Unique Transposon Landscapes are Pervasive Across Drosophila melanogaster Genomes

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dc.contributor.author Rahman, Reazur
dc.contributor.author Chirn, Gung-wei
dc.contributor.author Kanodia, Abhay
dc.contributor.author Sytnikova, Yuliya A.
dc.contributor.author Brembs, Björn
dc.contributor.author Bergman, Casey M.
dc.contributor.author Lau, Nelson C.
dc.date.accessioned 2016-02-17T21:14:52Z
dc.date.available 2016-02-17T21:14:52Z
dc.date.issued 2015-11-17
dc.identifier.citation Reazur Rahman, Gung-wei Chirn, Abhay Kanodia, Yuliya A. Sytnikova, Björn Brembs, Casey M. Bergman, and Nelson C. Lau "Unique transposon landscapes are pervasive across Drosophila melanogaster genomes". Nucl. Acids Res. (15 December 2015) 43 (22): 10655-10672 first published online November 17, 2015 doi:10.1093/nar/gkv1193
dc.identifier.uri http://hdl.handle.net/10192/31611
dc.description.abstract To understand how transposon landscapes (TLs) vary across animal genomes, we describe a new method called the Transposon Insertion and Depletion AnaLyzer (TIDAL) and a database of >300 TLs in Drosophila melanogaster (TIDAL-Fly). Our analysis reveals pervasive TL diversity across cell lines and fly strains, even for identically named sub-strains from different laboratories such as the ISO1 strain used for the reference genome sequence. On average, >500 novel insertions exist in every lab strain, inbred strains of the Drosophila Genetic Reference Panel (DGRP), and fly isolates in the Drosophila Genome Nexus (DGN). A minority (<25%) of transposon families comprise the majority (>70%) of TL diversity across fly strains. A sharp contrast between insertion and depletion patterns indicates that many transposons are unique to the ISO1 reference genome sequence. Although TL diversity from fly strains reaches asymptotic limits with increasing sequencing depth, rampant TL diversity causes unsaturated detection of TLs in pools of flies. Finally, we show novel transposon insertions negatively correlate with Piwi-interacting RNA (piRNA) levels for most transposon families, except for the highly-abundant roo retrotransposon. Our study provides a useful resource for Drosophila geneticists to understand how transposons create extensive genomic diversity in fly cell lines and strains.
dc.description.sponsorship Human Frontier Science Program [RGY0093/2012 to C.M.B.]; National Institutes of Health [R00HD057298 to N.C.L.]; Searle Scholars Foundation to N.C.L. Funding for open access charge: Brandeis University Open Access Fund.
dc.language English
dc.language.iso eng
dc.publisher Oxford University Press
dc.rights Copyright by the authors 2015
dc.title Unique Transposon Landscapes are Pervasive Across Drosophila melanogaster Genomes
dc.type Article
dc.contributor.department Department of Biology
dc.identifier.doi http://dx.doi.org/10.1093/nar/gkv1193
dc.description.esploro yes

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