Using Nextgen Sequencing to Investigate Genome Size Variation and Transposable Element Content

Abstract Background: The causes and consequences of genome size variation across Eukaryotes, which spans five orders of magnitude, have been hotly debated since before the advent of genome sequencing. Previous studies have mostly examined variation among larger taxonomic units (e.g., orders, or genera), while comparisons among closely related species are rare. Rotifers of the Brachionus plicatilis species complex exhibit a seven-fold variation in genome size and thus represent a unique opportunity to study such changes on a relatively short evolutionary timescale. Here, we sequenced and analysed the genomes of four species of this complex with nuclear DNA contents spanning 110- 422 Mbp. To establish the likely mechanisms of genome size change, we analysed both sequencing read libraries and assemblies for signatures of polyploidy and repetitive element content. We also compared these genomes to that of B. calyciflorus, the closest relative with a sequenced genome (293 Mbp nuclear DNA content). Results summary: Despite the very large differences in genome size, we saw no evidence of ploidy level changes across the B. plicatilis complex. However, repetitive element content explained a large portion of genome size variation (at least 54%). The species with the largest genome, B. asplanchnoidis, has a strikingly high 44% repetitive element content, while the smaller B. plicatilis genomes contain between 14% and 25% repetitive elements. According to our analyses, the B. calyciflorus genome contains 39% repetitive elements, which is substantially higher than previously reported (21%), and suggests that high repetitive element load could be widespread in monogonont rotifers. Conclusions: Even though the genome sizes of these species are at the low end of the Metazoan spectrum, their genomes contain substantial amounts of repetitive elements. Polyploidy does not appear to play a role in genome size variations in these species, and these variations can be mostly explained by changes in repetitive element content. This contradicts the naïve expectation that small genomes are streamlined, or less complex, and that large variations in nuclear DNA content between closely related species are due to polyploidy.

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Small, but surprisingly repetitive genomes: Transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex

10.21203/rs.2.9135/v2 ◽

2019 ◽

Author(s):

Julie Blommaert ◽

Simone Riss ◽

Bette Hecox-Lea ◽

David B. Mark-Welch ◽

Claus-Peter Stelzer

Keyword(s):

Genome Size ◽

Species Complex ◽

Nuclear Dna ◽

Repetitive Element ◽

Size Variation ◽

Nuclear Dna Content ◽

Repetitive Elements ◽

Element Content ◽

Genome Size Variation ◽

Closely Related Species

Abstract Background: The causes and consequences of genome size variation across Eukaryotes, which spans five orders of magnitude, have been hotly debated since before the advent of genome sequencing. Previous studies have mostly examined variation among larger taxonomic units (e.g., orders, or genera), while comparisons among closely related species are rare. Rotifers of the Brachionus plicatilis species complex exhibit a seven-fold variation in genome size and thus represent a unique opportunity to study such changes on a relatively short evolutionary timescale. Here, we sequenced and analysed the genomes of four species of this complex with nuclear DNA contents spanning 110- 422 Mbp. To establish the likely mechanisms of genome size change, we analysed both sequencing read libraries and assemblies for signatures of polyploidy and repetitive element content. We also compared these genomes to that of B. calyciflorus, the closest relative with a sequenced genome (293 Mbp nuclear DNA content). Results summary: Despite the very large differences in genome size, we saw no evidence of ploidy level changes across the B. plicatilis complex. However, repetitive element content explained a large portion of genome size variation (at least 54%). The species with the largest genome, B. asplanchnoidis, has a strikingly high 44% repetitive element content, while the smaller B. plicatilis genomes contain between 14% and 25% repetitive elements. According to our analyses, the B. calyciflorus genome contains 39% repetitive elements, which is substantially higher than previously reported (21%), and suggests that high repetitive element load could be widespread in monogonont rotifers. Conclusions: Even though the genome sizes of these species are at the low end of the Metazoan spectrum, their genomes contain substantial amounts of repetitive elements. Polyploidy does not appear to play a role in genome size variations in these species, and these variations can be mostly explained by changes in repetitive element content. This contradicts the naïve expectation that small genomes are streamlined, or less complex, and that large variations in nuclear DNA content between closely related species are due to polyploidy.

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Small, but surprisingly repetitive genomes: Transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex

10.21203/rs.2.9135/v1 ◽

2019 ◽

Cited By ~ 1

Author(s):

Julie Esmeralda Blommaert ◽

Simone Riss ◽

Bette Hecox-Lea ◽

David B. Mark-Welch ◽

Claus-Peter Stelzer

Keyword(s):

Genome Size ◽

Species Complex ◽

Nuclear Dna ◽

Repetitive Element ◽

Size Variation ◽

Nuclear Dna Content ◽

Repetitive Elements ◽

Element Content ◽

Genome Size Variation ◽

Closely Related Species

Abstract Background The causes and consequences of genome size variation across Eukaryotes, which spans five orders of magnitude, have been hotly debated since before the advent of genome sequencing. Previous studies have mostly examined variation among larger taxonomic units (e.g., orders, or genera), while comparisons among closely related species are rare. Rotifers of the Brachionus plicatilis species complex exhibit a seven-fold variation in genome size and thus represent a unique opportunity to study such changes on a relatively short evolutionary timescale. Here, we sequenced and analysed the genomes of four species of this complex with nuclear DNA contents spanning 110- 422 Mbp. To establish the likely mechanisms of genome size change, we analysed both sequencing read libraries and assemblies for signatures of polyploidy and repetitive element content. We also compared these genomes to that of B. calyciflorus, the closest relative with a sequenced genome (293 Mbp nuclear DNA content). Results summary Despite the very large differences in genome size, we saw no evidence of ploidy level changes across the B. plicatilis complex. However, repetitive element content explained a large portion of genome size variation (at least 54%). The species with the largest genome, B. asplanchnoidis, has a strikingly high 44% repetitive element content, while the smaller B. plicatilis genomes contain between 14% and 25% repetitive elements. According to our analyses, the B. calyciflorus genome contains 39% repetitive elements, which is substantially higher than previously reported (21%), and suggests that high repetitive element load could be widespread in monogonont rotifers. Conclusions Even though the genome sizes of these species are at the low end of the Metazoan spectrum, their genomes contain substantial amounts of repetitive elements. Polyploidy does not appear to play a role in genome size variations in these species, and these variations can be mostly explained by changes in repetitive element content. This contradicts the naïve expectation that small genomes are streamlined, or less complex, and that large variations in nuclear DNA content between closely related species are due to polyploidy.

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No evidence that sex and transposable elements drive genome size variation in evening primroses

10.1101/007161 ◽

2014 ◽

Author(s):

J Arvid Agren ◽

Stephan Greiner ◽

Marc TJ Johnson ◽

Stephen I Wright

Keyword(s):

Transposable Elements ◽

Transposable Element ◽

Sexual Reproduction ◽

Genome Size ◽

Reproductive System ◽

Size Variation ◽

Comparative Approach ◽

Element Abundance ◽

Whole Genome ◽

Genome Size Variation

Genome size varies dramatically across species, but despite an abundance of attention there is little agreement on the relative contributions of selective and neutral processes in governing this variation. The rate of sexual reproduction can potentially play an important role in genome size evolution because of its effect on the efficacy of selection and transmission of transposable elements. Here, we used a phylogenetic comparative approach and whole genome sequencing to investigate the contribution of sex and transposable element content to genome size variation in the evening primrose (Oenothera) genus. We determined genome size using flow cytometry from 30 Oenothera species of varying reproductive system and find that variation in sexual/asexual reproduction cannot explain the almost two-fold variation in genome size. Moreover, using whole genome sequences of three species of varying genome sizes and reproductive system, we found that genome size was not associated with transposable element abundance; instead the larger genomes had a higher abundance of simple sequence repeats. Although it has long been clear that sexual reproduction may affect various aspects of genome evolution in general and transposable element evolution in particular, it does not appear to have played a major role in the evening primroses.

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Whole genome duplication and transposable element proliferation drive genome expansion in Corydoradinae catfishes

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2017.2732 ◽

2018 ◽

Vol 285 (1872) ◽

pp. 20172732 ◽

Cited By ~ 10

Author(s):

Sarah Marburger ◽

Markos A. Alexandrou ◽

John B. Taggart ◽

Simon Creer ◽

Gary Carvalho ◽

...

Keyword(s):

Transposable Element ◽

Genome Size ◽

Size Variation ◽

Whole Genome ◽

Evolutionary Potential ◽

Posterior Density ◽

Genome Size Variation ◽

Genome Duplications ◽

Duplication Events ◽

Highest Posterior Density

Genome size varies significantly across eukaryotic taxa and the largest changes are typically driven by macro-mutations such as whole genome duplications (WGDs) and proliferation of repetitive elements. These two processes may affect the evolutionary potential of lineages by increasing genetic variation and changing gene expression. Here, we elucidate the evolutionary history and mechanisms underpinning genome size variation in a species-rich group of Neotropical catfishes (Corydoradinae) with extreme variation in genome size—0.6 to 4.4 pg per haploid cell. First, genome size was quantified in 65 species and mapped onto a novel fossil-calibrated phylogeny. Two evolutionary shifts in genome size were identified across the tree—the first between 43 and 49 Ma (95% highest posterior density (HPD) 36.2–68.1 Ma) and the second at approximately 19 Ma (95% HPD 15.3–30.14 Ma). Second, restriction-site-associated DNA (RAD) sequencing was used to identify potential WGD events and quantify transposable element (TE) abundance in different lineages. Evidence of two lineage-scale WGDs was identified across the phylogeny, the first event occurring between 54 and 66 Ma (95% HPD 42.56–99.5 Ma) and the second at 20–30 Ma (95% HPD 15.3–45 Ma) based on haplotype numbers per contig and between 35 and 44 Ma (95% HPD 30.29–64.51 Ma) and 20–30 Ma (95% HPD 15.3–45 Ma) based on SNP read ratios. TE abundance increased considerably in parallel with genome size, with a single TE-family (TC1-IS630-Pogo) showing several increases across the Corydoradinae, with the most recent at 20–30 Ma (95% HPD 15.3–45 Ma) and an older event at 35–44 Ma (95% HPD 30.29–64.51 Ma). We identified signals congruent with two WGD duplication events, as well as an increase in TE abundance across different lineages, making the Corydoradinae an excellent model system to study the effects of WGD and TEs on genome and organismal evolution.

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Transposable element distribution, abundance and role in genome size variation in the genus Oryza

BMC Evolutionary Biology ◽

10.1186/1471-2148-7-152 ◽

2007 ◽

Vol 7 (1) ◽

pp. 152 ◽

Cited By ~ 71

Author(s):

Andrea Zuccolo ◽

Aswathy Sebastian ◽

Jayson Talag ◽

Yeisoo Yu ◽

HyeRan Kim ◽

...

Keyword(s):

Transposable Element ◽

Genome Size ◽

Size Variation ◽

Element Distribution ◽

Genome Size Variation ◽

Genus Oryza

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Documenting Intraspecfic Genome Size Variation in Soybean

Crop Science ◽

10.2135/cropsci2004.0261 ◽

2004 ◽

Vol 44 (1) ◽

pp. 261 ◽

Cited By ~ 6

Author(s):

A. Lane Rayburn ◽

D. P. Biradar ◽

R. L. Nelson ◽

R. McCloskey ◽

K. M. Yeater

Keyword(s):

Genome Size ◽

Size Variation ◽

Genome Size Variation

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Genome size variation in deep-sea amphipods

Royal Society Open Science ◽

10.1098/rsos.170862 ◽

2017 ◽

Vol 4 (9) ◽

pp. 170862 ◽

Cited By ~ 3

Author(s):

H. Ritchie ◽

A. J. Jamieson ◽

S. B. Piertney

Keyword(s):

Life History ◽

Genome Size ◽

Deep Sea ◽

Research Effort ◽

Life History Strategy ◽

Size Variation ◽

Genome Size Variation ◽

New Hebrides ◽

Contrast Analysis ◽

Independent Contrast

Genome size varies considerably across taxa, and extensive research effort has gone into understanding whether variation can be explained by differences in key ecological and life-history traits among species. The extreme environmental conditions that characterize the deep sea have been hypothesized to promote large genome sizes in eukaryotes. Here we test this supposition by examining genome sizes among 13 species of deep-sea amphipods from the Mariana, Kermadec and New Hebrides trenches. Genome sizes were estimated using flow cytometry and found to vary nine-fold, ranging from 4.06 pg (4.04 Gb) in Paralicella caperesca to 34.79 pg (34.02 Gb) in Alicella gigantea . Phylogenetic independent contrast analysis identified a relationship between genome size and maximum body size, though this was largely driven by those species that display size gigantism. There was a distinct shift in the genome size trait diversification rate in the supergiant amphipod A. gigantea relative to the rest of the group. The variation in genome size observed is striking and argues against genome size being driven by a common evolutionary history, ecological niche and life-history strategy in deep-sea amphipods.

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Patterns of genome size variation in snapping shrimp

Genome ◽

10.1139/gen-2015-0206 ◽

2016 ◽

Vol 59 (6) ◽

pp. 393-402 ◽

Cited By ~ 19

Author(s):

Nicholas W. Jeffery ◽

Kristin Hultgren ◽

Solomon Tin Chi Chak ◽

T. Ryan Gregory ◽

Dustin R. Rubenstein

Keyword(s):

Genome Size ◽

Phylogenetic Signal ◽

Size Variation ◽

Diverse Group ◽

Chromosome Size ◽

Genome Size Variation ◽

Large Genome ◽

Large Genome Size ◽

Single Genus ◽

Geographic Regions

Although crustaceans vary extensively in genome size, little is known about how genome size may affect the ecology and evolution of species in this diverse group, in part due to the lack of large genome size datasets. Here we investigate interspecific, intraspecific, and intracolony variation in genome size in 39 species of Synalpheus shrimps, representing one of the largest genome size datasets for a single genus within crustaceans. We find that genome size ranges approximately 4-fold across Synalpheus with little phylogenetic signal, and is not related to body size. In a subset of these species, genome size is related to chromosome size, but not to chromosome number, suggesting that despite large genomes, these species are not polyploid. Interestingly, there appears to be 35% intraspecific genome size variation in Synalpheus idios among geographic regions, and up to 30% variation in Synalpheus duffyi genome size within the same colony.

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