Chromosome-level genome assembly of the king horseshoe bat (Rhinolophus rex) provides insights into its conservation status and chromosomal evolution of Rhinolophus.

A high-quality reference genome is quite valuable in assessing the conservation status of a rare species when adequate data from other sources are unavailable. Bats comprise almost a fifth of all mammals and contribute greatly to the ecosystem. However, due to the nocturnal and elusive habits, it is difficult to obtain the accurate census population size of a rare bat species and assess its conservation status. Here, we generate a chromosome-level genome assembly for the king horseshoe bat (Rhinolophus rex) and assess its conservation status by comparing the genome-wide summary statistics with other related species. The genome assembly size was 2.1 Gb (contig N50: 75.26 Mb) and 99.9% of the total sequences were anchored onto 30 autosomes, X and Y chromosomes. Despite lower genome-wide heterozygosity and recent inbreeding, R. rex did not exhibit a higher genetic load compared with the other two Rhinolophus species. Historical demography analysis revealed that R. rex maintained a long-term (2 million years) stable population size (150,000). In the future, whole-genome sequencing data from more individuals will be needed to comprehensively assess the conservation status at recent timescales. We also reconstructed the ancestral karyotype of Rhinolophus as 2n = 54 and found that Robertsonian fissions and fusions were the main mechanisms of chromosomal rearrangements in this genus. Overall, our study shows important implications of reference-quality genomes in both conservation genomics and comparative genomics.