Accelerated genome shuffling associated with rapid evolution of sexual conflict in seed beetles

Structural variation (SV) has an extensive impact on the evolution of the genome. The diverse SV provide a material basis for genome evolution, which can affect gene expression, 3D genome structure, and even changes in complex chromosomal features through regional recombination, copy number variation, and chromosome rearrangement. Here, we assemble and compare the chromosome-level assemblies of three species ( Acanthoscelides obtectus , Callosobruchus chinensis , and C. maculatus ) in Bruchinae, a clade of Coleoptera that is often used as models to study sexual conflict, to investigate the influence of SV on the changes of various genomic characteristics during species evolution. Through comparative genomic analysis of Coleoptera species, we reveal extensive structural variants (SVs) within the Bruchinae family, which is linked to the ongoing activity of LINE transposons. We show that SV drive the rapid evolution of sex chromosomes and correlated with dynamic evolution of sex-biased gene expression in seed beetle species. Our analysis highlights the acquisition of novel genes on the Y chromosome through frequent gene translocations, gradually shaping them into genes exhibiting male-biased expression patterns. This underscores the Y chromosome’s role in promoting sexual dimorphism evolution. Our findings reveal the significant contributions of SV to genome evolution, specifically through their influence on sex chromosome evolution and the evolutionary dynamics of sex-biased genes.