Feb 3, 2016

PoPoolationTE2: comparative population genomics of transposable elements using Pool-Seq

BioRxiv : the Preprint Server for Biology
Robert KoflerChristian Schloetterer

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, 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.

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Mentioned in this Paper

Patterns
Nucleic Acid Sequencing
Bio-Informatics
Genomics
Comparative Genomic Analysis
Transient Elastography
Simulation
Analysis
DNA Transposable Elements
Population Group

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