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Patterns of selection in the evolution of a transposable element
Transposable elements are a major component of most eukaryotic genomes. Here, we present a new approach which allows us to study patterns of natural selection in the evolution of transposable elements over short time scales. The method uses the alignment of all elements with intact gag/pol genes of...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9073684/ https://www.ncbi.nlm.nih.gov/pubmed/35262706 http://dx.doi.org/10.1093/g3journal/jkac056 |
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author | Dazenière, Julie Bousios, Alexandros Eyre-Walker, Adam |
author_facet | Dazenière, Julie Bousios, Alexandros Eyre-Walker, Adam |
author_sort | Dazenière, Julie |
collection | PubMed |
description | Transposable elements are a major component of most eukaryotic genomes. Here, we present a new approach which allows us to study patterns of natural selection in the evolution of transposable elements over short time scales. The method uses the alignment of all elements with intact gag/pol genes of a transposable element family from a single genome. We predict that the ratio of nonsynonymous to synonymous variants in the alignment should decrease as a function of the frequency of the variants, because elements with nonsynonymous variants that reduce transposition will have fewer progeny. We apply our method to Sirevirus long-terminal repeat retrotransposons that are abundant in maize and other plant species and show that nonsynonymous to synonymous variants declines as variant frequency increases, indicating that negative selection is acting strongly on the Sirevirus genome. The asymptotic value of nonsynonymous to synonymous variants suggests that at least 85% of all nonsynonymous mutations in the transposable element reduce transposition. Crucially, these patterns in nonsynonymous to synonymous variants are only predicted to occur if the gene products from a particular transposable element insertion preferentially promote the transposition of the same insertion. Overall, by using large numbers of intact elements, this study sheds new light on the selective processes that act on transposable elements. |
format | Online Article Text |
id | pubmed-9073684 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-90736842022-05-06 Patterns of selection in the evolution of a transposable element Dazenière, Julie Bousios, Alexandros Eyre-Walker, Adam G3 (Bethesda) Investigation Transposable elements are a major component of most eukaryotic genomes. Here, we present a new approach which allows us to study patterns of natural selection in the evolution of transposable elements over short time scales. The method uses the alignment of all elements with intact gag/pol genes of a transposable element family from a single genome. We predict that the ratio of nonsynonymous to synonymous variants in the alignment should decrease as a function of the frequency of the variants, because elements with nonsynonymous variants that reduce transposition will have fewer progeny. We apply our method to Sirevirus long-terminal repeat retrotransposons that are abundant in maize and other plant species and show that nonsynonymous to synonymous variants declines as variant frequency increases, indicating that negative selection is acting strongly on the Sirevirus genome. The asymptotic value of nonsynonymous to synonymous variants suggests that at least 85% of all nonsynonymous mutations in the transposable element reduce transposition. Crucially, these patterns in nonsynonymous to synonymous variants are only predicted to occur if the gene products from a particular transposable element insertion preferentially promote the transposition of the same insertion. Overall, by using large numbers of intact elements, this study sheds new light on the selective processes that act on transposable elements. Oxford University Press 2022-03-09 /pmc/articles/PMC9073684/ /pubmed/35262706 http://dx.doi.org/10.1093/g3journal/jkac056 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Investigation Dazenière, Julie Bousios, Alexandros Eyre-Walker, Adam Patterns of selection in the evolution of a transposable element |
title | Patterns of selection in the evolution of a transposable element |
title_full | Patterns of selection in the evolution of a transposable element |
title_fullStr | Patterns of selection in the evolution of a transposable element |
title_full_unstemmed | Patterns of selection in the evolution of a transposable element |
title_short | Patterns of selection in the evolution of a transposable element |
title_sort | patterns of selection in the evolution of a transposable element |
topic | Investigation |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9073684/ https://www.ncbi.nlm.nih.gov/pubmed/35262706 http://dx.doi.org/10.1093/g3journal/jkac056 |
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