title: Pangolin genomes and the evolution of mammalian scales and immunity.
abstract: 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.
authors: Genome 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, Malaysia.
authors: Siew Woh
authors: 0000-0002-9210-3837
authors: SW
authors: Choo
authors: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004.
authors: Mike
authors: M
authors: Rayko
authors: Genome 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.
authors: Tze King
authors: TK
authors: Tan
authors: Genome 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.
authors: Ranjeev
authors: R
authors: Hari
authors: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004.
authors: Aleksey
authors: A
authors: Komissarov
authors: Genome 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.
authors: Wei Yee
authors: WY
authors: Wee
authors: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004.
authors: Andrey A
authors: AA
authors: Yurchenko
authors: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004.
authors: Sergey
authors: S
authors: Kliver
authors: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004.
authors: Gaik
authors: G
authors: Tamazian
authors: CIIMAR/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, Portugal.
authors: Agostinho
authors: A
authors: Antunes
authors: McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA.
authors: Richard K
authors: RK
authors: Wilson
authors: McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA.
authors: Wesley C
authors: WC
authors: Warren
authors: National Zoological Park, Smithsonian Conservation Biology Institute, Washington, DC 20008, USA.
authors: Klaus-Peter
authors: KP
authors: Koepfli
authors: McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA.
authors: Patrick
authors: P
authors: Minx
authors: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004.
authors: Ksenia
authors: K
authors: Krasheninnikova
authors: National Zoological Gardens of South Africa, Pretoria 0001, South Africa; Department of Genetics, University of the Free State, Bloemfontein, 9300, South Africa.
authors: Antoinette
authors: A
authors: Kotze
authors: National Zoological Gardens of South Africa, Pretoria 0001, South Africa; Department of Genetics, University of the Free State, Bloemfontein, 9300, South Africa.
authors: Desire L
authors: DL
authors: Dalton
authors: National Zoological Gardens of South Africa, Pretoria 0001, South Africa.
authors: Elaine
authors: E
authors: Vermaak
authors: Department 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, Malaysia.
authors: Ian C
authors: IC
authors: Paterson
authors: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004.
authors: Pavel
authors: P
authors: Dobrynin
authors: Ex-Situ Conservation Division, Department of Wildlife and National Parks, 56100 Kuala Lumpur, Malaysia.
authors: Frankie Thomas
authors: FT
authors: Sitam
authors: Ex-Situ Conservation Division, Department of Wildlife and National Parks, 56100 Kuala Lumpur, Malaysia.
authors: Jeffrine J
authors: JJ
authors: Rovie-Ryan
authors: National Zoological Park, Smithsonian Conservation Biology Institute, Washington, DC 20008, USA.
authors: Warren E
authors: WE
authors: Johnson
authors: Genome 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.
authors: Aini Mohamed
authors: AM
authors: Yusoff
authors: Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing, China 100871.
authors: Shu-Jin
authors: SJ
authors: Luo
authors: Ex-Situ Conservation Division, Department of Wildlife and National Parks, 56100 Kuala Lumpur, Malaysia.
authors: Kayal Vizi
authors: KV
authors: Karuppannan
authors: NYU Shanghai, Pudong, Shanghai, China 200122.
authors: Gang
authors: G
authors: Fang
authors: Department of Neurology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
authors: Deyou
authors: D
authors: Zheng
authors: Program 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, USA.
authors: Mark B
authors: MB
authors: Gerstein
authors: Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA; Department of Neurology, School of Medicine, Wayne State University, Detroit, Michigan 48201, USA.
authors: Leonard
authors: L
authors: Lipovich
authors: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004; Oceanographic Center, Nova Southeastern University, Ft. Lauderdale, Florida 33004, USA.
authors: Stephen J
authors: SJ
authors: O'Brien
authors: Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia.
authors: Guat Jah
authors: GJ
authors: Wong
mesh_terms: D000222:Adaptation, Physiological; D000075342:Animal Scales / Q000033:anatomy & histology*; D000818:Animals; D056727:Endangered Species; D019143:Evolution, Molecular; D016678:Genome; D007113:Immunity, Innate / Q000235:genetics*; D007372:Interferons / Q000235:genetics; D008322:Mammals / Q000033:anatomy & histology / Q000145:classification / Q000235:genetics* / Q000276:immunology; D018035:Receptors, Odorant / Q000235:genetics
chemical_list: D018035:Receptors, Odorant; D007372:Interferons