期刊
MOLECULAR BIOLOGY AND EVOLUTION
卷 33, 期 10, 页码 2759-2764出版社
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msw137
关键词
transposable elements; comparative genomics; bioinformatics; next generation sequencing; Pool-Seq; comparative population genomics
资金
- European Research Council Grant ArchAdapt
- DFG (Adaptomics) [SPP 1529]
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.
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