Publication

Pangolin genomes and the evolution of mammalian scales and immunity

Genome Res. 2016 Aug 10. pii: gr.203521.115. [Epub ahead of print]

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 (IFN-?), exclusively expressed in epithelial cells and important in skin and mucosal immunity, is pseudogenised 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 IFN-?-deficient animal model for studying mammalian immunity.

Authors

Choo SW, Rayko M, Tan TK, Hari R, Komissarov A, Wee WY, Yurchenko A, Kliver S, Tamazian G, Antunes A, Wilson RK, Warren WC, Koepfli KP, Minx P, Krasheninnikova K, Kotze A, Dalton DL, Vermaak E, Paterson IC, Dobrynin P, Thomas Sitam F, Rovie Ryan Japning J, Johnson WE, Mohamed Yusoff A, Luo SJ, Vizi Karuppannan K, Fang G, Zheng D, Gerstein MB, Lipovich L, O'Brien SJ, Wong GJ

Institute Authors

Wes Warren, Ph.D., Patrick Minx