Pangolin genomes and the evolution of mammalian scales and immunity
Siew Woh ChooGenome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Oral and Craniofacial Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia; Genome Solutions Sdn Bhd, Research Management & Innovation Complex, University of Malaya, 50603 Kuala Lumpur, MalaysiaMikhail RaykoTheodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004Tze King TanGenome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Oral and Craniofacial Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, MalaysiaRanjeev HariGenome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Oral and Craniofacial Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, MalaysiaAleksey KomissarovTheodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004Wei Yee WeeGenome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Oral and Craniofacial Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, MalaysiaAndrey A. YurchenkoTheodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004Sergei KliverTheodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004Gaik TamazianTheodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004Agostinho AntunesCIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-123 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, PortugalRichard K. WilsonMcDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USAWesley C. WarrenMcDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USAKlaus‐Peter KoepfliNational Zoological Park, Smithsonian Conservation Biology Institute, Washington, DC 20008, USAPatrick MinxMcDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USAKsenia KrasheninnikovaTheodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004Antoinette KotzéNational Zoological Gardens of South Africa, Pretoria 0001, South Africa; Department of Genetics, University of the Free State, Bloemfontein, 9300, South AfricaDesiré L. DaltonNational Zoological Gardens of South Africa, Pretoria 0001, South Africa; Department of Genetics, University of the Free State, Bloemfontein, 9300, South AfricaElaine VermaakNational Zoological Gardens of South Africa, Pretoria 0001, South AfricaIan C. PatersonDepartment of Oral and Craniofacial Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia; Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, MalaysiaPavel DobryninTheodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004Frankie Thomas SitamEx-Situ Conservation Division, Department of Wildlife and National Parks, 56100 Kuala Lumpur, MalaysiaJeffrine J. Rovie‐RyanEx-Situ Conservation Division, Department of Wildlife and National Parks, 56100 Kuala Lumpur, MalaysiaWarren E. JohnsonNational Zoological Park, Smithsonian Conservation Biology Institute, Washington, DC 20008, USAAini Mohamed YusoffGenome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Oral and Craniofacial Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, MalaysiaShu‐Jin LuoPeking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing, China 100871Kayal Vizi KaruppannanEx-Situ Conservation Division, Department of Wildlife and National Parks, 56100 Kuala Lumpur, MalaysiaGang FangNYU Shanghai, Pudong, Shanghai, China 200122Deyou ZhengDepartment of Neurology, Albert Einstein College of Medicine, Bronx, New York 10461, USAMark GersteinProgram in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA; Department of Computer Science, Yale University, New Haven, Connecticut 06520, USALeonard LipovichCenter for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA; Department of Neurology, School of Medicine, Wayne State University, Detroit, Michigan 48201, USAStephen J. O’BrienTheodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004; Oceanographic Center, Nova Southeastern University, Ft. Lauderdale, Florida 33004, USAGuat Jah WongGenome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia
2016en
ABI
Аннотация
Pangolins, unique mammals with scales over most of their body, no teeth, poor vision, and an acute olfactory system, comprise the only placental order (Pholidota) without a whole-genome map. To investigate pangolin biology and evolution, we developed genome assemblies of the Malayan (Manis javanica) and Chinese (M. pentadactyla) pangolins. Strikingly, we found that interferon epsilon (IFNE), exclusively expressed in epithelial cells and important in skin and mucosal immunity, is pseudogenized in all African and Asian pangolin species that we examined, perhaps impacting resistance to infection. We propose that scale development was an innovation that provided protection against injuries or stress and reduced pangolin vulnerability to infection. Further evidence of specialized adaptations was evident from positively selected genes involving immunity-related pathways, inflammation, energy storage and metabolism, muscular and nervous systems, and scale/hair development. Olfactory receptor gene families are significantly expanded in pangolins, reflecting their well-developed olfaction system. This study provides insights into mammalian adaptation and functional diversification, new research tools and questions, and perhaps a new natural IFNE-deficient animal model for studying mammalian immunity.
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