Comparative Genomics Provide Insights Into Karyotype Evolution in Vespertilionid Bats (Vespertilionidae, Chiroptera)

Studies elucidating the molecular basis and evolutionary consequences of karyotypic changes in mammals remain scarce. Here, we investigate chromosomal evolution by focusing on two contrasting lineages within the family Vespertilionidae (Chiroptera): the karyotypically variable tribe Pipistrellini and the highly conserved genus Myotis. Pipistrellini exhibits extensive karyotype diversity, with diploid numbers (2n) ranging from 26 to 44, whereas Myotis demonstrates remarkable stability, maintaining 2n = 44 across nearly all studied species. To uncover the mechanisms driving these divergent evolutionary trajectories, we generated a high-quality chromosome-level genome assembly for Pipistrellus abramus (2n = 26). By integrating multiple high-quality vespertilionid genomes, we reconstructed the family phylogeny and inferred an ancestral karyotype of 2n = 44, revealing fusions and fissions as the primary drivers of karyotypic diversification. We further identified an enrichment of rolling-circle (RC) and recent DNA transposons in genes involved in DNA metabolism, suggesting a mechanistic basis for transposable element (TE) tolerance in Vespertilionidae. In P. abramus, a derived chromosome originated from three ancestral chromosomes via Robertsonian and end-to-end fusions, with TEs significantly enriched at fusion sites. Genome stability-related genes and contracted gene families also appear to facilitate adaptive responses to structural changes. These findings provide novel insights into the molecular mechanisms underlying chromosome evolution and speciation in mammals.