title: PoPoolationTE2: Comparative Population Genomics of Transposable Elements Using Pool-Seq.
abstract: 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.
authors.affiliation: Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria.
authors.forename: Robert
authors.initials: R
authors.lastname: Kofler
authors.affiliation: Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria.
authors.forename: Daniel
authors.initials: D
authors.lastname: Gómez-Sánchez
authors.affiliation: Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria christian.schloetterer@vetmeduni.ac.at.
authors.forename: Christian
authors.initials: C
authors.lastname: Schlötterer
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D004251:DNA Transposable Elements; D004331:Drosophila melanogaster; D019143:Evolution, Molecular; D023281:Genomics / Q000379:methods*; D056186:Metagenomics / Q000379:methods*; D008957:Models, Genetic; D012641:Selection, Genetic / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004251:DNA Transposable Elements
keywords: Pool-Seq; bioinformatics; comparative genomics; comparative population genomics; next generation sequencing; transposable elements