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Title:
Comparative genomics provides insights into chromosomal evolution and immunological adaptation in horseshoe bats | Nature Ecology & Evolution
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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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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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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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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, XiΓ’ΒΒan, 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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