Unique transposon landscapes are pervasive acrossDrosophila melanogastergenomes

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.

Direct interrogation of the role of H3K9 in metazoan heterochromatin function

“…In Drosophila, >130 different transposon families have been identified, with most families consisting of multiple insertions throughout the genome (Rahman et al 2015). This repetition complicates mapping of reads and consequently the analysis of high-throughput sequencing data.…”

“…We also searched for evidence of transposon insertion and depletion events in our whole-genome sequencing data sets using the program TIDAL, which uses split read analysis to identify junction reads that span both transposon and unique sequences (Rahman et al 2015). We examined input DNA from both our wing disc FAIRE experiment and our whole larvae HP1a ChIP experiment.…”

Reexamining the P-Element Invasion of Drosophila melanogaster Through the Lens of piRNA Silencing

“…However, performing this test of selection requires curating these alleles among wild-derived chromosomes, a goal that has been limited by the challenge of examining repetitive elements in short-read sequence data. Although population genomic approaches for TE annotation have improved greatly (Kofler et al 2012;Cridland et al 2013;Zhuang et al 2014;Fiston-Lavier et al 2015;Rahman et al 2015), the repetitive nature of piRNA clusters poses a particular problem for annotating insertions in these genomic regions. Similarly, determining the population frequencies of KP insertions requires not just annotating, but also assembling, specific P elements in order to localize structural variants to particular insertion sites.…”

PoPoolationTE2: comparative population genomics of transposable elements using Pool-Seq

“…Masking of TEs may be done based on a TE annotation, RepeatMasker (Smit et al 1996(Smit et al -2010 or, as RepatMasker sometimes misses TE insertions (Rahman et al 2015), iterative mapping of reads derived from TE sequences (see Manual). When reads are mapped to such a modified genome, TE insertions will result in groups of discordantly mapped paired ends, where one read maps to the reference chromosome and the other to a TE sequence (signatures of TE insertions; fig.…”