Population-specific dynamics and selection patterns of transposable element insertions in European natural populations
Transposable elements (TEs) are ubiquitous sequences in genomes of virtually all species. While TEs have been investigated for several decades, only recently we have the opportunity to study their genome-wide population dynamics. Most of the studies so far have been restricted either to the analysis of the insertions annotated in the reference genome or to the analysis of a limited number of populations. Taking advantage of the European Drosophila population genomics consortium (DrosEU) sequencing data set, we have identified and measured the dynamics of TEs in a large sample of European Drosophila melanogaster natural populations. We showed that the mobilome landscape is population-specific and highly diverse depending on the TE family. In contrast with previous studies based on SNP variants, no geographical structure was observed for TE abundance or TE divergence in European populations. We further identified de novo individual insertions using two available programs and, as expected, most of the insertions were present at low frequencies. Nevertheless, we identified a subset of TEs present at high frequencies and located in genomic regions with a high recombination rate. These TEs are candidates for being the target of positive selection, although neutral processes should be discarded before reaching any conclusion on the type of selection acting on them. Finally, parallel patterns of association between the frequency of TE insertions and several geographical and temporal variables were found between European and North American populations, suggesting that TEs can be potentially implicated in the adaptation of populations across continents.
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John Wiley & Sons
2019-03
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dig-ibe-es-10261-2068212021-12-27T15:58:40Z Population-specific dynamics and selection patterns of transposable element insertions in European natural populations Lerat, Emmanuelle Goubert, Clément Guirao-Rico, Sara Merenciano, Miriam Dufour, Anne‐Béatrice Vieira, Cristina González Pérez, Josefa European Research Council Agence Nationale de la Recherche (France) Transposable elements (TEs) are ubiquitous sequences in genomes of virtually all species. While TEs have been investigated for several decades, only recently we have the opportunity to study their genome-wide population dynamics. Most of the studies so far have been restricted either to the analysis of the insertions annotated in the reference genome or to the analysis of a limited number of populations. Taking advantage of the European Drosophila population genomics consortium (DrosEU) sequencing data set, we have identified and measured the dynamics of TEs in a large sample of European Drosophila melanogaster natural populations. We showed that the mobilome landscape is population-specific and highly diverse depending on the TE family. In contrast with previous studies based on SNP variants, no geographical structure was observed for TE abundance or TE divergence in European populations. We further identified de novo individual insertions using two available programs and, as expected, most of the insertions were present at low frequencies. Nevertheless, we identified a subset of TEs present at high frequencies and located in genomic regions with a high recombination rate. These TEs are candidates for being the target of positive selection, although neutral processes should be discarded before reaching any conclusion on the type of selection acting on them. Finally, parallel patterns of association between the frequency of TE insertions and several geographical and temporal variables were found between European and North American populations, suggesting that TEs can be potentially implicated in the adaptation of populations across continents. J.G. is funded by the ERC (H2020‐ERC‐2014‐CoG‐647900), and C.V. is funded by the ANR Exhyb (14‐CE19‐0016). 2020-04-07T10:17:37Z 2020-04-07T10:17:37Z 2019-03 2020-04-07T10:17:38Z artículo http://purl.org/coar/resource_type/c_6501 doi: 10.1111/mec.14963 e-issn: 1365-294X issn: 0962-1083 Molecular Ecology 28(6): 1506-1522 (2019) http://hdl.handle.net/10261/206821 10.1111/mec.14963 http://dx.doi.org/10.13039/501100000781 http://dx.doi.org/10.13039/501100001665 30506554 #PLACEHOLDER_PARENT_METADATA_VALUE# info:eu-repo/grantAgreement/EC/H2020/647900 Publisher's version http://doi.org/10.1111/mec.14963 Sí open John Wiley & Sons |
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Transposable elements (TEs) are ubiquitous sequences in genomes of virtually all species. While TEs have been investigated for several decades, only recently we have the opportunity to study their genome-wide population dynamics. Most of the studies so far have been restricted either to the analysis of the insertions annotated in the reference genome or to the analysis of a limited number of populations. Taking advantage of the European Drosophila population genomics consortium (DrosEU) sequencing data set, we have identified and measured the dynamics of TEs in a large sample of European Drosophila melanogaster natural populations. We showed that the mobilome landscape is population-specific and highly diverse depending on the TE family. In contrast with previous studies based on SNP variants, no geographical structure was observed for TE abundance or TE divergence in European populations. We further identified de novo individual insertions using two available programs and, as expected, most of the insertions were present at low frequencies. Nevertheless, we identified a subset of TEs present at high frequencies and located in genomic regions with a high recombination rate. These TEs are candidates for being the target of positive selection, although neutral processes should be discarded before reaching any conclusion on the type of selection acting on them. Finally, parallel patterns of association between the frequency of TE insertions and several geographical and temporal variables were found between European and North American populations, suggesting that TEs can be potentially implicated in the adaptation of populations across continents. |
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European Research Council |
author_facet |
European Research Council Lerat, Emmanuelle Goubert, Clément Guirao-Rico, Sara Merenciano, Miriam Dufour, Anne‐Béatrice Vieira, Cristina González Pérez, Josefa |
format |
artículo |
author |
Lerat, Emmanuelle Goubert, Clément Guirao-Rico, Sara Merenciano, Miriam Dufour, Anne‐Béatrice Vieira, Cristina González Pérez, Josefa |
spellingShingle |
Lerat, Emmanuelle Goubert, Clément Guirao-Rico, Sara Merenciano, Miriam Dufour, Anne‐Béatrice Vieira, Cristina González Pérez, Josefa Population-specific dynamics and selection patterns of transposable element insertions in European natural populations |
author_sort |
Lerat, Emmanuelle |
title |
Population-specific dynamics and selection patterns of transposable element insertions in European natural populations |
title_short |
Population-specific dynamics and selection patterns of transposable element insertions in European natural populations |
title_full |
Population-specific dynamics and selection patterns of transposable element insertions in European natural populations |
title_fullStr |
Population-specific dynamics and selection patterns of transposable element insertions in European natural populations |
title_full_unstemmed |
Population-specific dynamics and selection patterns of transposable element insertions in European natural populations |
title_sort |
population-specific dynamics and selection patterns of transposable element insertions in european natural populations |
publisher |
John Wiley & Sons |
publishDate |
2019-03 |
url |
http://hdl.handle.net/10261/206821 http://dx.doi.org/10.13039/501100000781 http://dx.doi.org/10.13039/501100001665 |
work_keys_str_mv |
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1777668749820690432 |