Evolution of genome structure in theDrosophila simulansspecies complex

The rapid evolution of repetitive DNA sequences, including satellite DNA, tandem duplications, and transposable elements, underlies phenotypic evolution and contributes to hybrid incompatibilities between species. However, repetitive genomic regions are fragmented and misassembled in most contemporary genome assemblies. We generated highly contiguousde novoreference genomes for theDrosophila simulansspecies complex (D. simulans, D. mauritiana, andD. sechellia), which speciated ∼250,000 years ago. Our assemblies are comparable in contiguity and accuracy to the currentD. melanogastergenome, allowing us to directly compare repetitive sequences between these four species. We find that at least 15% of theD. simulanscomplex species genomes fail to align uniquely toD. melanogasterdue to structural divergence—twice the number of single-nucleotide substitutions. We also find rapid turnover of satellite DNA and extensive structural divergence in heterochromatic regions, while the euchromatic gene content is mostly conserved. Despite the overall preservation of gene synteny, euchromatin in each species has been shaped by clade and species-specific inversions, transposable elements, expansions and contractions of satellite and tRNA tandem arrays, and gene duplications. We also find rapid divergence among Y-linked genes, including copy number variation and recent gene duplications from autosomes. Our assemblies provide a valuable resource for studying genome evolution and its consequences for phenotypic evolution in these genetic model species.