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

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.

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

2018 ◽  
Vol 285 (1872) ◽  
pp. 20172732 ◽  
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.

scholarly journals Comparative Analysis of Transposable Elements in Genus Calliptamus Grasshoppers Revealed That Satellite DNA Contributes to Genome Size Variation

Insects ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 837
Author(s):  
Muhammad Majid ◽  
Huang Yuan
Keyword(s):  
Comparative Analysis ◽  
Transposable Elements ◽  
Genome Size ◽  
Structural Changes ◽  
Evolutionary Dynamics ◽  
Size Variation ◽  
Genome Size Variation ◽  
Genome Size Evolution ◽  
Size Evolution ◽  
Low Coverage

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.

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

2012 ◽  
pp. 41-58 ◽  
Author(s):  
Concepcion Muñoz-Diez ◽  
Clémentine Vitte ◽  
Jeffrey Ross-Ibarra ◽  
Brandon S. Gaut ◽  
Maud I. Tenaillon
Keyword(s):  
Transposable Element ◽  
Genome Size ◽  
Size Variation ◽  
Element Content ◽  
Genome Size Variation ◽  
Nextgen Sequencing

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

Genome ◽  
2008 ◽  
Vol 51 (1) ◽  
pp. 11-18 ◽  
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.

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

Evolution ◽  
2015 ◽  
Vol 69 (4) ◽  
pp. 1053-1062 ◽  
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

scholarly journals Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium

2006 ◽  
Vol 16 (10) ◽  
pp. 1252-1261 ◽  
Author(s):  
J. S. Hawkins ◽  
H. Kim ◽  
J. D. Nason ◽  
R. A. Wing ◽  
J. F. Wendel
Keyword(s):  
Transposable Elements ◽  
Genome Size ◽  
Size Variation ◽  
Genome Size Variation ◽  
Specific Amplification

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

2007 ◽  
Vol 7 (1) ◽  
pp. 152 ◽  
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

scholarly journals Measuring the invisible - The sequences causal of genome size differences in eyebrights (Euphrasia) revealed by k-mers

2021 ◽  
Author(s):  
Hannes Becher ◽  
Jacob Sampson ◽  
Alex D Twyford
Keyword(s):  
Genome Size ◽  
Copy Number ◽  
Repetitive Sequences ◽  
Size Variation ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Genome Size Variation ◽  
Novel Approach ◽  
Low Copy Number

Genome size variation within plant (and other) taxa may be due to presence/absence variation in low-copy sequences or copy number variation in genomic repeats of various frequency classes. However, identifying the sequences underpinning genome size variation has been challenging because genome assemblies commonly contain collapsed representations of repetitive sequences and because genome skimming studies miss low-copy number sequences. Here, we take a novel approach based on k-mers, short sub-sequences of equal length k, generated from whole genome sequencing data of diploid eyebrights (Euphrasia), a group of plants which have considerable genome size variation within a ploidy level. We compare k-mer inventories within and between closely related species, and quantify the contribution of different copy number classes to genome size differences. We further assign high-copy number k-mers to specific repeat types as retrieved from the RepeatExplorer2 pipeline. We find complex patterns of k-mer differences between samples. While all copy number classes contributed to genome size variation, the largest contribution came from repeats with 1000-10,000 genomic copies including the 45S rDNA satellite DNA and, unexpectedly, a repeat associated with an Angela transposable element. We also find size differences in the low-copy number class, likely indicating differences in gene space between our samples. In this study, we demonstrate that it is possible to pinpoint the sequences causing genome size variation within species without use of a reference genome. Such sequences can serve as targets for future cytogenetic studies. We also show that studies of genome size variation should go beyond repeats and consider the whole genome. To allow future work with other taxonomic groups, we share our analysis pipeline, which is straightforward to run, relying largely on standard GNU command line tools.

Sign in / Sign up

Export Citation Format

Share Document