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Nucleic Acids Res. 2015 Dec 15;43(22):10655-72. doi: 10.1093/nar/gkv1193. Epub 2015 Nov 17.

Unique transposon landscapes are pervasive across Drosophila melanogaster genomes.

Author information

1
Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA 02454, USA.
2
Institute of Zoology, Universität Regensburg, Regensburg, Germany.
3
Faculty of Life Sciences, University of Manchester, Manchester M21 0RG, UK.
4
Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA 02454, USA nlau@brandeis.edu.

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.

PMID:
26578579
PMCID:
PMC4678822
DOI:
10.1093/nar/gkv1193
[Indexed for MEDLINE]
Free PMC Article

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