Pangolin genomes and the evolution of mammalian scales and immunity

Siew Who Choo, Mike Rayko, Tze King Tan, Ranjeev Hari, Aleksey Komissarov, Wei Yee Wee, Andrey A. Yurchenko, Sergey Kliver, Gaik Tamazian, Agostinho Antunes, Richard K. Wilson, Wesley C. Warren, Klaus Peter Koepfli, Patrick Minx, Ksenia Krasheninnikova, Antoinette Kotze, Desire L. Dalton, Elaine Vermaak, Ian C. Paterson, Pavel DobryninFrankie Thomas Sitam, Jeffrine J. Rovie-Ryan, Warren E. Johnson, Aini Mohamed Yusoff, Shu Jin Luo, Kayal Vizi Karuppannan, Gang Fang, Deyou Zheng, Mark B. Gerstein, Leonard Lipovich, Stephen J. O'Brien, Guat Jah Wong

Research output: Contribution to journalArticle

14 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)1312-1322
Number of pages11
JournalGenome Research
Volume26
Issue number10
DOIs
StatePublished - Oct 1 2016

Fingerprint

Interferons
Immunity
Odorant Receptors
Genome
Mucosal Immunity
Smell
Infection
Hair
Energy Metabolism
Nervous System
Genes
Mammals
Tooth
Animal Models
Epithelial Cells
Inflammation
Skin
Wounds and Injuries
Research

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Choo, S. W., Rayko, M., Tan, T. K., Hari, R., Komissarov, A., Wee, W. Y., ... Wong, G. J. (2016). Pangolin genomes and the evolution of mammalian scales and immunity. Genome Research, 26(10), 1312-1322. https://doi.org/10.1101/gr.203521.115

Pangolin genomes and the evolution of mammalian scales and immunity. / Choo, Siew Who; Rayko, Mike; Tan, Tze King; Hari, Ranjeev; Komissarov, Aleksey; Wee, Wei Yee; Yurchenko, Andrey A.; Kliver, Sergey; Tamazian, Gaik; Antunes, Agostinho; Wilson, Richard K.; Warren, Wesley C.; Koepfli, Klaus Peter; Minx, Patrick; Krasheninnikova, Ksenia; Kotze, Antoinette; Dalton, Desire L.; Vermaak, Elaine; Paterson, Ian C.; Dobrynin, Pavel; Sitam, Frankie Thomas; Rovie-Ryan, Jeffrine J.; Johnson, Warren E.; Yusoff, Aini Mohamed; Luo, Shu Jin; Karuppannan, Kayal Vizi; Fang, Gang; Zheng, Deyou; Gerstein, Mark B.; Lipovich, Leonard; O'Brien, Stephen J.; Wong, Guat Jah.

In: Genome Research, Vol. 26, No. 10, 01.10.2016, p. 1312-1322.

Research output: Contribution to journalArticle

Choo, SW, Rayko, M, Tan, TK, Hari, R, Komissarov, A, Wee, WY, Yurchenko, AA, 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, Sitam, FT, Rovie-Ryan, JJ, Johnson, WE, Yusoff, AM, Luo, SJ, Karuppannan, KV, Fang, G, Zheng, D, Gerstein, MB, Lipovich, L, O'Brien, SJ & Wong, GJ 2016, 'Pangolin genomes and the evolution of mammalian scales and immunity', Genome Research, vol. 26, no. 10, pp. 1312-1322. https://doi.org/10.1101/gr.203521.115
Choo SW, Rayko M, Tan TK, Hari R, Komissarov A, Wee WY et al. Pangolin genomes and the evolution of mammalian scales and immunity. Genome Research. 2016 Oct 1;26(10):1312-1322. https://doi.org/10.1101/gr.203521.115
Choo, Siew Who ; Rayko, Mike ; Tan, Tze King ; Hari, Ranjeev ; Komissarov, Aleksey ; Wee, Wei Yee ; Yurchenko, Andrey A. ; Kliver, Sergey ; Tamazian, Gaik ; Antunes, Agostinho ; Wilson, Richard K. ; Warren, Wesley C. ; Koepfli, Klaus Peter ; Minx, Patrick ; Krasheninnikova, Ksenia ; Kotze, Antoinette ; Dalton, Desire L. ; Vermaak, Elaine ; Paterson, Ian C. ; Dobrynin, Pavel ; Sitam, Frankie Thomas ; Rovie-Ryan, Jeffrine J. ; Johnson, Warren E. ; Yusoff, Aini Mohamed ; Luo, Shu Jin ; Karuppannan, Kayal Vizi ; Fang, Gang ; Zheng, Deyou ; Gerstein, Mark B. ; Lipovich, Leonard ; O'Brien, Stephen J. ; Wong, Guat Jah. / Pangolin genomes and the evolution of mammalian scales and immunity. In: Genome Research. 2016 ; Vol. 26, No. 10. pp. 1312-1322.
@article{cf3a291f53a54b219bcd4e8400016d59,
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.",
author = "Choo, {Siew Who} and Mike Rayko and Tan, {Tze King} and Ranjeev Hari and Aleksey Komissarov and Wee, {Wei Yee} and Yurchenko, {Andrey A.} and Sergey Kliver and Gaik Tamazian and Agostinho Antunes and Wilson, {Richard K.} and Warren, {Wesley C.} and Koepfli, {Klaus Peter} and Patrick Minx and Ksenia Krasheninnikova and Antoinette Kotze and Dalton, {Desire L.} and Elaine Vermaak and Paterson, {Ian C.} and Pavel Dobrynin and Sitam, {Frankie Thomas} and Rovie-Ryan, {Jeffrine J.} and Johnson, {Warren E.} and Yusoff, {Aini Mohamed} and Luo, {Shu Jin} and Karuppannan, {Kayal Vizi} and Gang Fang and Deyou Zheng and Gerstein, {Mark B.} and Leonard Lipovich and O'Brien, {Stephen J.} and Wong, {Guat Jah}",
year = "2016",
month = "10",
day = "1",
doi = "10.1101/gr.203521.115",
language = "English (US)",
volume = "26",
pages = "1312--1322",
journal = "Genome Research",
issn = "1088-9051",
publisher = "Cold Spring Harbor Laboratory Press",
number = "10",

}

TY - JOUR

T1 - Pangolin genomes and the evolution of mammalian scales and immunity

AU - Choo, Siew Who

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

PY - 2016/10/1

Y1 - 2016/10/1

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

UR - http://www.scopus.com/inward/citedby.url?scp=84989954912&partnerID=8YFLogxK

U2 - 10.1101/gr.203521.115

DO - 10.1101/gr.203521.115

M3 - Article

C2 - 27510566

AN - SCOPUS:84989954912

VL - 26

SP - 1312

EP - 1322

JO - Genome Research

JF - Genome Research

SN - 1088-9051

IS - 10

ER -