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Mating system shifts and transposable element evolution in the plant genus Capsella

BACKGROUND: Despite having predominately deleterious fitness effects, transposable elements (TEs) are major constituents of eukaryote genomes in general and of plant genomes in particular. Although the proportion of the genome made up of TEs varies at least four-fold across plants, the relative impo...

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Autores principales: Ågren, J Arvid, Wang, Wei, Koenig, Daniel, Neuffer, Barbara, Weigel, Detlef, Wright, Stephen I
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4112209/
https://www.ncbi.nlm.nih.gov/pubmed/25030755
http://dx.doi.org/10.1186/1471-2164-15-602
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author Ågren, J Arvid
Wang, Wei
Koenig, Daniel
Neuffer, Barbara
Weigel, Detlef
Wright, Stephen I
author_facet Ågren, J Arvid
Wang, Wei
Koenig, Daniel
Neuffer, Barbara
Weigel, Detlef
Wright, Stephen I
author_sort Ågren, J Arvid
collection PubMed
description BACKGROUND: Despite having predominately deleterious fitness effects, transposable elements (TEs) are major constituents of eukaryote genomes in general and of plant genomes in particular. Although the proportion of the genome made up of TEs varies at least four-fold across plants, the relative importance of the evolutionary forces shaping variation in TE abundance and distributions across taxa remains unclear. Under several theoretical models, mating system plays an important role in governing the evolutionary dynamics of TEs. Here, we use the recently sequenced Capsella rubella reference genome and short-read whole genome sequencing of multiple individuals to quantify abundance, genome distributions, and population frequencies of TEs in three recently diverged species of differing mating system, two self-compatible species (C. rubella and C. orientalis) and their self-incompatible outcrossing relative, C. grandiflora. RESULTS: We detect different dynamics of TE evolution in our two self-compatible species; C. rubella shows a small increase in transposon copy number, while C. orientalis shows a substantial decrease relative to C. grandiflora. The direction of this change in copy number is genome wide and consistent across transposon classes. For insertions near genes, however, we detect the highest abundances in C. grandiflora. Finally, we also find differences in the population frequency distributions across the three species. CONCLUSION: Overall, our results suggest that the evolution of selfing may have different effects on TE evolution on a short and on a long timescale. Moreover, cross-species comparisons of transposon abundance are sensitive to reference genome bias, and efforts to control for this bias are key when making comparisons across species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-602) contains supplementary material, which is available to authorized users.
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spelling pubmed-41122092014-08-05 Mating system shifts and transposable element evolution in the plant genus Capsella Ågren, J Arvid Wang, Wei Koenig, Daniel Neuffer, Barbara Weigel, Detlef Wright, Stephen I BMC Genomics Research Article BACKGROUND: Despite having predominately deleterious fitness effects, transposable elements (TEs) are major constituents of eukaryote genomes in general and of plant genomes in particular. Although the proportion of the genome made up of TEs varies at least four-fold across plants, the relative importance of the evolutionary forces shaping variation in TE abundance and distributions across taxa remains unclear. Under several theoretical models, mating system plays an important role in governing the evolutionary dynamics of TEs. Here, we use the recently sequenced Capsella rubella reference genome and short-read whole genome sequencing of multiple individuals to quantify abundance, genome distributions, and population frequencies of TEs in three recently diverged species of differing mating system, two self-compatible species (C. rubella and C. orientalis) and their self-incompatible outcrossing relative, C. grandiflora. RESULTS: We detect different dynamics of TE evolution in our two self-compatible species; C. rubella shows a small increase in transposon copy number, while C. orientalis shows a substantial decrease relative to C. grandiflora. The direction of this change in copy number is genome wide and consistent across transposon classes. For insertions near genes, however, we detect the highest abundances in C. grandiflora. Finally, we also find differences in the population frequency distributions across the three species. CONCLUSION: Overall, our results suggest that the evolution of selfing may have different effects on TE evolution on a short and on a long timescale. Moreover, cross-species comparisons of transposon abundance are sensitive to reference genome bias, and efforts to control for this bias are key when making comparisons across species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-602) contains supplementary material, which is available to authorized users. BioMed Central 2014-07-16 /pmc/articles/PMC4112209/ /pubmed/25030755 http://dx.doi.org/10.1186/1471-2164-15-602 Text en © Ågren et al.; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Ågren, J Arvid
Wang, Wei
Koenig, Daniel
Neuffer, Barbara
Weigel, Detlef
Wright, Stephen I
Mating system shifts and transposable element evolution in the plant genus Capsella
title Mating system shifts and transposable element evolution in the plant genus Capsella
title_full Mating system shifts and transposable element evolution in the plant genus Capsella
title_fullStr Mating system shifts and transposable element evolution in the plant genus Capsella
title_full_unstemmed Mating system shifts and transposable element evolution in the plant genus Capsella
title_short Mating system shifts and transposable element evolution in the plant genus Capsella
title_sort mating system shifts and transposable element evolution in the plant genus capsella
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4112209/
https://www.ncbi.nlm.nih.gov/pubmed/25030755
http://dx.doi.org/10.1186/1471-2164-15-602
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