Transposable elements as drivers of genome evolution in <i>Drosophila virilis</i>

Transposable elements (TEs) drive genomic innovation, but their dynamics in non-model species remain unclear. Here, we integrated multi-omics data to explore TE dynamics in Drosophila virilis, an important model for repetitive DNA research. By combining computational predictions with manual curation, we identified 100 TE families and delineated three temporal waves of TE mobilization: recent activity, speciation-associated, and ancient invasions. TEs in D. virilis dynamically colonise both euchromatin and heterochromatin, suggesting heterochromatin is not solely a repository for degenerate repeats. While most TEs are widespread across strains, some exhibit strain-specific expansions, indicating varied activity and silencing. We found substantial evidence for horizontal transfer of TEs among close relatives, demonstrating that the D. virilis species group functions effectively as a TE "ecosystem", allowing for recurrent invasion, loss, and re-invasion of TE lineages across the group. Epigenetic profiling revealed that H3K9me3 spreading from TEs represses adjacent genes in a distance-dependent manner, influenced by insertion length and genomic context, affecting developmental and metabolic genes. We also discovered the first spontaneous polymorphic inversion in D. virilis linked to retrotransposons. Our findings illuminate TEs as drivers of genomic innovation, influencing gene regulation and evolutionary trajectories, providing a framework for studying TE dynamics across animal species.