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The sequence and de novo assembly of the giant panda genome.


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.

SUBMITTER: Li R 

PROVIDER: S-EPMC3951497 | biostudies-literature | 2010 Jan

REPOSITORIES: biostudies-literature

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The sequence and de novo assembly of the giant panda genome.

Li Ruiqiang R   Fan Wei W   Tian Geng G   Zhu Hongmei H   He Lin L   Cai Jing J   Huang Quanfei Q   Cai Qingle Q   Li Bo B   Bai Yinqi Y   Zhang Zhihe Z   Zhang Yaping Y   Wang Wen W   Li Jun J   Wei Fuwen F   Li Heng H   Jian Min M   Li Jianwen J   Zhang Zhaolei Z   Nielsen Rasmus R   Li Dawei D   Gu Wanjun W   Yang Zhentao Z   Xuan Zhaoling Z   Ryder Oliver A OA   Leung Frederick Chi-Ching FC   Zhou Yan Y   Cao Jianjun J   Sun Xiao X   Fu Yonggui Y   Fang Xiaodong X   Guo Xiaosen X   Wang Bo B   Hou Rong R   Shen Fujun F   Mu Bo B   Ni Peixiang P   Lin Runmao R   Qian Wubin W   Wang Guodong G   Yu Chang C   Nie Wenhui W   Wang Jinhuan J   Wu Zhigang Z   Liang Huiqing H   Min Jiumeng J   Wu Qi Q   Cheng Shifeng S   Ruan Jue J   Wang Mingwei M   Shi Zhongbin Z   Wen Ming M   Liu Binghang B   Ren Xiaoli X   Zheng Huisong H   Dong Dong D   Cook Kathleen K   Shan Gao G   Zhang Hao H   Kosiol Carolin C   Xie Xueying X   Lu Zuhong Z   Zheng Hancheng H   Li Yingrui Y   Steiner Cynthia C CC   Lam Tommy Tsan-Yuk TT   Lin Siyuan S   Zhang Qinghui Q   Li Guoqing G   Tian Jing J   Gong Timing T   Liu Hongde H   Zhang Dejin D   Fang Lin L   Ye Chen C   Zhang Juanbin J   Hu Wenbo W   Xu Anlong A   Ren Yuanyuan Y   Zhang Guojie G   Bruford Michael W MW   Li Qibin Q   Ma Lijia L   Guo Yiran Y   An Na N   Hu Yujie Y   Zheng Yang Y   Shi Yongyong Y   Li Zhiqiang Z   Liu Qing Q   Chen Yanling Y   Zhao Jing J   Qu Ning N   Zhao Shancen S   Tian Feng F   Wang Xiaoling X   Wang Haiyin H   Xu Lizhi L   Liu Xiao X   Vinar Tomas T   Wang Yajun Y   Lam Tak-Wah TW   Yiu Siu-Ming SM   Liu Shiping S   Zhang Hemin H   Li Desheng D   Huang Yan Y   Wang Xia X   Yang Guohua G   Jiang Zhi Z   Wang Junyi J   Qin Nan N   Li Li L   Li Jingxiang J   Bolund Lars L   Kristiansen Karsten K   Wong Gane Ka-Shu GK   Olson Maynard M   Zhang Xiuqing X   Li Songgang S   Yang Huanming H   Wang Jian J   Wang Jun J  

Nature 20091213 7279


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 ind  ...[more]

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