Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster

Raquel S. Linheiro, Casey M. Bergman

    Research output: Contribution to journalArticlepeer-review

    Abstract

    Transposable elements are mobile DNA sequences that integrate into host genomes using diverse mechanisms with varying degrees of target site specificity. While the target site preferences of some engineered transposable elements are well studied, the natural target preferences of most transposable elements are poorly characterized. Using population genomic resequencing data from 166 strains of Drosophila melanogaster, we identified over 8,000 new insertion sites not present in the reference genome sequence that we used to decode the natural target preferences of 22 families of transposable element in this species. We found that terminal inverted repeat transposon and long terminal repeat retrotransposon families present clade-specific target site duplications and target site sequence motifs. Additionally, we found that the sequence motifs at transposable element target sites are always palindromes that extend beyond the target site duplication. Our results demonstrate the utility of population genomics data for high-throughput inference of transposable element targeting preferences in the wild and establish general rules for terminal inverted repeat transposon and long terminal repeat retrotransposon target site selection in eukaryotic genomes. © 2012 Linheiro, Bergman.
    Original languageEnglish
    Article numbere30008
    JournalPLoS ONE
    Volume7
    Issue number2
    DOIs
    Publication statusPublished - 9 Feb 2012

    Fingerprint

    Dive into the research topics of 'Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster'. Together they form a unique fingerprint.

    Cite this