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Cited by 1,180Genomics and Phylogenetic StudiesChromosomal and Genetic VariationsGenetic and phenotypic traits in livestock

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The sequence and de novo assembly of the giant panda genome

Open access
Li, Ruiqiang, Fan, Wei, Tian, Geng, Zhu, Hongmei, He, Lin, Cai, Jing, Huang, Quanfei, Cai, Qingle, Li, Bo, Bai, Yinqi, Zhang, Zhihe, Zhang, Yaping, Wang, Wen, Li, Jun, Wei, Fuwen, Li, Heng, Jian, Min, Li, Jianwen, Zhang, Zhaolei, Nielsen, Rasmus, Li, Dawei, Gu, Wanjun, Yang, Zhentao, Xuan, Zhaoling, Ryder, Oliver A., Leung, Frederick Chi-Ching, Zhou, Yan, Cao, Jianjun, Sun, Xiao, Fu, Yonggui, Fang, Xiaodong, Guo, Xiaosen, Wang, Bo, Hou, Rong, Shen, Fujun, Mu, Bo, Ni, Peixiang, Lin, Runmao, Qian, Wubin, Wang, Guodong, Yu, Chang, Nie, Wenhui, Wang, Jinhuan, Wu, Zhigang, Liang, Huiqing, Min, Jiumeng, Wu, Qi, Cheng, Shifeng, Ruan, Jue, Wang, Mingwei, Shi, Zhongbin, Wen, Ming, Liu, Binghang, Ren, Xiaoli, Zheng, Huisong, Dong, Dong, Cook, Kathleen, Shan, Gao, Zhang, Hao, Kosiol, Carolin, Xie, Xueying, Lu, Zuhong, Zheng, Hancheng, Li, Yingrui, Steiner, Cynthia C., Lam, Tommy Tsan-Yuk, Lin, Siyuan, Zhang, Qinghui, Li, Guoqing, Tian, Jing, Gong, Timing, Liu, Hongde, Zhang, Dejin, Fang, Lin, Ye, Chen, Zhang, Juanbin, Hu, Wenbo, Xu, Anlong, Ren, Yuanyuan, Zhang, Guojie, Bruford, Michael W., Li, Qibin, Ma, Lijia, Guo, Yiran, An, Na, Hu, Yujie, Zheng, Yang, Shi, Yongyong, Li, Zhiqiang, Liu, Qing, Chen, Yanling, Zhao, Jing, Qu, Ning, Zhao, Shancen, Tian, Feng, Wang, Xiaoling, Wang, Haiyin, Xu, Lizhi, Liu, Xiao, Vinar, Tomas, Wang, Yajun, Lam, Tak-Wah, Yiu, Siu-Ming, Liu, Shiping, Zhang, Hemin, Li, Desheng, Huang, Yan, Wang, Xia, Yang, Guohua, Jiang, Zhi, Wang, Junyi, Qin, Nan, Li, Li, Li, Jingxiang, Bolund, Lars, Kristiansen, Karsten, Wong, Gane Ka-Shu, Olson, Maynard, Zhang, Xiuqing, Li, Songgang, Yang, Huanming, Wang, Jian, Wang, Jun·2010·Nature
DOI 10.1038/nature08696PMC PMC3951497
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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. The genome of the giant panda — specifically of the female Beijing Olympics mascot Jingjing — has been determined using short-read sequencing technology, a first for such a complex genome. It consists of some 2.4 billion DNA base pairs, compared to 3 billion in humans, and contains around 21,000 protein-encoding genes, similar to the human genome. Genomic diversity reflected in the sequence is high, raising hopes that despite a population of only about 2,500, conservation efforts can keep the species from extinction. Intriguingly, the panda appears to have all the genes needed for a carnivorous digestive system but lacks digestive cellulase genes. It may therefore depend on its gut microbiome to handle its famously limited bamboo diet. Taste may be a diet-limiting factor: loss of function of the T1R1 gene means that pandas may not experience the umami taste associated with high-protein foods. Technical aspects of this work pave the way for the use of next-generation sequencing for rapid de novo assembly of large eukaryotic genomes. Here, a draft sequence of the giant panda genome is assembled using next-generation sequencing technology alone. Genome analysis reveals a low divergence rate in comparison with dog and human genomes and insights into panda-specific traits; for example, the giant panda's bamboo diet may be more dependent on its gut microbiome than its own genetic composition.

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Authors
Li, R., Fan, W., Tian, G., Zhu, H., He, L., Cai, J., Huang, Q., Cai, Q., Li, B., Bai, Y., Zhang, Z., Zhang, Y., Wang, W., Li, J., Wei, F., Li, H., Jian, M., Li, J., Zhang, Z., Nielsen, R., Li, D., Gu, W., Yang, Z., Xuan, Z., Ryder, O. A., Leung, F. C.-C., Zhou, Y., Cao, J., Sun, X., Fu, Y., Fang, X., Guo, X., Wang, B., Hou, R., Shen, F., Mu, B., Ni, P., Lin, R., Qian, W., Wang, G., Yu, C., Nie, W., Wang, J., Wu, Z., Liang, H., Min, J., Wu, Q., Cheng, S., Ruan, J., Wang, M., Shi, Z., Wen, M., Liu, B., Ren, X., Zheng, H., Dong, D., Cook, K., Shan, G., Zhang, H., Kosiol, C., Xie, X., Lu, Z., Zheng, H., Li, Y., Steiner, C. C., Lam, T. T.-Y., Lin, S., Zhang, Q., Li, G., Tian, J., Gong, T., Liu, H., Zhang, D., Fang, L., Ye, C., Zhang, J., Hu, W., Xu, A., Ren, Y., Zhang, G., Bruford, M. W., Li, Q., Ma, L., Guo, Y., An, N., Hu, Y., Zheng, Y., Shi, Y., Li, Z., Liu, Q., Chen, Y., Zhao, J., Qu, N., Zhao, S., Tian, F., Wang, X., Wang, H., Xu, L., Liu, X., Vinar, T., Wang, Y., Lam, T.-W., Yiu, S.-M., Liu, S., Zhang, H., Li, D., Huang, Y., Wang, X., Yang, G., Jiang, Z., Wang, J., Qin, N., Li, L., Li, J., Bolund, L., Kristiansen, K., Wong, G. K.-S., Olson, M., Zhang, X., Li, S., Yang, H., Wang, J., & Wang, J.
Affiliations
  • BGI Group (China) (CN)
  • Kunming Institute of Zoology (CN)
  • University of Toronto (CA)
  • Chinese Academy of Sciences (CN)
  • Wellcome Trust (GB)
  • University of California, Berkeley (US)
  • Southeast University (CN)
  • San Diego Zoo Institute for Conservation Research (US)
  • University of Hong Kong (HK)
  • State Key Laboratory of Digital Medical Engineering (CN)
  • Sun Yat-sen University (CN)
  • Chengdu Research Base of Giant Panda Breeding (CN)
  • University of Veterinary Medicine Vienna (AT)
  • Cardiff University (GB)
  • Shanghai Jiao Tong University (CN)
  • Sichuan University (CN)
  • South China University of Technology (CN)
  • University of Washington (US)
Corresponding author
  • Wang, Jinhuan
  • Wang, Junyi
  • Wang, Jian
  • Wang, Jun
ORCID
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2009-12-13
Volume
463
Issue
7279
Pages
311-317
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
DOI
10.1038/nature08696
PMC
PMC3951497
OpenAlex
W2159946869
Cited by
1,180
References
33
Citations by year
2026: 16 · 2025: 21 · 2024: 30 · 2023: 40 · 2022: 53 · 2021: 66 · 2020: 110 · 2019: 61 · 2018: 53 · 2017: 60 · 2016: 76 · 2015: 89 · 2014: 106 · 2013: 90 · 2012: 121
FWCI
40.98
Type
journal article
Language
en
Update notices
erratum (2010-02-25)
Open access
Licence
Locations
  • Nature (publishedVersion, cc-by-nc-sa)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • ORCA Online Research @Cardiff (Cardiff University) (submittedVersion)
  • The HKU Scholars Hub (University of Hong Kong) (submittedVersion)
  • Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
Funders
  • Shenzhen Government
  • National Natural Science Foundation of China (30725008)
  • Strategic Research Council
  • National Human Genome Research Institute (R01HG003229)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
Keywords
giant panda, genome assembly, de novo assembly, draft genome sequence, bamboo diet, gut microbiota, cellulase genes, umami taste, single nucleotide polymorphisms
MeSH terms
Algorithms, Animals, Ursidae, China, Diet, Dogs, Female, Fertility, Multigene Family, Heterozygote, Humans, Sequence Alignment, Genome, Conserved Sequence, Sequence Analysis, DNA, Evolution, Molecular, Contig Mapping, Polymorphism, Single Nucleotide, Genomics, Synteny, Receptors, G-Protein-Coupled

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