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      headline:Comparative genomics provides insights into chromosomal evolution and immunological adaptation in horseshoe bats
      description:Horseshoe bats are natural hosts of zoonotic viruses, yet the genetic basis of their antiviral immunity is poorly understood. Here we generated two new chromosomal-level genome assemblies for horseshoe bat species (Rhinolophus) and three close relatives, and show that, during their diversification, horseshoe bats underwent extensive chromosomal rearrangements and gene expansions linked to segmental duplications. These expansions have generated new adaptive variations in type I interferons and the interferon-stimulated gene ANXA2R, which potentially enhance antiviral states, as suggested by our functional assays. Genome-wide selection screens, including of candidate introgressed regions, uncover numerous putative molecular adaptations linked to immunity, including in viral receptors. By expanding taxon coverage to ten horseshoe bat species, we identify new variants of the SARS-CoV-2 receptor ACE2, and report convergent functionally important residues that could explain wider patterns of susceptibility across mammals. We conclude that horseshoe bats have numerous signatures of adaptation, including some potentially related to immune response to viruses, in genomic regions with diverse and multiscale mutational changes. A comparative analysis of bat genomes, including five newly assembled chromosome-scale genomes, provides insights into the diversification of horseshoe bats and reveals molecular adaptations with a potential role in antiviral immune response.
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               name:State Key Laboratory of Virology and Biosafety, Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
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            type:Organization
            name:Novogene Bioinformatics Institute
            address:
               name:Novogene Bioinformatics Institute, Beijing, China
               type:PostalAddress
            type:Organization
      name:Junyu Si
      affiliation:
            name:Wuhan University
            address:
               name:State Key Laboratory of Virology and Biosafety, Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
               type:PostalAddress
            type:Organization
      name:Libiao Zhang
      affiliation:
            name:Guangdong Academy of Sciences
            address:
               name:Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
               type:PostalAddress
            type:Organization
      name:Jiaming Zeng
      affiliation:
            name:Wuhan University
            address:
               name:State Key Laboratory of Virology and Biosafety, Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
               type:PostalAddress
            type:Organization
      name:Xiangyi Zhang
      url:http://orcid.org/0000-0002-4221-8978
      affiliation:
            name:Wuhan University
            address:
               name:State Key Laboratory of Virology and Biosafety, Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
               type:PostalAddress
            type:Organization
      name:Chen Huang
      affiliation:
            name:Wuhan University
            address:
               name:State Key Laboratory of Virology and Biosafety, Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
               type:PostalAddress
            type:Organization
      name:Gang Li
      url:http://orcid.org/0000-0001-7400-5486
      affiliation:
            name:Shaanxi Normal University
            address:
               name:College of Life Sciences, Shaanxi Normal University, Xi’an, China
               type:PostalAddress
            type:Organization
      name:Caoqi Lei
      affiliation:
            name:Wuhan University
            address:
               name:State Key Laboratory of Virology and Biosafety, Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
               type:PostalAddress
            type:Organization
      name:Xuming Zhou
      url:http://orcid.org/0000-0002-1100-6294
      affiliation:
            name:Institute of Zoology, Chinese Academy of Sciences
            address:
               name:CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
               type:PostalAddress
            type:Organization
      name:Rong Geng
      affiliation:
            name:Guangzhou International Bio Island
            address:
               name:Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, China
               type:PostalAddress
            type:Organization
      name:Peng Zhou
      affiliation:
            name:Guangzhou International Bio Island
            address:
               name:Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, China
               type:PostalAddress
            type:Organization
      name:Huan Yan
      url:http://orcid.org/0000-0001-8744-8665
      affiliation:
            name:Wuhan University
            address:
               name:State Key Laboratory of Virology and Biosafety, Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
               type:PostalAddress
            type:Organization
      name:Stephen J. Rossiter
      url:http://orcid.org/0000-0002-3881-4515
      affiliation:
            name:Queen Mary University of London
            address:
               name:School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
               type:PostalAddress
            type:Organization
      email:[email protected]
      name:Huabin Zhao
      url:http://orcid.org/0000-0002-7848-6392
      affiliation:
            name:Wuhan University
            address:
               name:State Key Laboratory of Virology and Biosafety, Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
               type:PostalAddress
            type:Organization
      email:[email protected]
PostalAddress:
      name:State Key Laboratory of Virology and Biosafety, Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
      name:Novogene Bioinformatics Institute, Beijing, China
      name:State Key Laboratory of Virology and Biosafety, Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
      name:Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
      name:State Key Laboratory of Virology and Biosafety, Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
      name:State Key Laboratory of Virology and Biosafety, Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
      name:State Key Laboratory of Virology and Biosafety, Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
      name:College of Life Sciences, Shaanxi Normal University, Xi’an, China
      name:State Key Laboratory of Virology and Biosafety, Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
      name:CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
      name:Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, China
      name:Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, China
      name:State Key Laboratory of Virology and Biosafety, Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
      name:School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
      name:State Key Laboratory of Virology and Biosafety, Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
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