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.

Transposable elements (TEs) are genetic parasites that can potentially threaten the stability of the genomes they colonize. Nonetheless, TEs persist within genomes and are rarely fully eliminated, with diverse TE families coexisting in varing copy numbers. The TE replication strategies that enable host organisms to tolerate and accommodate the extensive diversity of TEs, while minimizing harm to the host and avoiding mutual competition among TEs, remain poorly understood. Here, by studying the spontaneous or experimental mobilization of four Drosophila LTR RetroTransposable Elements (LTR-RTEs), we reveal that each of them preferentially targets open chromatin regions characterized by specific epigenetic features. Among these, gtwin and ZAM are expressed in distinct cell types within female somatic gonadal tissues and inserted into the distinct accessible chromatin landscapes of the corresponding stages of embryogenesis. These findings suggest that individual LTR-RTEs exploit unique biological niches, enabling their coexistence within the tightly regulated ecosystem of the same host genome.

The specific role of chromatin modifying factors in the timely execution of transcriptional changes in gene expression to regulate organ size remains largely unknown. Here, we report that in Drosophila melanogaster depletion of the histone demethylase dLsd1 results in the reduction of wing size. dLsd1 depletion affects cell proliferation and causes an increase in DNA damage and cell death. Mechanistically, we have identified Transposable Elements (TEs) as critical dLsd1 targets for organ size determination. We found that upon dLsd1 loss many TE families are upregulated, and new TE insertions appear. By blocking this new TE activity, we could rescue the wing size phenotype. Collectively, our results reveal that the histone demethylase dLsd1 and maintenance of TE homeostasis are required to ensure proper wing size.