Article

Nature 463, 311-317 (21 January 2010) | doi:10.1038/nature08696; Received 19 August 2009; Accepted 24 November 2009; Published online 13 December 2009

There is a Corrigendum (25 February 2010) associated with this document.

The sequence and de novo assembly of the giant panda genome

Ruiqiang Li1,2,27, Wei Fan1,27, Geng Tian1,3,27, Hongmei Zhu1,27, Lin He4,5,27, Jing Cai3,6,27, Quanfei Huang1, Qingle Cai1,7, Bo Li1, Yinqi Bai1, Zhihe Zhang8, Yaping Zhang6, Wen Wang6, Jun Li1, Fuwen Wei9, Heng Li10, Min Jian1, Jianwen Li1, Zhaolei Zhang11, Rasmus Nielsen12, Dawei Li1, Wanjun Gu13, Zhentao Yang1, Zhaoling Xuan1, Oliver A. Ryder14, Frederick Chi-Ching Leung15, Yan Zhou1, Jianjun Cao1, Xiao Sun16, Yonggui Fu17, Xiaodong Fang1, Xiaosen Guo1, Bo Wang1, Rong Hou8, Fujun Shen8, Bo Mu1, Peixiang Ni1, Runmao Lin1, Wubin Qian1, Guodong Wang3,6, Chang Yu1, Wenhui Nie6, Jinhuan Wang6, Zhigang Wu1, Huiqing Liang1, Jiumeng Min1,7, Qi Wu9, Shifeng Cheng1,7, Jue Ruan1,3, Mingwei Wang1, Zhongbin Shi1, Ming Wen1, Binghang Liu1, Xiaoli Ren1, Huisong Zheng1, Dong Dong11, Kathleen Cook11, Gao Shan1, Hao Zhang1, Carolin Kosiol18, Xueying Xie13, Zuhong Lu13, Hancheng Zheng1, Yingrui Li1,3, Cynthia C. Steiner14, Tommy Tsan-Yuk Lam15, Siyuan Lin1, Qinghui Zhang1, Guoqing Li1, Jing Tian1, Timing Gong1, Hongde Liu16, Dejin Zhang16, Lin Fang1, Chen Ye1, Juanbin Zhang1, Wenbo Hu17, Anlong Xu17, Yuanyuan Ren1, Guojie Zhang1,3,6, Michael W. Bruford19, Qibin Li1,3, Lijia Ma1,3, Yiran Guo1,3, Na An1, Yujie Hu1,3, Yang Zheng1,3, Yongyong Shi5, Zhiqiang Li5, Qing Liu1, Yanling Chen1, Jing Zhao1, Ning Qu1,7, Shancen Zhao1, Feng Tian1, Xiaoling Wang1, Haiyin Wang1, Lizhi Xu1, Xiao Liu1, Tomas Vinar20, Yajun Wang21, Tak-Wah Lam22, Siu-Ming Yiu22, Shiping Liu23, Hemin Zhang24, Desheng Li24, Yan Huang24, Xia Wang1, Guohua Yang1, Zhi Jiang1, Junyi Wang1, Nan Qin1, Li Li1, Jingxiang Li1, Lars Bolund1, Karsten Kristiansen1,2, Gane Ka-Shu Wong1,25, Maynard Olson26, Xiuqing Zhang1, Songgang Li1, Huanming Yang1, Jian Wang1 & Jun Wang1,2

  1. BGI-Shenzhen, Shenzhen 518083, China
  2. Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark
  3. The Graduate University of Chinese Academy of Sciences, Beijing 100062, China
  4. Institutes of Biomedical Sciences, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China
  5. Bio-X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China
  6. State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
  7. Genome Research Institute, Shenzhen University Medical School, Shenzhen 518000, China
  8. Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
  9. Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, the Chinese Academy of Sciences, Beichenxilu 1-5, Chaoyang District, Beijing 100101, China
  10. Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
  11. 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
  12. Departments of Integrative Biology and Statistics, UC-Berkeley, 3060 VLSB, Berkeley, California 94720, USA
  13. Key Laboratory of Child Development and Learning Science, Southeast University, Ministry of Education, Nanjing 210096, China
  14. San Diego Zoo’s Institute for Conservation Research, 15600 San Pasqual Valley Road, Escondido, California 92027, USA
  15. School of Biological Sciences, The University of Hong Kong, Hong Kong, China
  16. State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
  17. State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University, 510275 Guanghou, China
  18. Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Veterinärplatz 1, 1210 Wien, Austria
  19. Biodiversity and Ecological Processes Group, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
  20. Department of Applied Informatics, Faculty of Mathematics, Physics, and Informatics, Comenius University, Mlynska Dolina, 84248 Bratislava, Slovakia
  21. School of Life Science, Sichuan University, Chengdu 610064, China
  22. Department of Computer Science, The University of Hong Kong, Hong Kong, China
  23. South China University of Technology, Guangzhou 510641, China
  24. China Conservation and Research Centre for the Giant Panda, Wolong Nature Reserve 623006, China
  25. Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
  26. University of Washington Genome Center, Seattle 352145, USA
  27. These authors contributed equally to this work.

Correspondence to: Jian Wang1Jun Wang1,2 Correspondence and requests for materials should be addressed to Ju.W. (Email: wangj@genomics.org.cn) or Ji.W. (Email: wangjian@genomics.org.cn).

This article is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike licence (http://creativecommons.org/licenses/by-nc-sa/3.0/), which permits distribution, and reproduction in any medium, provided the original author and source are credited. This licence does not permit commercial exploitation, and derivative works must be licensed under the same or similar licence.

Top

Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05Gb) 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 2.7million 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 ARTICLES LIKE THIS

These links to content published by NPG are automatically generated.

REVIEWS

Mammalian karyotype evolution

Nature Reviews Genetics Review (01 Dec 2007)

See all 6 matches for Reviews

NEWS AND VIEWS

Genetics Decoding a national treasure

Nature News and Views (21 Jan 2010)

Research highlights

Nature Genetics News and Views (01 Dec 2007)