Cargando…

PoPoolationTE2: Comparative Population Genomics of Transposable Elements Using Pool-Seq

The evolutionary dynamics of transposable elements (TEs) are still poorly understood. One reason is that TE abundance needs to be studied at the population level, but sequencing individuals on a population scale is still too expensive to characterize TE abundance in multiple populations. Although se...

Descripción completa

Detalles Bibliográficos
Autores principales: Kofler, Robert, Gómez-Sánchez, Daniel, Schlötterer, Christian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5026257/
https://www.ncbi.nlm.nih.gov/pubmed/27486221
http://dx.doi.org/10.1093/molbev/msw137
_version_ 1782454100404731904
author Kofler, Robert
Gómez-Sánchez, Daniel
Schlötterer, Christian
author_facet Kofler, Robert
Gómez-Sánchez, Daniel
Schlötterer, Christian
author_sort Kofler, Robert
collection PubMed
description The evolutionary dynamics of transposable elements (TEs) are still poorly understood. One reason is that TE abundance needs to be studied at the population level, but sequencing individuals on a population scale is still too expensive to characterize TE abundance in multiple populations. Although sequencing pools of individuals dramatically reduces sequencing costs, a comparison of TE abundance between pooled samples has been difficult, if not impossible, due to various biases. Here, we introduce a novel bioinformatic tool, PoPoolationTE2, which is specifically tailored for the comparison of TE abundance among pooled population samples or different tissues. Using computer simulations, we demonstrate that PoPoolationTE2 not only faithfully recovers TE insertion frequencies and positions but, by homogenizing the power to identify TEs across samples, it provides an unbiased comparison of TE abundance between pooled population samples. We anticipate that PoPoolationTE2 will greatly facilitate the analysis of TE insertion patterns in a broad range of applications.
format Online
Article
Text
id pubmed-5026257
institution National Center for Biotechnology Information
language English
publishDate 2016
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-50262572016-09-20 PoPoolationTE2: Comparative Population Genomics of Transposable Elements Using Pool-Seq Kofler, Robert Gómez-Sánchez, Daniel Schlötterer, Christian Mol Biol Evol Resources The evolutionary dynamics of transposable elements (TEs) are still poorly understood. One reason is that TE abundance needs to be studied at the population level, but sequencing individuals on a population scale is still too expensive to characterize TE abundance in multiple populations. Although sequencing pools of individuals dramatically reduces sequencing costs, a comparison of TE abundance between pooled samples has been difficult, if not impossible, due to various biases. Here, we introduce a novel bioinformatic tool, PoPoolationTE2, which is specifically tailored for the comparison of TE abundance among pooled population samples or different tissues. Using computer simulations, we demonstrate that PoPoolationTE2 not only faithfully recovers TE insertion frequencies and positions but, by homogenizing the power to identify TEs across samples, it provides an unbiased comparison of TE abundance between pooled population samples. We anticipate that PoPoolationTE2 will greatly facilitate the analysis of TE insertion patterns in a broad range of applications. Oxford University Press 2016-10 2016-08-02 /pmc/articles/PMC5026257/ /pubmed/27486221 http://dx.doi.org/10.1093/molbev/msw137 Text en © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Resources
Kofler, Robert
Gómez-Sánchez, Daniel
Schlötterer, Christian
PoPoolationTE2: Comparative Population Genomics of Transposable Elements Using Pool-Seq
title PoPoolationTE2: Comparative Population Genomics of Transposable Elements Using Pool-Seq
title_full PoPoolationTE2: Comparative Population Genomics of Transposable Elements Using Pool-Seq
title_fullStr PoPoolationTE2: Comparative Population Genomics of Transposable Elements Using Pool-Seq
title_full_unstemmed PoPoolationTE2: Comparative Population Genomics of Transposable Elements Using Pool-Seq
title_short PoPoolationTE2: Comparative Population Genomics of Transposable Elements Using Pool-Seq
title_sort popoolationte2: comparative population genomics of transposable elements using pool-seq
topic Resources
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5026257/
https://www.ncbi.nlm.nih.gov/pubmed/27486221
http://dx.doi.org/10.1093/molbev/msw137
work_keys_str_mv AT koflerrobert popoolationte2comparativepopulationgenomicsoftransposableelementsusingpoolseq
AT gomezsanchezdaniel popoolationte2comparativepopulationgenomicsoftransposableelementsusingpoolseq
AT schlottererchristian popoolationte2comparativepopulationgenomicsoftransposableelementsusingpoolseq