A comparative analysis of transposable element diversity and evolution across 75 bee genomes

Transposable elements (TEs) are repetitive DNA sequences that can alter their position and abundance within genomes. While TEs are known to have various impacts on genome structure and function, our understanding of how their evolution has shaped genome diversity across the Tree of Life remains limited. Characterizing repetitive DNA profiles in a phylogenomic comparative context provides valuable insight into the evolutionary roles of these important genomic features. Bees are a well-studied and species-rich lineage which makes them an effective tool for exploring the evolution of TEs and their relationship to functional traits in non-model organisms. Here, we characterize TE dynamics across high-quality genome assemblies of 75 bee species to quantify their diversity in an evolutionary context. We find that bees show a striking amount of variation in repetitive element diversity and abundance, comprising between 4.4% to 82.1% of their genomes. We determine this variation is largely responsible for genome size differences, and lineages have unique signatures of TE accumulation with many genomes containing TE copies with a putatively recent history of activity. Additionally, we find a reduction of repetitive DNA to be associated with species that produce multiple generations per year. Our study provides the most comprehensive analysis of TE evolution across bees to date, allowing deep insight into genome evolution of the most species rich lineage of pollinating insects. This work will provide the foundation for future research on the evolution of TEs across bees, and the impact of TEs on genome evolution in general.