Abstract
Transposable elements (TEs) are the main components of genomes. However, due to their repetitive nature, they are very difficult to study using data obtained with short-read sequencing technologies. Here, we describe an efficient pipeline to accurately recover TE insertion (TEI) sites and sequences from long reads obtained by Oxford Nanopore Technology (ONT) sequencing. With this pipeline, we could precisely describe the landscapes of the most recent TEIs in wild-type strains of Drosophila melanogaster and Drosophila simulans. Their comparison suggests that this subset of TE sequences is more similar than previously thought in these two species. The chromosome assemblies obtained using this pipeline also allowed recovering piRNA cluster sequences, which was impossible using short-read sequencing. Finally, we used our pipeline to analyze ONT sequencing data from a D. melanogaster unstable line in which LTR transposition was derepressed for 73 successive generations. We could rely on single reads to identify new insertions with intact target site duplications. Moreover, the detailed analysis of TEIs in the wild-type strains and the unstable line did not support the trap model claiming that piRNA clusters are hotspots of TE insertions.
Highlights
Transposable elements (TEs) are major components of almost all eukaryotic genomes [1,2].They can be separated into three main groups that include several TE superfamilies and families: Cells 2020, 9, 1776; doi:10.3390/cells9081776 www.mdpi.com/journal/cellsDNA transposons, Long-Terminal Repeat (LTR) elements, and Long Interspersed Nuclear Elements (LINEs) [2,3]
Our work demonstrates that long reads are crucial in order to finely describe TE landscapes at the intra-genome scale
The parallel analysis of two close species (D. melanogaster and D. simulans) and two genetic backgrounds allowed us to show that overall, TE recent dynamics are quite similar between species and among strains
Summary
Transposable elements (TEs) are major components of almost all eukaryotic genomes [1,2].They can be separated into three main groups that include several TE superfamilies and families: Cells 2020, 9, 1776; doi:10.3390/cells9081776 www.mdpi.com/journal/cellsDNA transposons, Long-Terminal Repeat (LTR) elements, and Long Interspersed Nuclear Elements (LINEs) [2,3]. Transposable elements (TEs) are major components of almost all eukaryotic genomes [1,2]. They can be separated into three main groups that include several TE superfamilies and families: Cells 2020, 9, 1776; doi:10.3390/cells9081776 www.mdpi.com/journal/cells. Different methods (e.g., Southern blotting [4,5], in-situ hybridization on polytene chromosomes [6,7], and PCR [8,9]) were first used to estimate TE content in Drosophila genomes and to understand how TEs invade and shape genomes by affecting genome function and evolution. Several computational methods were developed, such as RepeatExplorer [10] and dnaPipeTE [11], to analyze Illumina data from different Drosophila species, and to study TE biology at the populational level
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