RT Journal Article
SR Electronic
T1 PoPoolationTE2: comparative population genomics of transposable elements using Pool-Seq
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 038745
DO 10.1101/038745
A1 Robert Kofler
A1 Daniel Gómez-Sánchez
A1 Christian Schlöetterer
YR 2016
UL http://biorxiv.org/content/early/2016/02/03/038745.abstract
AB 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, and despite recent advances in sequencing technologies, characterizing TE abundance in multiple populations by sequencing individuals separately is still too expensive. While sequencing pools of individuals (Pool-Seq) 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 acrosss 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.