TY - JOUR
T1 - Pangolin genomes and the evolution of mammalian scales and immunity
AU - Choo, Siew Woh
AU - Rayko, Mike
AU - Tan, Tze King
AU - Hari, Ranjeev
AU - Komissarov, Aleksey
AU - Wee, Wei Yee
AU - Yurchenko, Andrey A.
AU - Kliver, Sergey
AU - Tamazian, Gaik
AU - Antunes, Agostinho
AU - Wilson, Richard K.
AU - Warren, Wesley C.
AU - Koepfli, Klaus-Peter
AU - Minx, Patrick
AU - Krasheninnikova, Ksenia
AU - Kotze, Antoinette
AU - Dalton, Desire L.
AU - Vermaak, Elaine
AU - Paterson, Ian C.
AU - Dobrynin, Pavel
AU - Sitam, Frankie Thomas
AU - Rovie-Ryan, Jeffrine J.
AU - Johnson, Warren E.
AU - Yusoff, Aini Mohamed
AU - Luo, Shu Jin
AU - Karuppannan, Kayal Vizi
AU - Fang, Gang
AU - Zheng, Deyou
AU - Gerstein, Mark B.
AU - Lipovich, Leonard
AU - O'Brien, Stephen J.
AU - Wong, Guat Jah
N1 - Publisher Copyright:
© 2016 Aldrup-MacDonald et al.
PY - 2016/10/31
Y1 - 2016/10/31
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84989954912&partnerID=8YFLogxK
U2 - 10.1101/gr.203521.115
DO - 10.1101/gr.203521.115
M3 - Article
C2 - 27510566
AN - SCOPUS:84989954912
SN - 1088-9051
VL - 26
SP - 1312
EP - 1322
JO - Genome Research
JF - Genome Research
IS - 10
ER -