Transposable elements as catalysts of genome evolution in Drosophila virilis

Transposable elements (TEs) drive genomic innovation, but their dynamics in non-model species remain unclear. Herein, we integrated multiomics 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 mobilisation: recent activity, speciation-associated divergence, and ancient invasions. TEs in D. virilis dynamically colonise euchromatin and heterochromatin, contradicting the idea that heterochromatin is just a passive dump for degenerate repeats. Most TE families are prevalent across all analyzed D. virilis strains, while certain DNA transposons and retroelements exhibit strain-specific expansion, suggesting different TE activity and silencing across populations. Nonetheless, there is substantial evidence for extensive horizontal transfer of TEs among close relatives, demonstrating that the D. virilis species group function effectively as TE “ecosystem”. Epigenetic profiling revealed 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 polymorphic inversion in D. virilis, likely linked to retrotransposons. Our findings illuminate TEs as catalysts of genomic innovation, influencing gene regulation and evolutionary trajectories, providing a framework for studying TE dynamics across species. Overall design: RNA-seq, ChIP-seq and long-read genomic sequences of various strains of Drosophila virilis