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The tiger genome and comparative analysis with lion and snow leopard genomes

Author

Listed:
  • Yun Sung Cho

    (Personal Genomics Institute, Genome Research Foundation)

  • Li Hu

    (BGI-Shenzhen)

  • Haolong Hou

    (BGI-Shenzhen)

  • Hang Lee

    (Tiger and Leopard Conservation Fund in Korea and College of Veterinary Medicine, Seoul National University)

  • Jiaohui Xu

    (BGI-Shenzhen)

  • Soowhan Kwon

    (Samsung Everland Zoo)

  • Sukhun Oh

    (Samsung Everland Zoo)

  • Hak-Min Kim

    (Personal Genomics Institute, Genome Research Foundation)

  • Sungwoong Jho

    (Personal Genomics Institute, Genome Research Foundation)

  • Sangsoo Kim

    (School of Systems Biomedical Science, Soongsil University)

  • Young-Ah Shin

    (Personal Genomics Institute, Genome Research Foundation)

  • Byung Chul Kim

    (Personal Genomics Institute, Genome Research Foundation
    Theragen BiO Institute, TheragenEtex)

  • Hyunmin Kim

    (Theragen BiO Institute, TheragenEtex)

  • Chang-uk Kim

    (Personal Genomics Institute, Genome Research Foundation)

  • Shu-Jin Luo

    (Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University)

  • Warren E. Johnson

    (Smithsonian Conservation Biology Institute)

  • Klaus-Peter Koepfli

    (Theodosius Dobzhansky Center for Genome Bioinformatics, St Petersburg State University)

  • Anne Schmidt-Küntzel

    (Life Technologies Conservation Genetics Laboratory, Cheetah Conservation Fund)

  • Jason A. Turner

    (Global White Lion Protection Trust, Tsau Conservancy, Greater Timbavati Region)

  • Laurie Marker

    (Cheetah Conservation Fund)

  • Cindy Harper

    (Veterinary Genetics Laboratory, Faculty of Veterinary Science, University of Pretoria)

  • Susan M. Miller

    (Veterinary Genetics Laboratory, Faculty of Veterinary Science, University of Pretoria
    Tshwane University of Technology)

  • Wilhelm Jacobs

    (Ukutula Lodge & Lion Centre)

  • Laura D. Bertola

    (Institute of Environmental Sciences (CML), Leiden University)

  • Tae Hyung Kim

    (Theragen BiO Institute, TheragenEtex)

  • Sunghoon Lee

    (Personal Genomics Institute, Genome Research Foundation
    Theragen BiO Institute, TheragenEtex)

  • Qian Zhou

    (BGI-Shenzhen)

  • Hyun-Ju Jung

    (Theragen BiO Institute, TheragenEtex)

  • Xiao Xu

    (Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University)

  • Priyvrat Gadhvi

    (Personal Genomics Institute, Genome Research Foundation)

  • Pengwei Xu

    (BGI-Shenzhen)

  • Yingqi Xiong

    (BGI-Shenzhen)

  • Yadan Luo

    (BGI-Shenzhen)

  • Shengkai Pan

    (BGI-Shenzhen)

  • Caiyun Gou

    (BGI-Shenzhen)

  • Xiuhui Chu

    (BGI-Shenzhen)

  • Jilin Zhang

    (BGI-Shenzhen)

  • Sanyang Liu

    (BGI-Shenzhen)

  • Jing He

    (BGI-Shenzhen)

  • Ying Chen

    (BGI-Shenzhen)

  • Linfeng Yang

    (BGI-Shenzhen)

  • Yulan Yang

    (BGI-Shenzhen)

  • Jiaju He

    (BGI-Shenzhen)

  • Sha Liu

    (BGI-Shenzhen)

  • Junyi Wang

    (BGI-Shenzhen)

  • Chul Hong Kim

    (Theragen BiO Institute, TheragenEtex)

  • Hwanjong Kwak

    (Theragen BiO Institute, TheragenEtex)

  • Jong-Soo Kim

    (Personal Genomics Institute, Genome Research Foundation)

  • Seungwoo Hwang

    (Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology)

  • Junsu Ko

    (Theragen BiO Institute, TheragenEtex)

  • Chang-Bae Kim

    (Sangmyung University)

  • Sangtae Kim

    (Sungshin Women’s University)

  • Damdin Bayarlkhagva

    (School of Biology and Biotechnology, National University of Mongolia)

  • Woon Kee Paek

    (National Science Museum)

  • Seong-Jin Kim

    (Theragen BiO Institute, TheragenEtex
    CHA Cancer Institute, CHA University)

  • Stephen J. O’Brien

    (Theodosius Dobzhansky Center for Genome Bioinformatics, St Petersburg State University
    Oceanographic Center, Nova Southeastern University, Ft Lauderdale)

  • Jun Wang

    (BGI-Shenzhen
    University of Copenhagen
    King Abdulaziz University)

  • Jong Bhak

    (Personal Genomics Institute, Genome Research Foundation
    Theragen BiO Institute, TheragenEtex
    Advanced Institutes of Convergence Technology Nano Science and Technology
    Program in Nano Science and Technology, Seoul National University)

Abstract

Tigers and their close relatives (Panthera) are some of the world’s most endangered species. Here we report the de novo assembly of an Amur tiger whole-genome sequence as well as the genomic sequences of a white Bengal tiger, African lion, white African lion and snow leopard. Through comparative genetic analyses of these genomes, we find genetic signatures that may reflect molecular adaptations consistent with the big cats’ hypercarnivorous diet and muscle strength. We report a snow leopard-specific genetic determinant in EGLN1 (Met39>Lys39), which is likely to be associated with adaptation to high altitude. We also detect a TYR260G>A mutation likely responsible for the white lion coat colour. Tiger and cat genomes show similar repeat composition and an appreciably conserved synteny. Genomic data from the five big cats provide an invaluable resource for resolving easily identifiable phenotypes evident in very close, but distinct, species.

Suggested Citation

  • Yun Sung Cho & Li Hu & Haolong Hou & Hang Lee & Jiaohui Xu & Soowhan Kwon & Sukhun Oh & Hak-Min Kim & Sungwoong Jho & Sangsoo Kim & Young-Ah Shin & Byung Chul Kim & Hyunmin Kim & Chang-uk Kim & Shu-Ji, 2013. "The tiger genome and comparative analysis with lion and snow leopard genomes," Nature Communications, Nature, vol. 4(1), pages 1-7, December.
    • Handle: RePEc:nat:natcom:v:4:y:2013:i:1:d:10.1038_ncomms3433
    DOI: 10.1038/ncomms3433
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    Cited by:

    1. Kang Du & Juliana Morena Bonita Ricci & Yuan Lu & Mateo Garcia-Olazabal & Ronald B. Walter & Wesley C. Warren & Tristram O. Dodge & Molly Schumer & Hyun Park & Axel Meyer & Manfred Schartl, 2024. "Phylogenomic analyses of all species of swordtail fishes (genus Xiphophorus) show that hybridization preceded speciation," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    2. Min-Rui-Xuan Xu & Zhen-Yang Liao & Jordan R. Brock & Kang Du & Guo-Yin Li & Zhi-Qiang Chen & Ying-Hao Wang & Zhong-Nan Gao & Gaurav Agarwal & Kevin H-C Wei & Feng Shao & Shuai Pang & Adrian E. Platts , 2023. "Maternal dominance contributes to subgenome differentiation in allopolyploid fishes," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    3. Liye Zhang & Neahga Leonard & Rick Passaro & Mai Sy Luan & Pham Tuyen & Le Thi Ngoc Han & Nguyen Huy Cam & Larry Vogelnest & Michael Lynch & Amanda E. Fine & Nguyen Thi Thanh Nga & Nguyen Long & Benja, 2024. "Genomic adaptation to small population size and saltwater consumption in the critically endangered Cat Ba langur," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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