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The sequence and de novo assembly of the giant panda genome

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 rep... Full description

Journal Title: Nature 2009, Vol.463(7279), p.311
Main Author: Ruiqiang Li
Other Authors: 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
Format: Electronic Article Electronic Article
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Subjects:
ID: ISSN: 0028-0836 ; E-ISSN: 1476-4687 ; DOI: 10.1038/nature08696
Link: http://dx.doi.org/10.1038/nature08696
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recordid: nature_a10.1038/nature08696
title: The sequence and de novo assembly of the giant panda genome
format: Article
creator:
  • Ruiqiang Li
  • 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
subjects:
  • Algorithms–Genetics
  • Animals–Veterinary
  • China–Genetics
  • Conserved Sequence–Physiology
  • Contig Mapping–Genetics
  • Diet–Genetics
  • Dogs–Genetics
  • Evolution, Molecular–Genetics
  • Female–Genetics
  • Fertility–Classification
  • Fertility–Genetics
  • Genome–Physiology
  • Genomics–Physiology
  • Heterozygote–Physiology
  • Humans–Physiology
  • Multigene Family–Physiology
  • Polymorphism, Single Nucleotide–Physiology
  • Receptors, G-Protein-Coupled–Physiology
  • Sequence Alignment–Physiology
  • Sequence Analysis, DNA–Physiology
  • Synteny–Physiology
  • Ursidae–Physiology
  • Ursidae–Physiology
  • Ursidae–Physiology
  • Genomics
  • Genetics
  • Deoxyribonucleic Acid–DNA
  • Cost Reduction
  • Comparative Analysis
  • Biology
  • Receptors, G-Protein-Coupled
  • Taste Receptors, Type 1
ispartof: Nature, 2009, Vol.463(7279), p.311
description: 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. [PUBLICATION ]
language:
source:
identifier: ISSN: 0028-0836 ; E-ISSN: 1476-4687 ; DOI: 10.1038/nature08696
fulltext: fulltext
issn:
  • 0028-0836
  • 00280836
  • 1476-4687
  • 14764687
url: Link


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titleThe sequence and de novo assembly of the giant panda genome
creatorRuiqiang Li ; 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
ispartofNature, 2009, Vol.463(7279), p.311
identifier
source
descriptionUsing 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. [PUBLICATION ]
subjectAlgorithms–Genetics ; Animals–Veterinary ; China–Genetics ; Conserved Sequence–Physiology ; Contig Mapping–Genetics ; Diet–Genetics ; Dogs–Genetics ; Evolution, Molecular–Genetics ; Female–Genetics ; Fertility–Classification ; Fertility–Genetics ; Genome–Physiology ; Genomics–Physiology ; Heterozygote–Physiology ; Humans–Physiology ; Multigene Family–Physiology ; Polymorphism, Single Nucleotide–Physiology ; Receptors, G-Protein-Coupled–Physiology ; Sequence Alignment–Physiology ; Sequence Analysis, DNA–Physiology ; Synteny–Physiology ; Ursidae–Physiology ; Ursidae–Physiology ; Ursidae–Physiology ; Genomics ; Genetics ; Deoxyribonucleic Acid–DNA ; Cost Reduction ; Comparative Analysis ; Biology ; Receptors, G-Protein-Coupled ; Taste Receptors, Type 1;
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13Jun Li
14Fuwen Wei
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16Min Jian
17Jianwen Li
18Zhaolei Zhang
19Rasmus Nielsen
20Dawei Li
21Wanjun Gu
22Zhentao Yang
23Zhaoling Xuan
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25Frederick Chi-Ching Leung
26Yan Zhou
27Jianjun Cao
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49Mingwei Wang
50Zhongbin Shi
51Ming Wen
52Binghang Liu
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54Huisong Zheng
55Dong Dong
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57Gao Shan
58Hao Zhang
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98Xiao Liu
99Tomas Vinar
100Yajun Wang
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102Siu-Ming Yiu
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106Yan Huang
107Xia Wang
108Guohua Yang
109Zhi Jiang
110Junyi Wang
111Nan Qin
112Li Li
113Jingxiang Li
114Lars Bolund
115Karsten Kristiansen
116Gane Ka-Shu Wong
117Maynard Olson
118Xiuqing Zhang
119Songgang Li
120Huanming Yang
121Jian Wang
122Jun Wang
titleThe sequence and de novo assembly of the giant panda genome
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titleThe sequence and de novo assembly of the giant panda genome
authorRuiqiang Li ; 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
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11Yaping Zhang
12Wen Wang
13Jun Li
14Fuwen Wei
15Heng Li
16Min Jian
17Jianwen Li
18Zhaolei Zhang
19Rasmus Nielsen
20Dawei Li
21Wanjun Gu
22Zhentao Yang
23Zhaoling Xuan
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25Frederick Chi-Ching Leung
26Yan Zhou
27Jianjun Cao
28Xiao Sun
29Yonggui Fu
30Xiaodong Fang
31Xiaosen Guo
32Bo Wang
33Rong Hou
34Fujun Shen
35Bo Mu
36Peixiang Ni
37Runmao Lin
38Wubin Qian
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41Wenhui Nie
42Jinhuan Wang
43Zhigang Wu
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46Qi Wu
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49Mingwei Wang
50Zhongbin Shi
51Ming Wen
52Binghang Liu
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54Huisong Zheng
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58Hao Zhang
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62Hancheng Zheng
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65Tommy Tsan-Yuk Lam
66Siyuan Lin
67Qinghui Zhang
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69Jing Tian
70Timing Gong
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121Jian Wang
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26Yan Zhou
27Jianjun Cao
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50Zhongbin Shi
51Ming Wen
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54Huisong Zheng
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57Gao Shan
58Hao Zhang
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60Xueying Xie
61Zuhong Lu
62Hancheng Zheng
63Yingrui Li
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65Tommy Tsan-Yuk Lam
66Siyuan Lin
67Qinghui Zhang
68Guoqing Li
69Jing Tian
70Timing Gong
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72Dejin Zhang
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77Anlong Xu
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84Na An
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92Ning Qu
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96Haiyin Wang
97Lizhi Xu
98Xiao Liu
99Tomas Vinar
100Yajun Wang
101Tak-Wah Lam
102Siu-Ming Yiu
103Shiping Liu
104Hemin Zhang
105Desheng Li
106Yan Huang
107Xia Wang
108Guohua Yang
109Zhi Jiang
110Junyi Wang
111Nan Qin
112Li Li
113Jingxiang Li
114Lars Bolund
115Karsten Kristiansen
116Gane Ka-Shu Wong
117Maynard Olson
118Xiuqing Zhang
119Songgang Li
120Huanming Yang
121Jian Wang
122Jun Wang
atitleThe sequence and de novo assembly of the giant panda genome
jtitleNature
risdate20091213
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doi10.1038/nature08696
pages311-317
eissn14764687
date2010-01-21