Introduction Lectures Note Transposable elements
Transposable elements (TEs) are mobile genetic elements that can move from one
genomic position to another, and as the resultant insertions are quite large, mobilization
can lead to mutations of high impact. For example, a TE insertion into the 5’ region of a
gene can function as a new regulatory sequence and lead to changes in gene expression,
or it can inactivate the gene by disrupting the existing cis-regulatory controls or altering
chromatin conformation. Similarly, TE insertions into introns can be incorporated as new
exons or lead to premature/truncated transcripts. Although TEs are predominantly
silenced, protecting the genome from rampant insertional mutagenesis, the host
suppression system can be circumvented in some situations, particularly those situations
that present environmental challenges. Indeed, it has been suggested that species or
populations that are prone to strong diversifying selection would benefit from such
TEdriven genome variability (Naito et al. 2009, Fernandez et al. 2010, Tenaillon et al.
2010, Linquist et al. 2013, Oliver et al. 2013, Vitte et al. 2014, Ong-Abdullah et al. 2015,
Lu et al. 2017). In other words, transposition may create genomic diversity with the
potential to promote plant adaptation and survival.
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
The purpose of my dissertation work is to describe quantitative and
qualitative variation in TE composition at both recent and distant evolutionary
timescales. I have performed three specific aims to evaluate TE diversity in the related
but independently domesticated and economically important grasses, maize and sorghum.
Further, I extended these analyses into a non-grass system to investigate TE dynamics in
response to genome doubling and domestication.
Specific Aim 1 – Determine TE composition and copy number diversity among
Sorghum accessions to evaluate intraspecific TE-associated genome evolution over
short evolutionary time scales. Though numerous studies have described interspecific
TE-associated variation, relatively little is known about TE variation among members of a
single species. In this study, I evaluated TE composition and copy number diversity
within several representatives of Sorghum bicolor and compared those results to that of
Sorghum propinquum, a close wild relative, using short-read sequence data.
Specific Aim 2 – Describe interspecific TE diversity among related members of
the Andropogoneae tribe that have undergone a shared recent polyploidization event.
Here, I evaluated TE diversity in Zea mays, Tripsacum dactyloides and Urelytrum
digitatum, and compare these results with that from Sorghum. Z. mays and T. dactyloides
are paleopolyploids that arose from a single genome doubling event involving U.
digitatum approximately 5-10 million years ago (mya) and have since undergone
rediploidization. Comparisons of TE evolutionary dynamics in various Zea-Tripsacum
species along with closely related diploid species Urelytrum and Sorghum revealed
existing variation in repeat content between pre- and post-polyploid species included in
the study.
Specific Aim 3 – Describe interspecific TE diversity in the cotton genus,
Gossypium, to evaluate TE-associated genome evolution in domesticated polyploids
compared to their diploid progenitors. To investigate whether TE dynamics and
polyploid-domesticate phenomenon is a common theme for all species, I performed
interspecific TE diversity analyses similar to my specific aim 2 in a non-grass system,
cotton (Gossypium). To characterize both common patterns and lineage-specific
differences in TE composition and evolution in response to genome doubling, I have
investigated Gossypium allopolyploids (AD), which includes leading domesticated cash
crops and island-endemics, originating from a single interspecific hybridization event
between two divergent diploid (A and D) species.
References
Naito K et al. 2009. Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature. 461:1130–1134.
Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 2010.
Transposon-induced gene activation as a mechanism generating cluster shape somatic
variation in grapevine. The Plant Journal. 61:545–557.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. 2011. Genome Size and Transposable
Element Content as Determined by High-Throughput Sequencing in Maize and Zea
luxurians. Genome Biol Evol. 3:219–229.
Linquist S et al. 2013. Distinguishing ecological from evolutionary approaches to
transposable elements. Biol Rev. 88:573–584.
Oliver KR, McComb JA, Greene WK. 2013. Transposable Elements: Powerful
Contributors to Angiosperm Evolution and Diversity. Genome Biol Evol. 5:1886–1901.
Vitte C, Fustier M-A, Alix K, Tenaillon MI. 2014. The bright side of transposons in crop
evolution. Brief Funct Genomics 13:276–295.
Ong-Abdullah, M. et al. 2015. Loss of Karma transposon methylation underlies the
mantled somaclonal variant of oil palm. Nature 525, 533–537.
Lu L et al. 2017. Tracking the genome-wide outcomes of a transposable element burst
over decades of amplification. PNAS. 114:E10550–E10559.
CHAPTER 2: INTRODUCTION The Discovery of TEs
Historically, genes were thought of as stable entities whose linear-arrangement
was highly conserved across diverse organisms; however, Barbara McClintock challenged
this view in the late 1940s. McClintock was primarily interested in understanding the
mechanisms of chromosome breakage and fusion in maize, and through her studies she
observed a frequent breakage event at a specific locus on chromosome 9 during plant
development. She named the locus Dissociation (Ds), and further, she discovered that this
locus could change its position on the chromosome. She also discovered an unlinked
factor called Activator (Ac) that seemingly initiated the break at the Ds locus on
chromosome 9 (McClintock 1948, 1951). This work led to the discovery of the first
transposable elements, the Ac/Ds system. McClintock referred to these genetic factors as
“controlling elements” due to their ability to alter gene function when inserted near or
within genic regions; however, the concept of transposition was considered complex at
that time, and was largely dismissed due to strong adherence to the stable genome
hypothesis. It took two decades for McClintock to receive the prestigious Nobel Prize for
her discovery of transposable elements.
Major TE classes and their genetic structure
Since McClintock’s discovery, many different types of TEs have been discovered
and described, and they are now classified into two major groups based on their mode of
transposition, e.g., whether their transposition intermediate is RNA (Class I -
retrotransposons) or DNA (Class II – DNA transposons) (Figure 1). Both classes contain
autonomous and non-autonomous elements. Autonomous elements contain open reading
frames (ORFs) that encode the proteins necessary for transposition. Non-autonomous
elements lack these ORFs, and therefore require proteins encoded by their autonomous
counterpart to move throughout the genome. Class II elements, which transpose via a
cutand-paste mechanism, contain a transposase gene that is flanked by two terminal
inverted repeats (TIRs). Examples include Ac/Ds and Spm/dspm (En/I) in maize. The
inverted terminal repeats are unique to each DNA transposon family and range in size
from 11 bp to a few hundred base pairs. Proteins encoded by the autonomous elements of
one DNA transposon family recognize the corresponding non-autonomous element by
their shared termini, and thereby assist in its transposition. For example, Ac and Ds
elements share 11 bp TIRs and therefore the Ac-encoded transposase can interact with the
Ds TIRs to facilitate its movement. The Ac-encoded transposase cannot bind the TIRs of
Spm/dspm elements or any other TE family for which it does not share TIR sequence
identity.
Class I retrotransposons are RNA elements that are particularly abundant in
eukaryotes, especially in plants. Retrotransposons are divided into Long Terminal Repeat
(LTR) and non-LTR elements. LTR-retrotransposons vary in size from several hundred
base pairs to ~20 kb and contain unique, directly-oriented LTRs at their ends that range in
size from ~100 bp to 5 kb. An intact element contains gag, an ORF that encodes a
polyprotein responsible for maturation and packaging of retrotransposon RNA, and pol,
an ORF that encodes protease (PR), reverse transcriptase (RT), RNase H (RH) and
integrase (IN) which aid in synthesis, processing and subsequent integration of new
retrotransposons at random locations in the genome (Feschotte 2002).
LTRretrotransposons are classified into Gypsy (RT-RH-IN) and Copia (IN-RT-RH)
superfamilies based on the arrangement of RT and IN in the pol ORF (Xiong and
Eickbush, 1990). Though several non-autonomous LTR-retrotransposon families have
been identified in plants, their autonomous partners have yet to be discovered in most
cases (Jin and Bennetzen, 1989; Hu et al. 1995; Lander et al. 2001; Witte et al. 2001;
Jiang et al. 2002; Kalendar et al. 2004; Kejnovsky et al. 2006). Non-LTR
retrotransposons such as Long Interspersed Nuclear Elements (LINEs) and Short
Interspersed Nuclear Elements (SINEs) are also found in flowering plant genomes but
mostly remain epigenetically silenced and therefore inactive. Although LINEs encode the
proteins for their own transposition, SINEs are non-autonomous and therefore depend on
the machinery encoded by other retrotransposons.
The C-value paradox and TE contribution to genome size disparity
One of the largest genomes known belongs to the single celled Amoeba dubia
(670 billion bp) whose genome is ~200 times larger than that of most multi-cellular
organisms. Such lack of correlation between genome size and organismal complexity has
been historically termed the C-value paradox (Thomas, 1971). Plant genomes are
extremely diverse and exhibit a wide range of C-values (Pellicer et al. 2010, Fedoroff,
2012). It is now known that the two major mechanisms that contribute to genome
expansion in plants are genome doubling (polyploidy) and transposable element
accumulation (Grover & Wendel 2010, Kejnovsky et al. 2012, Leitch & Leitch 2012).
LTR-retrotransposons are predominant in most plant genomes, comprising 50-80% of the
maize genome (~2500 Mb) and more than 90% of the bread wheat genome (SanMiguel
1998, Paux 2008, McCarthy 2002). Although TE proliferation occurs frequently and in
large detectable bursts, accumulation is counteracted by DNA removal mechanisms such
as non-homologous end joining (NHEJ) and unequal homologous recombination. The
former excises parts of TEs by generating small deletions, and the latter often occurs
between two LTRs of an intact retroelement, removing the internal portion and resulting
in a solo LTR. In plants with smaller genomes, DNA removal occurs more frequently via
illegitimate recombination (NHEJ) than through unequal homologous recombination
(Hawkins 2009, Ma J 2004, Devos KM 2002). It is also thought that smaller genomes
purge excess DNA more efficiently relative to larger genomes due to extensive epigenetic
silencing (Ibarra-Lacette et al. 2013, Nystedt et al. 2013, Zhong X et al. 2012, Tian Z et
al. 2009). Such efficiency could have evolved to decrease the likelihood of a TE insertion
near a gene, as such an event is statistically more likely in plants with smaller genomes.
Rapid rates of TE amplification and decay can lead to variable TE composition
among closely related plant lineages. For instance, although similar numbers of TE
families occupy both the rice and maize genomes, transpositional bursts of a few Long
Terminal Repeat (LTR) retrotransposon families have inflated the maize genome to six
times that of rice (Baucom 2009, Baucom2008). Variation is also common among more
closely related taxa, such as those that belong to the same subfamily (SanMiguel et al.
1998), and significant copy number differences are found even among members of a
single genus. Interspecific comparisons performed in Gossypium and Oryza revealed that
proliferation of a small subset of TE families were responsible for the observed genome
size variation among species (Hawkins et al. 2006, Piegu et al. 2006). TE copy number
variation is not always due to the activity of just a few families, however. Proliferation of
several different TE families is responsible for the variation in TE content between Zea
and Arabidopsis (Tenaillon et al. 2011, Hu et al. 2011, Hollister et al. 2011). In either
case, TE accumulation and deletion occurs over very short evolutionary time-scales,
