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.
Highlights
Transposable elements (TEs) are short stretches of DNA that selfishly propagate within genomes and are thought to be involved in diverse phenomena ranging from human diseases (Kazazian, 1998) to genome evolution (Kazazian, 2004)
Promising lines of research include the activity of transposable elements (TEs) in mutation accumulation lines, the dynamics of TE invasions during experimental evolution, the contribution of TEs to local adaptation, the evolution of TE
A comparison of TE abundance between pooled samples is difficult as numbers of reads are usually insufficient to identify all TEs within a pool
Summary
Transposable elements (TEs) are short stretches of DNA that selfishly propagate within genomes and are thought to be involved in diverse phenomena ranging from human diseases (Kazazian, 1998) to genome evolution (Kazazian, 2004).Addressing many questions about the biology of TEs requires comparing TE abundance between different samples. A comparison of TE abundance between pooled samples is difficult as numbers of reads are usually insufficient to identify all TEs within a pool. Based on the physical pileup our new software tool PoPoolationTE2 homogenizes the physical coverage across samples and the power to identify TEs. PoPoolationTE2 is a fast and user-friendly tool for analysing TE insertions in one or more samples, where samples could be tissues, pooled populations or sequenced individuals.
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