Faculty Opinions recommendation of Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium.

Transposable elements (TEs) play a significant role in both eukaryotes and prokaryotes genome size evolution, structural changes, duplication, and functional variabilities. However, the large number of different repetitive DNA has hindered the process of assembling reference genomes, and the genus level TEs diversification of the grasshopper massive genomes is still under investigation. The genus Calliptamus diverged from Peripolus around 17 mya and its species divergence dated back about 8.5 mya, but their genome size shows rather large differences. Here, we used low-coverage Illumina unassembled short reads to investigate the effects of evolutionary dynamics of satDNAs and TEs on genome size variations. The Repeatexplorer2 analysis with 0.5X data resulted in 52%, 56%, and 55% as repetitive elements in the genomes of Calliptamus barbarus, Calliptamus italicus, and Calliptamus abbreviatus, respectively. The LINE and Ty3-gypsy LTR retrotransposons and TcMar-Tc1 dominated the repeatomes of all genomes, accounting for 16–35% of the total genomes of these species. Comparative analysis unveiled that most of the transposable elements (TEs) except satDNAs were highly conserved across three genomes in the genus Calliptamus grasshoppers. Out of a total of 20 satDNA families, 17 satDNA families were commonly shared with minor variations in abundance and divergence between three genomes, and 3 were Calliptamus barbarus specific. Our findings suggest that there is a significant amplification or contraction of satDNAs at genus phylogeny which is the main cause that made genome size different.

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Impact of transposable elements on genome size variation between two closely related crustacean species

Analytical Biochemistry ◽

10.1016/j.ab.2020.113770 ◽

2020 ◽

Vol 600 ◽

pp. 113770

Author(s):

Thomas Becking ◽

Clément Gilbert ◽

Richard Cordaux

Keyword(s):

Transposable Elements ◽

Genome Size ◽

Size Variation ◽

Genome Size Variation ◽

Crustacean Species

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Phylogenetic determination of the pace of transposable element proliferation in plants: copia and LINE-like elements in Gossypium

Genome ◽

10.1139/g07-099 ◽

2008 ◽

Vol 51 (1) ◽

pp. 11-18 ◽

Cited By ~ 42

Author(s):

Jennifer S. Hawkins ◽

Guanjing Hu ◽

Ryan A. Rapp ◽

Jessie L. Grafenberg ◽

Jonathan F. Wendel

Keyword(s):

Transposable Elements ◽

Genome Size ◽

Size Variation ◽

Plant Genome ◽

Genome Size Variation ◽

Copy Numbers ◽

History Of ◽

Regular Manner ◽

Genus One ◽

Copia Retrotransposons

Transposable elements contribute significantly to plant genome evolution in myriad ways, ranging from local insertional mutations to global effects exerted on genome size through accumulation. Differential accumulation and deletion of transposable elements may profoundly affect genome size, even among members of the same genus. One example is that of Gossypium (cotton), where much of the 3-fold genome size variation is due to differential accumulation of one gypsy-like LTR retrotransposon, Gorge3. Copia and non-LTR LINE retrotransposons are also major components of the Gossypium genome, but unlike Gorge3, their extant copy numbers do not correlate with genome size. In the present study, we describe the nature and timing of transposition for copia and LINE retrotransposons in Gossypium. Our findings indicate that copia retrotransposons have been active in each lineage since divergence from a common ancestor, and that they have proliferated in a punctuated manner. However, the evolutionary history of LINEs contrasts markedly with that of the copia retrotransposons. Although LINEs have also been active in each lineage, they have accumulated in a stochastically regular manner, and phylogenetic analysis suggests that extant LINE populations in Gossypium are dominated by ancient insertions. Interestingly, the magnitude of transpositional bursts in each lineage corresponds directly with extant estimated copy number.

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

Evolution ◽

10.1111/evo.12627 ◽

2015 ◽

Vol 69 (4) ◽

pp. 1053-1062 ◽

Cited By ~ 20

Author(s):

J. Arvid Ågren ◽

Stephan Greiner ◽

Marc T. J. Johnson ◽

Stephen I. Wright

Keyword(s):

Transposable Elements ◽

Genome Size ◽

Size Variation ◽

Genome Size Variation

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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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