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The sequence and de novo assembly of the giant panda genome

Li, Ruiqiang, Fan, Wei, Tian, Geng, Zhu, Hongmei, He, Lin, Cai, Jing, Huang, Quanfei, Cai, Qingle, Li, Bo, Bai, Yinqi, Zhang, Zhihe, Zhang, Yaping, Wang, Wen, Li, Jun, Wei, Fuwen, Li, Heng, Jian, Min, Li, Jianwen, Zhang, Zhaolei, Nielsen, Rasmus, Li, Dawei, Gu, Wanjun, Yang, Zhentao, Xuan, Zhaoling, Ryder, Oliver A., Leung, Frederick Chi-Ching, Zhou, Yan, Cao, Jianjun, Sun, Xiao, Fu, Yonggui, Fang, Xiaodong, Guo, Xiaosen, Wang, Bo, Hou, Rong, Shen, Fujun, Mu, Bo, Ni, Peixiang, Lin, Runmao, Qian, Wubin, Wang, Guodong, Yu, Chang, Nie, Wenhui, Wang, Jinhuan, Wu, Zhigang, Liang, Huiqing, Min, Jiumeng, Wu, Qi, Cheng, Shifeng, Ruan, Jue, Wang, Mingwei, Shi, Zhongbin, Wen, Ming, Liu, Binghang, Ren, Xiaoli, Zheng, Huisong, Dong, Dong, Cook, Kathleen, Shan, Gao, Zhang, Hao, Kosiol, Carolin, Xie, Xueying, Lu, Zuhong, Zheng, Hancheng, Li, Yingrui, Steiner, Cynthia C., Lam, Tommy Tsan-Yuk, Lin, Siyuan, Zhang, Qinghui, Li, Guoqing, Tian, Jing, Gong, Timing, Liu, Hongde, Zhang, Dejin, Fang, Lin, Ye, Chen, Zhang, Juanbin, Hu, Wenbo, Xu, Anlong, Ren, Yuanyuan, Zhang, Guojie, Bruford, Michael William, Li, Qibin, Ma, Lijia, Guo, Yiran, An, Na, Hu, Yujie, Zheng, Yang, Shi, Yongyong, Li, Zhiqiang, Liu, Qing, Chen, Yanling, Zhao, Jing, Qu, Ning, Zhao, Shancen, Tian, Feng, Wang, Xiaoling, Wang, Haiyin, Xu, Lizhi, Liu, Xiao, Vinar, Tomas, Wang, Yajun, Lam, Tak-Wah, Yiu, Siu-Ming, Liu, Shiping, Zhang, Hemin, Li, Desheng, Huang, Yan, Wang, Xia, Yang, Guohua, Jiang, Zhi, Wang, Junyi, Qin, Nan, Li, Li, Li, Jingxiang, Bolund, Lars, Kristiansen, Karsten, Wong, Gane Ka-Shu, Olson, Maynard, Zhang, Xiuqing, Li, Songgang, Yang, Huanming, Wang, Jian and Wang, Jun 2010. The sequence and de novo assembly of the giant panda genome. Nature 463 (7279) , pp. 311-317. 10.1038/nature08696

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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.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Biosciences
Sustainable Places Research Institute (PLACES)
Subjects: Q Science > QH Natural history > QH301 Biology
Q Science > QH Natural history > QH426 Genetics
Q Science > QL Zoology
Additional Information: There is a Corrigendum (25 February 2010) associated with this document: 'In this Article, the Latin species name of the giant panda was written incorrectly as Ailuropoda melanoleura. The correct name is Ailuropoda melanoleuca.' The corrigendum can be viewed at this link: http://www.nature.com/nature/journal/v463/n7284/full/nature08846.html
Publisher: Nature Publishing Group
ISSN: 0028-0836
Last Modified: 04 Jun 2017 03:30
URI: http://orca.cf.ac.uk/id/eprint/22184

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