The sequence and de novo assembly of the giant panda genome

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, Jianwen Li, Zhaolei Zhang, Rasmus Nielsen, Dawei Li, Wanjun Gu, Zhentao Yang, Zhaoling Xuan, Oliver A. Ryder, Frederick Chi-Ching Leung, Yan Zhou, Jianjun Cao, Xiao Sun, Yonggui Fu, Xiaodong Fang, Xiaosen Guo, Bo Wang, Rong Hou, Fujun Shen, Bo Mu, Peixiang Ni, Runmao Lin, Wubin Qian, Guodong Wang, Chang Yu, Wenhui Nie, Jinhuan Wang, Zhigang Wu, Huiqing Liang, Jiumeng Min, Qi Wu, Shifeng Cheng, Jue Ruan, Mingwei Wang, Zhongbin Shi, Ming Wen, Binghang Liu, Xiaoli Ren, Huisong Zheng, Dong Dong, Kathleen Cook, Gao Shan, Hao Zhang, Carolin Kosiol, Xueying Xie, Zuhong Lu, Hancheng Zheng, Yingrui Li, Cynthia C. Steiner, Tommy Tsan-Yuk Lam, Siyuan Lin, Qinghui Zhang, Guoqing Li, Jing Tian, Timing Gong, Hongde Liu, Dejin Zhang, Lin Fang, Chen Ye, Juanbin Zhang, Wenbo Hu, Anlong Xu, Yuanyuan Ren, Guojie Zhang, Michael W. Bruford, Qibin Li, Lijia Ma, Yiran Guo, Na An, Yujie Hu, Yang Zheng, Yongyong Shi, Zhiqiang Li, Qing Liu, Yanling Chen, Jing Zhao, Ning Qu, Shancen Zhao, Feng Tian, Xiaoling Wang, Haiyin Wang, Lizhi Xu, Xiao Liu, Tomas Vinar, Yajun Wang, Tak-Wah Lam, Siu-Ming Yiu, Shiping Liu, Hemin Zhang, Desheng Li, Yan Huang, Xia Wang, Guohua Yang, Zhi Jiang, Junyi Wang, Nan Qin, Li Li, Jingxiang Li, Lars Bolund, Karsten Kristiansen, Gane Ka-Shu Wong, Maynard Olson, Xiuqing Zhang, Songgang Li, Huanming Yang, Jian Wang () and Jun Wang ()
Additional contact information
Ruiqiang Li: BGI-Shenzhen
Wei Fan: BGI-Shenzhen
Geng Tian: BGI-Shenzhen
Hongmei Zhu: BGI-Shenzhen
Lin He: Institutes of Biomedical Sciences, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China
Jing Cai: The Graduate University of Chinese Academy of Sciences
Quanfei Huang: BGI-Shenzhen
Qingle Cai: BGI-Shenzhen
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
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
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
Jue Ruan: BGI-Shenzhen
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
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
Michael W. Bruford: Biodiversity and Ecological Processes Group, Cardiff School of Biosciences, Cardiff University
Qibin Li: BGI-Shenzhen
Lijia Ma: BGI-Shenzhen
Yiran Guo: BGI-Shenzhen
Na An: BGI-Shenzhen
Yujie Hu: BGI-Shenzhen
Yang Zheng: BGI-Shenzhen
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
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
Gane Ka-Shu Wong: BGI-Shenzhen
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

Nature, 2010, vol. 463, issue 7279, 311-317

Abstract: 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.

Date: 2010
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DOI: 10.1038/nature08696

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