Chromosome-level genomes of Bruchinae reveal the rapid evolution of sex chromosomes and sex-biased genes in seed beetles

Structural variations (SVs) provide a material basis for genomic evolution, which can influence gene expression and three-dimensional (3D) genome structure, and even alter complex chromosomal features through regional recombination, copy number variation, and chromosome rearrangement. Here, we assemble and compare the chromosome-level assemblies of three species (<italic>Acanthoscelides obtectus</italic>, <italic>Callosobruchus chinensis</italic>, and <italic>C. maculatus</italic>) in Bruchinae, a clade of Coleoptera that is often used as a model to study sexual conflict, to investigate the role of SVs in their genomic differences. Through a comparative genomic analysis of Coleoptera species, we reveal extensive SVs within the Bruchinae family, which are linked to the ongoing activity of long interspersed nuclear element (LINE) retrotransposons. We show that the significant SVs between the chromosomes of different species are correlated with the dynamic evolution of sex-biased genes. Our analysis highlights the acquisition of novel genes on the Y chromosome through frequent gene translocations. In addition, we observed additional copies of some gene families on the Y chromosome of seed beetles, which may alleviate conflicts associated with certain sexually dimorphic traits. Our findings reveal the significant contributions of SVs to the differences in genomic features in Bruchinae, specifically in sex chromosome evolution and the evolutionary dynamics of sex-biased genes.