The sequence and de novo assembly of the giant panda genome View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2009-12-13

AUTHORS

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, Jun Wang

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. More... »

PAGES

311-317

Journal

TITLE

Nature

ISSUE

7279

VOLUME

463

Author Affiliations

  • Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark
  • BGI-Shenzhen, Shenzhen 518083, China
  • The Graduate University of Chinese Academy of Sciences, Beijing 100062, China
  • Bio-X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China
  • State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
  • Genome Research Institute, Shenzhen University Medical School, Shenzhen 518000, China
  • Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
  • Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, the Chinese Academy of Sciences, Beichenxilu 1-5, Chaoyang District, Beijing 100101, China
  • Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
  • Banting and Best Department of Medical Research, Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
  • Departments of Integrative Biology and Statistics, UC-Berkeley, 3060 VLSB, Berkeley, California 94720, USA
  • Key Laboratory of Child Development and Learning Science, Southeast University, Ministry of Education, Nanjing 210096, China
  • San Diego Zoo’s Institute for Conservation Research, 15600 San Pasqual Valley Road, Escondido, California 92027, USA
  • School of Biological Sciences, The University of Hong Kong, Hong Kong, China
  • State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
  • State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University, 510275 Guanghou, China
  • Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Veterinärplatz 1, 1210 Wien, Austria
  • Biodiversity and Ecological Processes Group, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
  • Department of Applied Informatics, Faculty of Mathematics, Physics, and Informatics, Comenius University, Mlynska Dolina, 84248 Bratislava, Slovakia
  • School of Life Science, Sichuan University, Chengdu 610064, China
  • Department of Computer Science, The University of Hong Kong, Hong Kong, China
  • South China University of Technology, Guangzhou 510641, China
  • China Conservation and Research Centre for the Giant Panda, Wolong Nature Reserve 623006, China
  • Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
  • University of Washington Genome Center, Seattle 352145, USA
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nature08696

    DOI

    http://dx.doi.org/10.1038/nature08696

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1044030989

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/20010809


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