Chromosome-level genome and population genomics of the intermediate horseshoe bat(Rhinolophus affinis)reveal the molecular basis of virus tolerance in Rhinolophus and echolocation call frequency variation  

作　　者：Le Zhao Jiaqing Yuan Guiqiang Wang Haohao Jing Chen Huang Lulu Xu Xiao Xu Ting Sun Wu Chen Xiuguang Mao Gang Li 

机构地区：[1]College of Life Sciences,Shaanxi Normal University,Xi’an,Shaanxi 710119,China [2]QinLing-Bashan Mountains Bioresources Comprehensive Development C.I.C.,School of Bioscience and Engineering,Shaanxi University of Technology,Hanzhong,Shaanxi 723001,China [3]Guangzhou Zoo,Guangzhou,Guangdong 510070,China [4]School of Ecological and Environmental Sciences,East China Normal University,Shanghai 200241,China

出　　处：《Zoological Research》2024年第5期1147-1160,共14页动物学研究（英文）

基　　金：supported by the China Postdoctoral Science Foundation(2022M722020)to Z.L.;Key Project of Scientific Research Program of Shaanxi Provincial Education Department(23JY020)to Z.L.;Natural Science Basic Research Program of Shaanxi(2024JCYBMS-152)to Z.L.;Key Projects of Shaanxi University of Technology(SLGKYXM2302)to Z.L.;Opening Foundation of Shaanxi University of Technology(SLGPT2019KF02-02)to Z.L.;Natural Science Basic Research Program of Shaanxi(2020JM-280)to G.L.;Fundamental Research Funds for the Central Universities(GK201902008)to G.L;National Natural Science Foundation of China(31570378)to X.M.

摘　　要：Horseshoe bats(genus Rhinolophus,family Rhinolophidae)represent an important group within chiropteran phylogeny due to their distinctive traits,including constant high-frequency echolocation,rapid karyotype evolution,and unique immune system.Advances in evolutionary biology,supported by high-quality reference genomes and comprehensive whole-genome data,have significantly enhanced our understanding of species origins,speciation mechanisms,adaptive evolutionary processes,and phenotypic diversity.However,genomic research and understanding of the evolutionary patterns of Rhinolophus are severely constrained by limited data,with only a single published genome of R.ferrumequinum currently available.In this study,we constructed a high-quality chromosome-level reference genome for the intermediate horseshoe bat(R.affinis).Comparative genomic analyses revealed potential genetic characteristics associated with virus tolerance in Rhinolophidae.Notably,we observed expansions in several immune-related gene families and identified various genes functionally associated with the SARS-CoV-2 signaling pathway,DNA repair,and apoptosis,which displayed signs of rapid evolution.In addition,we observed an expansion of the major histocompatibility complex class II(MHC-II)region and a higher copy number of the HLA-DQB2 gene in horseshoe bats compared to other chiropteran species.Based on whole-genome resequencing and population genomic analyses,we identified multiple candidate loci(e.g.,GLI3)associated with variations in echolocation call frequency across R.affinis subspecies.This research not only expands our understanding of the genetic characteristics of the Rhinolophus genus but also establishes a valuable foundation for future research.

关 键 词：Reference-quality genome Comparative genomics Population genomics Positive selection Bats 

分 类 号：Q953[生物学—动物学]