Format

Send to

Choose Destination
PLoS One. 2012;7(2):e30008. doi: 10.1371/journal.pone.0030008. Epub 2012 Feb 9.

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

Author information

1
Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.

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.

PMID:
22347367
PMCID:
PMC3276498
DOI:
10.1371/journal.pone.0030008
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Public Library of Science Icon for PubMed Central
Loading ...
Support Center