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The sequence and de novo assembly of the giant panda genome
Open accessAbstract
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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“it is noteworthy that a draft genome sequence for the giant panda has been generated and assembled successfully using only Illumina Genome Analyser sequencing technology [26].”
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Metadata
- 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
- Li, Ruiqiang
- Fan, Wei
- Tian, Geng
- Zhu, Hongmei
- He, Lin
- Cai, Jing
- Huang, Quanfei
- Li, Bo
- Bai, Yinqi
- Zhang, Zhihe
- Wang, Wen
- Li, Jun
- Wei, Fuwen
- Li, Heng
- Jian, Min
- Li, Jianwen
- Zhang, Zhaolei
- Nielsen, Rasmus
- Li, Dawei
- Gu, Wanjun
- Ryder, Oliver A.
- Leung, Frederick Chi-Ching
- Cao, Jianjun
- Sun, Xiao
- Fu, Yonggui
- Fang, Xiaodong
- Wang, Bo
- Hou, Rong
- Lin, Runmao
- Qian, Wubin
- Wang, Guodong
- Yu, Chang
- Wu, Zhigang
- Liang, Huiqing
- Wu, Qi
- Cheng, Shifeng
- Ruan, Jue
- Wen, Ming
- Liu, Binghang
- Ren, Xiaoli
- Dong, Dong
- Zhang, Hao
- Kosiol, Carolin
- Xie, Xueying
- Lu, Zuhong
- Zheng, Hancheng
- Li, Yingrui
- Steiner, Cynthia C.
- Lam, Tommy Tsan-Yuk
- Zhang, Qinghui
- Li, Guoqing
- Tian, Jing
- Liu, Hongde
- Zhang, Dejin
- Ye, Chen
- Hu, Wenbo
- Ren, Yuanyuan
- Zhang, Guojie
- Bruford, Michael W.
- Li, Qibin
- Ma, Lijia
- Guo, Yiran
- Zheng, Yang
- Shi, Yongyong
- Li, Zhiqiang
- Chen, Yanling
- Zhao, Jing
- Qu, Ning
- Zhao, Shancen
- Tian, Feng
- Wang, Xiaoling
- Xu, Lizhi
- Wang, Yajun
- Lam, Tak-Wah
- Yiu, Siu-Ming
- Zhang, Hemin
- Li, Desheng
- Huang, Yan
- Wang, Xia
- Yang, Guohua
- Jiang, Zhi
- Qin, Nan
- Li, Li
- Bolund, Lars
- Kristiansen, Karsten
- Wong, Gane Ka-Shu
- Olson, Maynard
- Zhang, Xiuqing
- Li, Songgang
- Yang, Huanming
- Wang, Jian
- Wang, Jun
- Venue
- Nature
- Published
- 2009-12-13
- Volume
- 463
- Issue
- 7279
- Pages
- 311-317
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- 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
- hybrid
- doi.org
- 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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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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