Sequencing of pooled DNA samples (Pool-Seq) uncovers complex dynamics of transposable element insertions in Drosophila melanogaster.



Kofler, Robert ORCID: 0000-0001-9960-7248, Betancourt, Andrea J ORCID: 0000-0001-9351-1413 and Schlötterer, Christian
(2012) Sequencing of pooled DNA samples (Pool-Seq) uncovers complex dynamics of transposable element insertions in Drosophila melanogaster. PLoS genetics, 8 (1). e1002487-.

Access the full-text of this item by clicking on the Open Access link.

Abstract

Transposable elements (TEs) are mobile genetic elements that parasitize genomes by semi-autonomously increasing their own copy number within the host genome. While TEs are important for genome evolution, appropriate methods for performing unbiased genome-wide surveys of TE variation in natural populations have been lacking. Here, we describe a novel and cost-effective approach for estimating population frequencies of TE insertions using paired-end Illumina reads from a pooled population sample. Importantly, the method treats insertions present in and absent from the reference genome identically, allowing unbiased TE population frequency estimates. We apply this method to data from a natural Drosophila melanogaster population from Portugal. Consistent with previous reports, we show that low recombining genomic regions harbor more TE insertions and maintain insertions at higher frequencies than do high recombining regions. We conservatively estimate that there are almost twice as many "novel" TE insertion sites as sites known from the reference sequence in our population sample (6,824 novel versus 3,639 reference sites, with on average a 31-fold coverage per insertion site). Different families of transposable elements show large differences in their insertion densities and population frequencies. Our analyses suggest that the history of TE activity significantly contributes to this pattern, with recently active families segregating at lower frequencies than those active in the more distant past. Finally, using our high-resolution TE abundance measurements, we identified 13 candidate positively selected TE insertions based on their high population frequencies and on low Tajima's D values in their neighborhoods.

Item Type: Article
Uncontrolled Keywords: Animals, Drosophila melanogaster, DNA Transposable Elements, Mutagenesis, Insertional, Sequence Analysis, DNA, Evolution, Molecular, Recombination, Genetic, Gene Frequency, Portugal, Genome, Insect, Selection, Genetic
Depositing User: Symplectic Admin
Date Deposited: 31 Oct 2016 09:55
Last Modified: 07 Feb 2024 11:44
DOI: 10.1371/journal.pgen.1002487
Open Access URL: http://journals.plos.org/plosgenetics/article?id=1...
Related URLs:
URI: https://livrepository.liverpool.ac.uk/id/eprint/3004207