Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2010 Jan 21;463(7279):311-7.
doi: 10.1038/nature08696. Epub 2009 Dec 13.

The sequence and de novo assembly of the giant panda genome

Ruiqiang Li  1 , 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
Affiliations

The sequence and de novo assembly of the giant panda genome

Ruiqiang Li et al. Nature. .

Erratum in

  • Nature. 2010 Feb 25;463(7284):1106

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.

PubMed Disclaimer

Figures

Figure 1
Figure 1. Assessment of assembly quality
a, Distribution of sequencing depth of the assembled genome. b, Comparison of the assembled genome with a BAC sequence. Read depth on the BAC was calculated by mapping the Illumina Genome Analyser short reads onto the BAC sequence. The predicted gene and annotated transposable elements (TEs) on the BAC sequence are shown in green and red, respectively. The remaining unclosed gaps on the scaffolds are marked as white blocks.
Figure 2
Figure 2. Conserved sequences among the panda, dog and human genomes
a, The total lengths of aligned and unaligned non-repetitive sequences. Each of the three genomes contains 1.4Gb of non-repetitive sequences. Pairwise whole-genome alignment was performed using Blastz. The lengths shown are in Mb. b, Syntenic view of the dog chromosome 37, 35 panda scaffolds (>10 kb), and the human chromosome 2. Note that the 3Mb region at the end of dog chromosome 37 was unanchored.
Figure 3
Figure 3. Dynamic evolution of orthologous gene clusters
The estimated numbers of orthologue groups in the common ancestral species are shown on the internal nodes. The numbers of orthologous groups that expanded or contracted in each lineage after speciation are shown on the corresponding branch, with ‘+’ referring to expansion and ‘−’ referring to contraction.
Figure 4
Figure 4. Structure of the umami receptor T1R1 gene
Two frameshift mutations occurred in the third and sixth exons (red) of the panda T1R1 gene. The third exon contained a 2-bp (‘GG’) insertion; the sixth exon contained a 4-bp (‘GTGT’) deletion.
Figure 5
Figure 5. Panda heterozygous SNP density
a, Statistics of identified heterozygous SNPs. Analysed regions are the genomic regions with proper unique read coverage that were used for heterozygote detection. The panda X-chromosome-derived scaffolds were identified by Blastz alignment to the dog X chromosome. b, Distribution of heterozygosity density in the panda diploid genome. Heterozygous SNPs between the two sets of chromosomes of the panda diploid genome were annotated, then non-overlapping 50-kb windows were chosen and heterozygosity density in each window was calculated.
See this image and copyright information in PMC

Comment in

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Zhan X, et al. Molecular censusing doubles giant panda population estimate in a key nature reserve. Curr. Biol. 2006;16:R451–R452. - PubMed
    1. Krause J, et al. Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. BMC Evol. Biol. 2008;8:220. - PMC - PubMed
    1. Wang J, et al. The diploid genome sequence of an Asian individual. Nature. 2008;456:60–65. - PMC - PubMed
    1. Bentley DR, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008;456:53–59. - PMC - PubMed
    1. Lindblad-Toh K, et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature. 2005;438:803–819. - PubMed

Publication types

MeSH terms

Substances

-