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The sequence and de novo assembly of the giant panda genome

Author

Listed:
  • Ruiqiang Li

    (BGI-Shenzhen
    University of Copenhagen)

  • Wei Fan

    (BGI-Shenzhen)

  • Geng Tian

    (BGI-Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Hongmei Zhu

    (BGI-Shenzhen)

  • Lin He

    (Institutes of Biomedical Sciences, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China
    Bio-X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University)

  • Jing Cai

    (The Graduate University of Chinese Academy of Sciences
    State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences)

  • Quanfei Huang

    (BGI-Shenzhen)

  • Qingle Cai

    (BGI-Shenzhen
    Genome Research Institute, Shenzhen University Medical School)

  • Bo Li

    (BGI-Shenzhen)

  • Yinqi Bai

    (BGI-Shenzhen)

  • Zhihe Zhang

    (Chengdu Research Base of Giant Panda Breeding)

  • Yaping Zhang

    (State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences)

  • Wen Wang

    (State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences)

  • Jun Li

    (BGI-Shenzhen)

  • Fuwen Wei

    (Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, the Chinese Academy of Sciences, Beichenxilu 1-5, Chaoyang District, Beijing 100101, China)

  • Heng Li

    (Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK)

  • Min Jian

    (BGI-Shenzhen)

  • Jianwen Li

    (BGI-Shenzhen)

  • Zhaolei Zhang

    (Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada)

  • Rasmus Nielsen

    (UC-Berkeley, 3060 VLSB, Berkeley, California 94720, USA)

  • Dawei Li

    (BGI-Shenzhen)

  • Wanjun Gu

    (Key Laboratory of Child Development and Learning Science, Southeast University, Ministry of Education)

  • Zhentao Yang

    (BGI-Shenzhen)

  • Zhaoling Xuan

    (BGI-Shenzhen)

  • Oliver A. Ryder

    (San Diego Zoo’s Institute for Conservation Research, 15600 San Pasqual Valley Road, Escondido, California 92027, USA)

  • Frederick Chi-Ching Leung

    (School of Biological Sciences, The University of Hong Kong)

  • Yan Zhou

    (BGI-Shenzhen)

  • Jianjun Cao

    (BGI-Shenzhen)

  • Xiao Sun

    (State Key Laboratory of Bioelectronics, Southeast University)

  • Yonggui Fu

    (State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University)

  • Xiaodong Fang

    (BGI-Shenzhen)

  • Xiaosen Guo

    (BGI-Shenzhen)

  • Bo Wang

    (BGI-Shenzhen)

  • Rong Hou

    (Chengdu Research Base of Giant Panda Breeding)

  • Fujun Shen

    (Chengdu Research Base of Giant Panda Breeding)

  • Bo Mu

    (BGI-Shenzhen)

  • Peixiang Ni

    (BGI-Shenzhen)

  • Runmao Lin

    (BGI-Shenzhen)

  • Wubin Qian

    (BGI-Shenzhen)

  • Guodong Wang

    (The Graduate University of Chinese Academy of Sciences
    State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences)

  • Chang Yu

    (BGI-Shenzhen)

  • Wenhui Nie

    (State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences)

  • Jinhuan Wang

    (State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences)

  • Zhigang Wu

    (BGI-Shenzhen)

  • Huiqing Liang

    (BGI-Shenzhen)

  • Jiumeng Min

    (BGI-Shenzhen
    Genome Research Institute, Shenzhen University Medical School)

  • Qi Wu

    (Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, the Chinese Academy of Sciences, Beichenxilu 1-5, Chaoyang District, Beijing 100101, China)

  • Shifeng Cheng

    (BGI-Shenzhen
    Genome Research Institute, Shenzhen University Medical School)

  • Jue Ruan

    (BGI-Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Mingwei Wang

    (BGI-Shenzhen)

  • Zhongbin Shi

    (BGI-Shenzhen)

  • Ming Wen

    (BGI-Shenzhen)

  • Binghang Liu

    (BGI-Shenzhen)

  • Xiaoli Ren

    (BGI-Shenzhen)

  • Huisong Zheng

    (BGI-Shenzhen)

  • Dong Dong

    (Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada)

  • Kathleen Cook

    (Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada)

  • Gao Shan

    (BGI-Shenzhen)

  • Hao Zhang

    (BGI-Shenzhen)

  • Carolin Kosiol

    (Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Veterinärplatz 1, 1210 Wien, Austria)

  • Xueying Xie

    (Key Laboratory of Child Development and Learning Science, Southeast University, Ministry of Education)

  • Zuhong Lu

    (Key Laboratory of Child Development and Learning Science, Southeast University, Ministry of Education)

  • Hancheng Zheng

    (BGI-Shenzhen)

  • Yingrui Li

    (BGI-Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Cynthia C. Steiner

    (San Diego Zoo’s Institute for Conservation Research, 15600 San Pasqual Valley Road, Escondido, California 92027, USA)

  • Tommy Tsan-Yuk Lam

    (School of Biological Sciences, The University of Hong Kong)

  • Siyuan Lin

    (BGI-Shenzhen)

  • Qinghui Zhang

    (BGI-Shenzhen)

  • Guoqing Li

    (BGI-Shenzhen)

  • Jing Tian

    (BGI-Shenzhen)

  • Timing Gong

    (BGI-Shenzhen)

  • Hongde Liu

    (State Key Laboratory of Bioelectronics, Southeast University)

  • Dejin Zhang

    (State Key Laboratory of Bioelectronics, Southeast University)

  • Lin Fang

    (BGI-Shenzhen)

  • Chen Ye

    (BGI-Shenzhen)

  • Juanbin Zhang

    (BGI-Shenzhen)

  • Wenbo Hu

    (State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University)

  • Anlong Xu

    (State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University)

  • Yuanyuan Ren

    (BGI-Shenzhen)

  • Guojie Zhang

    (BGI-Shenzhen
    The Graduate University of Chinese Academy of Sciences
    State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences)

  • Michael W. Bruford

    (Biodiversity and Ecological Processes Group, Cardiff School of Biosciences, Cardiff University)

  • Qibin Li

    (BGI-Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Lijia Ma

    (BGI-Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Yiran Guo

    (BGI-Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Na An

    (BGI-Shenzhen)

  • Yujie Hu

    (BGI-Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Yang Zheng

    (BGI-Shenzhen
    The Graduate University of Chinese Academy of Sciences)

  • Yongyong Shi

    (Bio-X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University)

  • Zhiqiang Li

    (Bio-X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University)

  • Qing Liu

    (BGI-Shenzhen)

  • Yanling Chen

    (BGI-Shenzhen)

  • Jing Zhao

    (BGI-Shenzhen)

  • Ning Qu

    (BGI-Shenzhen
    Genome Research Institute, Shenzhen University Medical School)

  • Shancen Zhao

    (BGI-Shenzhen)

  • Feng Tian

    (BGI-Shenzhen)

  • Xiaoling Wang

    (BGI-Shenzhen)

  • Haiyin Wang

    (BGI-Shenzhen)

  • Lizhi Xu

    (BGI-Shenzhen)

  • Xiao Liu

    (BGI-Shenzhen)

  • Tomas Vinar

    (Faculty of Mathematics, Physics, and Informatics, Comenius University, Mlynska Dolina, 84248 Bratislava, Slovakia)

  • Yajun Wang

    (School of Life Science, Sichuan University)

  • Tak-Wah Lam

    (The University of Hong Kong)

  • Siu-Ming Yiu

    (The University of Hong Kong)

  • Shiping Liu

    (South China University of Technology)

  • Hemin Zhang

    (China Conservation and Research Centre for the Giant Panda, Wolong Nature Reserve 623006)

  • Desheng Li

    (China Conservation and Research Centre for the Giant Panda, Wolong Nature Reserve 623006)

  • Yan Huang

    (China Conservation and Research Centre for the Giant Panda, Wolong Nature Reserve 623006)

  • Xia Wang

    (BGI-Shenzhen)

  • Guohua Yang

    (BGI-Shenzhen)

  • Zhi Jiang

    (BGI-Shenzhen)

  • Junyi Wang

    (BGI-Shenzhen)

  • Nan Qin

    (BGI-Shenzhen)

  • Li Li

    (BGI-Shenzhen)

  • Jingxiang Li

    (BGI-Shenzhen)

  • Lars Bolund

    (BGI-Shenzhen)

  • Karsten Kristiansen

    (BGI-Shenzhen
    University of Copenhagen)

  • Gane Ka-Shu Wong

    (BGI-Shenzhen
    University of Alberta, Edmonton, Alberta T6G 2E9, Canada)

  • Maynard Olson

    (University of Washington Genome Center)

  • Xiuqing Zhang

    (BGI-Shenzhen)

  • Songgang Li

    (BGI-Shenzhen)

  • Huanming Yang

    (BGI-Shenzhen)

  • Jian Wang

    (BGI-Shenzhen)

  • Jun Wang

    (BGI-Shenzhen
    University of Copenhagen)

Abstract

Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.

Suggested Citation

  • Ruiqiang Li & Wei Fan & Geng Tian & Hongmei Zhu & Lin He & Jing Cai & Quanfei Huang & Qingle Cai & Bo Li & Yinqi Bai & Zhihe Zhang & Yaping Zhang & Wen Wang & Jun Li & Fuwen Wei & Heng Li & Min Jian &, 2010. "The sequence and de novo assembly of the giant panda genome," Nature, Nature, vol. 463(7279), pages 311-317, January.
    • Handle: RePEc:nat:nature:v:463:y:2010:i:7279:d:10.1038_nature08696
    DOI: 10.1038/nature08696
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    Cited by:

    1. Fangyuan Zhang & Fei Qiu & Junlan Zeng & Zhichao Xu & Yueli Tang & Tengfei Zhao & Yuqin Gou & Fei Su & Shiyi Wang & Xiuli Sun & Zheyong Xue & Weixing Wang & Chunxian Yang & Lingjiang Zeng & Xiaozhong , 2023. "Revealing evolution of tropane alkaloid biosynthesis by analyzing two genomes in the Solanaceae family," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    2. Mahrous R. Ahmed & E. Kh. Shokr & I. A. Abdel-Latif & Ibrahim Y. Khaled & E. M. M. Ibrahim & Sara A. Mohamed, 2024. "Dependence of optical and dielectric properties on heat treatment of calcium-doped manganites," The European Physical Journal B: Condensed Matter and Complex Systems, Springer;EDP Sciences, vol. 97(8), pages 1-9, August.
    3. Jiao Yang & Ying Wu & Pan Zhang & Jianxiang Ma & Ying Jun Yao & Yan Lin Ma & Lei Zhang & Yongzhi Yang & Changmin Zhao & Jihua Wu & Xiangwen Fang & Jianquan Liu, 2023. "Multiple independent losses of the biosynthetic pathway for two tropane alkaloids in the Solanaceae family," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    4. 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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