High-quality genome assemblies reveal intra-chromosomal rearrangements and molecular signatures of adaptation in vespertilionid bats

Abstract Chromosome-level genome assemblies offer novel insights into the molecular mechanisms driving adaptive evolution. Beyond revealing macroevolutionary trends, these resources enable precise detection of fine-scale intra-chromosomal rearrangements. Here, we analyzed 16 chromosome-scale genomes, including 11 Vespertilionidae species, to investigate cryptic structural variation in karyotypically conserved lineages (2n = 44) across four Myotis and two Pipistrellus bats using whole-genome alignment. We uncovered widespread intra-chromosomal rearrangements, predominantly inversions, accounting for 0.49–3.13% of the genomes. Multiple large inversions (>1 Mb) encompassed genes involved in antiviral innate immunity (e.g., TRIMs, NLRPs, IRF3). We further investigated molecular adaptations linked to distinctive traits in Vespertilionidae and detected multiple positively selected genes (PSGs) and dynamically evolving gene families associated with antiviral defense and immune specialization. These include PSGs (CDK13, NUP93, SND1) and expanded gene families (NLRP1, GZMs) related to virus tolerance. Immune specialization was reflected through PSGs such as ACE, ADAM17, NDFIP1, IL27RA, and TNIP1, along with expanded families including TRIMs. Many of these genes also contribute to cancer-resistance pathways, suggesting pleiotropic adaptations that may support bat longevity. Additionally, genomic signatures of urban adaptation were identified, encompassing traits such as pollution resistance (PSGs: XPA, DNMT3B; expanded family: TAS2Rs) and photoperiod adaptation (PSGs: GPR179, ABCA4). In light of existing literature, this study highlights that comprehensive comparative genomic analyses (especially inferences of gene family evolution) require highly continuous and accurate genome assemblies, which are essential for reliably identifying candidate genetic drivers of adaptive evolution.