The sequence and de novo assembly of the giant panda genome

Nature

Volumn 463, Issue 7279, 2010, Pages 311-317

  Li, Ruiqiang ^a,b   Fan, Wei ^a   Tian, Geng ^a,c   Zhu, Hongmei ^a   He, Lin ^d,e   Cai, Jing ^c,f   Huang, Quanfei ^a   Cai, Qingle ^a,g   Li, Bo ^a   Bai, Yinqi ^a   Zhang, Zhihe ^h   Zhang, Yaping ^f   Wang, Wen ^f   Li, Jun ^a   Wei, Fuwen ⁱ   Li, Heng ^j   Jian, Min ^a   Li, Jianwen ^k   Zhang, Zhaolei ^l   Nielsen, Rasmus ^a   Li, Dawei ^m   Gu, Wanjun ^a   Yang, Zhentao ^a   Xuan, Zhaoling ⁿ   Ryder, Oliver A ^o   Leung, Frederick Chi Ching ^a   Zhou, Yan ^a   Cao, Jianjun ^p   Sun, Xiao ^q   Fu, Yonggui ^a   Fang, Xiaodong ^a   Guo, Xiaosen ^h   Wang, Bo ^h   Hou, Rong ^a   Shen, Fujun ^a   Mu, Bo ^a   Ni, Peixiang ^a   Lin, Runmao ^c,f   Qian, Wubin ^a   Wang, Guodong ^f   Yu, Chang ^f   Nie, Wenhui ^a   Wang, Jinhuan ^a   Wu, Zhigang ^a,g   Liang, Huiqing ⁱ   Min, Jiumeng ^a,g   Wu, Qi ^a,c   Cheng, Shifeng ^a   Ruan, Jue ^a   Wang, Mingwei ^a   Shi, Zhongbin ^a   Wen, Ming ^a   Liu, Binghang ^a   Ren, Xiaoli ^k   Zheng, Huisong ^k   Dong, Dong ^a   Cook, Kathleen ^a   Shan, Gao ^r   Zhang, Hao ^m   Kosiol, Carolin ^m   Xie, Xueying ^a   Lu, Zuhong ^a,c   Zheng, Hancheng ⁿ   Li, Yingrui ^o   Steiner, Cynthia C ^a   Lam, Tommy Tsan Yuk ^a   Lin, Siyuan ^a   Zhang, Qinghui ^a   Li, Guoqing ^a   Tian, Jing ^p   Gong, Timing ^p   Liu, Hongde ^a   Zhang, Dejin ^a   Fang, Lin ^a   Ye, Chen ^q   Zhang, Juanbin ^q   Hu, Wenbo ^a   Xu, Anlong ^a,c,f   Ren, Yuanyuan ^s   Zhang, Guojie ^a,c   Bruford, Michael W ^a,c   Li, Qibin ^a,c   Ma, Lijia ^a   Guo, Yiran ^a,c   An, Na ^a,c   Hu, Yujie ^e   Zheng, Yang ^e   Shi, Yongyong ^a   Li, Zhiqiang ^a   Liu, Qing ^a   Chen, Yanling ^a,g   Zhao, Jing ^a   Qu, Ning ^a   Zhao, Shancen ^a   Tian, Feng ^a   Wang, Xiaoling ^a   Wang, Haiyin ^a   Xu, Lizhi ^t   Liu, Xiao ^u   Vinar, Tomas ^o   Wang, Yajun ^v   Lam, Tak Wah ^w   Yiu, Siu Ming ^w   Liu, Shiping ^w   Zhang, Hemin ^a   Li, Desheng ^a   Huang, Yan ^a   Wang, Xia ^a   Yang, Guohua ^a   Jiang, Zhi ^a   Wang, Junyi ^a   Qin, Nan ^a   Li, Li ^a,b   Li, Jingxiang ^a,x   Bolund, Lars ^a   Kristiansen, Karsten ^a   Wong, Gane Ka Shu ^a   Olson, Maynard ^y   Zhang, Xiuqing ^a   Li, Songgang ^a   Yang, Huanming ^a   Wang, Jian ^a   Wang, Jun ^a,b   more..

^a BGI SHENZHEN   (China)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^d FUDAN UNIVERSITY   (China)

^e SHANGHAI JIAO TONG UNIVERSITY   (China)

^f KUNMING INSTITUTE OF ZOOLOGY   (China)

^g SHENZHEN UNIVERSITY   (China)

^h CHENGDU RESEARCH BASE OF GIANT PANDA BREEDING   (China)

ⁱ INSTITUTE OF ZOOLOGY   (China)

^j WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^k UNIVERSITY OF TORONTO   (Canada)

^l UNIVERSITY OF CALIFORNIA   (United States)

^m Southeast University   (China)

ⁿ INSTITUTE FOR CONSERVATION RESEARCH   (United States)

^o UNIVERSITY OF HONG KONG   (Hong Kong)

^p SOUTHEAST UNIVERSITY   (China)

^q SUN YAT SEN UNIVERSITY   (China)

^r UNIVERSITY OF VETERINARY MEDICINE   (Austria)

^s CARDIFF UNIVERSITY   (United Kingdom)

^t Physics and Informatics   (Slovakia)

^u SICHUAN UNIVERSITY   (China)

^v SOUTH CHINA UNIVERSITY OF TECHNOLOGY   (China)

^w China Conservation and Research Centre for the Giant Panda   (China)

^x UNIVERSITY OF ALBERTA   (Canada)

^y UNIVERSITY OF WASHINGTON   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTE; GENETIC ANALYSIS; GENOME; MAMMAL;

AILUROPODA; ARTICLE; CARNIVORE; DIPLOIDY; DOG; GENE SEQUENCE; GENETICS; GENOME; HETEROZYGOTE; MAMMAL; MICROBIOME; NONHUMAN; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; TANDEM REPEAT;

ALGORITHMS; ANIMALS; CHINA; CONSERVED SEQUENCE; CONTIG MAPPING; DIET; DOGS; EVOLUTION, MOLECULAR; FEMALE; FERTILITY; GENOME; GENOMICS; HETEROZYGOTE; HUMANS; MULTIGENE FAMILY; POLYMORPHISM, SINGLE NUCLEOTIDE; RECEPTORS, G-PROTEIN-COUPLED; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SYNTENY; URSIDAE;

AILUROPODA MELANOLEUCA; CANIS FAMILIARIS; EUKARYOTA; MAMMALIA;

EID: 75149155568     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature08696     Document Type: Article

References (31)

1. Zhan, X. et al. Molecular censusing doubles giant panda population estimate in a key nature reserve. Curr. Biol. 16, R451-R452 (2006).
2. Krause, J. et al. Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. BMC Evol. Biol. 8, 220 (2008).
3. Wang, J. et al. The diploid genome sequence of an Asian individual. Nature 456, 60-65 (2008).
4. Bentley, D. R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53-59 (2008).
5. Lindblad-Toh, K. et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438, 803-819 (2005).
6. Li, R., Zhu, H. & Wang, J. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. doi:10.1101/gr.097261.109 (in the press).
7. Pevzner, P. A., Tang, H. & Waterman, M. S. An Eulerian path approach to DNA fragment assembly. Proc. Natl Acad. Sci. USA 98, 9748-9753 (2001).
8. Li, R., Li, Y., Kristiansen, K. & Wang, J. SOAP: short oligonucleotide alignment program. Bioinformatics 24, 713-714 (2008).
9. Li, R. et al. SNP detection for massively parallel whole-genome resequencing. Genome Res. 19, 1124-1132 (2009).
10. Zheng, Y. et al. Sequencing, annotation and comparative analysis of nine BACs of giant panda (Ailuropoda melanoleuca). Sci. China C Life Sci.doi:10.1007/s11427-010-0001-z (in the press).
11. Yu, J. et al. The genomes of Oryza sativa: a history of duplications. PLoS Biol. 3, e38 (2005).
12. Nash, W. G., Wienberg, J., Ferguson-Smith, M. A., Menninger, J. C. & O'Brien, S. J. Comparative genomics: tracking chromosome evolution in the family Ursidae using reciprocal chromosome painting. Cytogenet. Cell Genet. 83, 182-192 (1998).
13. Kapitonov, V. V. & Jurka, J. A universal classification of eukaryotic transposable elements implemented in Repbase. Nature Rev. Genet. 9, 411-412, author reply 414 (2008).
14. Smit, A. F. A., Hubley, R. & Green, P. RepeatMasker at Æhttp:// www.RepeatMasker.orgæ.
15. Nicholas, T. J. et al. The genomic architecture of segmental duplications and associated copy number variants in dogs. Genome Res. 19, 491-499 (2009).
16. Salamov, A. A. & Solovyev, V. V. Ab initio gene finding in Drosophila genomic DNA. Genome Res. 10, 516-522 (2000).
17. Stanke, M. & Waack, S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19 (suppl. 2), ii215-ii225 (2003).
18. Alexeyenko, A., Tamas, I., Liu, G. & Sonnhammer, E. L. Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics 22, e9-e15 (2006).
19. Nei, M. & Rooney, A. P. Concerted and birth-and-death evolution of multigene families. Annu. Rev. Genet. 39, 121-152 (2005).
20. Demuth, J. P., De Bie, T., Stajich, J. E., Cristianini, N. & Hahn, M. W. The evolution of mammalian gene families. PLoS One 1, e85 (2006).
21. Yang, Z. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15, 568-573 (1998).
22. Kosiol, C. et al. Patterns of positive selection in six mammalian genomes. PLoS Genet. 4, e1000144 (2008).
23. Nielsen, R. et al. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol. 3, e170 (2005).
24. Chandrashekar, J. et al. T2Rs function as bitter taste receptors. Cell 100, 703-711 (2000).
25. Go, Y. Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Lineage-specific expansions and contractions of the bitter taste receptor gene repertoire in vertebrates. Mol. Biol. Evol. 23, 964-972 (2006).
26. Chandrashekar, J., Hoon, M. A., Ryba, N. J. & Zuker, C. S. The receptors and cells for mammalian taste. Nature 444, 288-294 (2006).
27. Nelson, G. et al. An amino-acid taste receptor. Nature 416, 199-202 (2002).
28. Yasuo, T., Kusuhara, Y., Yasumatsu, K. & Ninomiya, Y. Multiple receptor systems for glutamate detection in the taste organ. Biol. Pharm. Bull. 31, 1833-1837 (2008).
29. Zhang, B. et al. Genetic viability and population history of the giant panda, putting an end to the "evolutionary dead end"? Mol. Biol. Evol. 24, 1801-1810 (2007).
30. Donnelly, P. & Tavare, S. Coalescents and genealogical structure under neutrality. Annu. Rev. Genet. 29, 401-421 (1995).
31. Jurka, J. et al. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110, 462-467 (2005).