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

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 e...

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Autores principales:	Raquel S Linheiro, Casey M Bergman
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/034b47140ddb44878ce5fbf405854b58
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spelling	oai:doaj.org-article:034b47140ddb44878ce5fbf405854b582021-11-18T07:28:36ZWhole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster.1932-620310.1371/journal.pone.0030008https://doaj.org/article/034b47140ddb44878ce5fbf405854b582012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22347367/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Transposable 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.Raquel S LinheiroCasey M BergmanPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 2, p e30008 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Raquel S Linheiro Casey M Bergman Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster.
description	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.
format	article
author	Raquel S Linheiro Casey M Bergman
author_facet	Raquel S Linheiro Casey M Bergman
author_sort	Raquel S Linheiro
title	Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster.
title_short	Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster.
title_full	Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster.
title_fullStr	Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster.
title_full_unstemmed	Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster.
title_sort	whole genome resequencing reveals natural target site preferences of transposable elements in drosophila melanogaster.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/034b47140ddb44878ce5fbf405854b58
work_keys_str_mv	AT raquelslinheiro wholegenomeresequencingrevealsnaturaltargetsitepreferencesoftransposableelementsindrosophilamelanogaster AT caseymbergman wholegenomeresequencingrevealsnaturaltargetsitepreferencesoftransposableelementsindrosophilamelanogaster
_version_	1718423389326016512

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

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