The sequence and de novo assembly of the giant panda genome

被引：849

作者：

Li, Ruiqiang ^{[1
,2
]}

Fan, Wei ^{[1
]}

Tian, Geng ^{[1
,3
]}

Zhu, Hongmei ^{[1
]}

He, Lin ^{[4
,5
]}

Cai, Jing ^{[3
,6
]}

Huang, Quanfei ^{[1
]}

Cai, Qingle ^{[1
,7
]}

Li, Bo ^{[1
]}

Bai, Yinqi ^{[1
]}

Zhang, Zhihe ^{[8
]}

Zhang, Yaping ^{[6
]}

Wang, Wen ^{[6
]}

Li, Jun ^{[1
]}

Wei, Fuwen ^{[9
]}

Li, Heng ^{[10
]}

Jian, Min ^{[1
]}

Li, Jianwen ^{[1
]}

Zhang, Zhaolei ^{[11
]}

Nielsen, Rasmus ^{[12
,13
]}

Li, Dawei ^{[1
]}

Gu, Wanjun ^{[14
]}

Yang, Zhentao ^{[1
]}

Xuan, Zhaoling ^{[1
]}

Ryder, Oliver A. ^{[15
]}

Leung, Frederick Chi-Ching ^{[16
]}

Zhou, Yan ^{[1
]}

Cao, Jianjun ^{[1
]}

Sun, Xiao ^{[17
]}

Fu, Yonggui ^{[18
]}

Fang, Xiaodong ^{[1
]}

Guo, Xiaosen ^{[1
]}

Wang, Bo ^{[1
]}

Hou, Rong ^{[8
]}

Shen, Fujun ^{[8
]}

Mu, Bo ^{[1
]}

Ni, Peixiang ^{[1
]}

Lin, Runmao ^{[1
]}

Qian, Wubin ^{[1
]}

Wang, Guodong ^{[3
,6
]}

Yu, Chang ^{[1
]}

Nie, Wenhui ^{[6
]}

Wang, Jinhuan ^{[6
]}

Wu, Zhigang ^{[1
]}

Liang, Huiqing ^{[1
]}

Min, Jiumeng ^{[1
,7
]}

Wu, Qi ^{[9
]}

Cheng, Shifeng ^{[1
,7
]}

Ruan, Jue ^{[1
,3
]}

Wang, Mingwei ^{[1
]}

机构：

[1] BGI Shenzhen, Shenzhen 518083, Peoples R China

[2] Univ Copenhagen, Dept Biol, DK-2200 Copenhagen, Denmark

[3] Chinese Acad Sci, Grad Univ, Beijing 100062, Peoples R China

[4] Fudan Univ, Inst Biomed Sci, Shanghai 200032, Peoples R China

[5] Shanghai Jiao Tong Univ, Minist Educ, Key Lab Genet Dev & Neuropsychiat Disorders, BioX Ctr, Shanghai 200030, Peoples R China

[6] Chinese Acad Sci, Kunming Inst Zool, State Key Lab Genet Resources & Evolut, Kunming 650223, Peoples R China

[7] Shenzhen Univ, Sch Med, Genome Res Inst, Shenzhen 518000, Peoples R China

[8] Chengdu Res Base Giant Panda Breeding, Chengdu 610081, Peoples R China

[9] Chinese Acad Sci, Inst Zool, Key Lab Anim Ecol & Conservat Biol, Beijing 100101, Peoples R China

[10] Wellcome Trust Genome Campus, Cambridge CB10 1SA, England

[11] Univ Toronto, Dept Mol Genet, Banting & Best Dept Med Res, Donnelly Ctr Cellular & Biomol Res, Toronto, ON M5S 3E1, Canada

[12] Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA

[13] Univ Calif Berkeley, Dept Stat, Berkeley, CA 94720 USA

[14] Southeast Univ, Minist Educ, Key Lab Child Dev & Learning Sci, Nanjing 210096, Peoples R China

[15] San Diego Zoos Inst Conservat Res, Escondido, CA 92027 USA

[16] Univ Hong Kong, Sch Biol Sci, Hong Kong, Hong Kong, Peoples R China

[17] Southeast Univ, State Key Lab Bioelect, Nanjing 210096, Peoples R China

[18] Sun Yat Sen Univ, Coll Life Sci, State Key Lab Biocontrol, Guangzhou 510275, Guangdong, Peoples R China

[19] Vet Med Univ Wien, Inst Populat Genet, A-1210 Vienna, Austria

[20] Cardiff Univ, Cardiff Sch Biosci, Biodivers & Ecol Proc Grp, Cardiff CF10 3AX, Wales

[21] Comenius Univ, Dept Appl Informat, Fac Math Phys & Informat, Bratislava 84248, Slovakia

[22] Sichuan Univ, Sch Life Sci, Chengdu 610064, Peoples R China

[23] Univ Hong Kong, Dept Comp Sci, Hong Kong, Hong Kong, Peoples R China

[24] S China Univ Technol, Guangzhou 510641, Peoples R China

[25] China Conservat & Res Ctr Giant Panda, Wolong Nat Reserve 623006, Peoples R China

[26] Univ Alberta, Dept Med, Edmonton, AB T6G 2E9, Canada

[27] Univ Alberta, Dept Biol Sci, Edmonton, AB T6G 2E9, Canada

[28] Univ Washington, Genome Ctr, Seattle, WA USA

来源：

NATURE | 2010年 / 463卷 / 7279期

基金：

中国国家自然科学基金;

关键词：

TASTE RECEPTOR; EVOLUTION; FAMILIES; DNA;

D O I：

10.1038/nature08696

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页码：311 / 317

页数：7

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