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, Bjšrn
dc.contributor.author Bergman, Casey M
dc.contributor.author Lau, Nelson C
dc.date.accessioned 2019-01-17T19:30:56Z
dc.date.available 2019-01-17T19:30:56Z
dc.date.issued 2015
dc.identifier.issn 1362-4962
dc.identifier.uri https://hdl.handle.net/10192/36121
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.format.extent 1 file
dc.language English
dc.language.iso eng
dc.publisher Oxford University Press
dc.relation.isversionof https://dx.doi.org/10.1093/nar/gkv1193
dc.rights Creative Commons Attribution 4.0 International License
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.subject Animals
dc.subject Cell Line
dc.subject DNA Transposable Elements
dc.subject Databases, Nucleic Acid
dc.subject Drosophila melanogaster
dc.subject Genetic Variation
dc.subject Genome, Insect
dc.subject Genomics
dc.subject RNA, Small Interfering
dc.subject Retroelements
dc.subject DNA Transposable Elements
dc.subject RNA, Small Interfering
dc.subject Retroelements
dc.title Unique transposon landscapes are pervasive across Drosophila melanogaster genomes.
dc.type Article
dc.contributor.department Department of Biology
dc.relation.journal Nucleic Acids Research
dc.identifier.pmid 26578579
dc.identifier.pmcid PMC4678822


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