title: Unique transposon landscapes are pervasive across Drosophila melanogaster genomes.
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.
authors.affiliation: Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA 02454, USA.
authors.forename: Reazur
authors.initials: R
authors.lastname: Rahman
authors.affiliation: Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA 02454, USA.
authors.forename: Gung-wei
authors.initials: GW
authors.lastname: Chirn
authors.affiliation: Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA 02454, USA.
authors.forename: Abhay
authors.initials: A
authors.lastname: Kanodia
authors.affiliation: Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA 02454, USA.
authors.forename: Yuliya A
authors.initials: YA
authors.lastname: Sytnikova
authors.affiliation: Institute of Zoology, Universität Regensburg, Regensburg, Germany.
authors.forename: Björn
authors.initials: B
authors.lastname: Brembs
authors.affiliation: Faculty of Life Sciences, University of Manchester, Manchester M21 0RG, UK.
authors.forename: Casey M
authors.initials: CM
authors.lastname: Bergman
authors.affiliation: Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA 02454, USA nlau@brandeis.edu.
authors.forename: Nelson C
authors.initials: NC
authors.lastname: Lau
mesh_terms: D000818:Animals; D002460:Cell Line; D004251:DNA Transposable Elements; D030561:Databases, Nucleic Acid; D004331:Drosophila melanogaster / Q000235:genetics*; D014644:Genetic Variation; D049750:Genome, Insect; D023281:Genomics / Q000379:methods*; D034741:RNA, Small Interfering / Q000378:metabolism; D018626:Retroelements
chemical_list: D004251:DNA Transposable Elements; D034741:RNA, Small Interfering; D018626:Retroelements