1. The sequence and de novo assembly of the giant panda genome
- Author
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Xiao Sun, Xiaosen Guo, Xiao Liu, Qibin Li, Siu-Ming Yiu, Ning Qu, Jing Wang, Zhaolei Zhang, Anlong Xu, Carolin Kosiol, Yiran Guo, Xiaodong Fang, Yanling Chen, Tomas Vinar, Jianjun Cao, Desheng Li, Ming Wen, Gane Ka-Shu Wong, Hao Zhang, Bo Li, Feng Tian, Yajun Wang, Wei Fan, Shiping Liu, Bo Mu, Qingle Cai, Zhentao Yang, Oliver A. Ryder, Min Jian, Qing Liu, Lin Fang, Kathleen Cook, Shancen Zhao, Gao Shan, Jingxiang Li, Jing Zhao, Lin He, Mingwei Wang, Qi Wu, Haiyin Wang, Wen Wang, Hongmei Zhu, Michael William Bruford, Junyi Wang, Quanfei Huang, Wanjun Gu, Yuanyuan Ren, Jing Cai, Jing Tian, Yang Zheng, Guohua Yang, Yingrui Li, Huiqing Liang, Guojie Zhang, Yonggui Fu, Yinqi Bai, Qinghui Zhang, Juanbin Zhang, Maynard V. Olson, Songgang Li, Shifeng Cheng, Guo-Dong Wang, Jianwen Li, Chang Yu, Zhongbin Shi, Chen Ye, Na An, Heng Li, Zhi Jiang, Huisong Zheng, Cynthia C. Steiner, Ruiqiang Li, Wubin Qian, Yujie Hu, Wenbo Hu, Hongde Liu, Rasmus Nielsen, Xueying Xie, Tommy Tsan-Yuk Lam, Hemin Zhang, Yongyong Shi, Frederick C. Leung, Jun Wang, Peixiang Ni, Xiuqing Zhang, Dong Dong, Xiaoli Ren, Fuwen Wei, Jiumeng Min, Jue Ruan, Runmao Lin, Zhiqiang Li, Wenhui Nie, Lars Bolund, Dawei Li, Fujun Shen, Zuhong Lu, Ya-Ping Zhang, Karsten Kristiansen, Dejin Zhang, Geng Tian, Nan Qin, Siyuan Lin, Tak-Wah Lam, Xia Wang, Jinhuan Wang, Binghang Liu, Li Li, Xiaoling Wang, Lijia Ma, Yan Zhou, Zhihe Zhang, Zhaoling Xuan, Zhigang Wu, Lizhi Xu, Guoqing Li, Rong Hou, Huanming Yang, Bo Wang, Hancheng Zheng, Jun Li, Yan Huang, and Timing Gong
- Subjects
Cancer genome sequencing ,Heterozygote ,China ,Sequence assembly ,Receptors, G-Protein-Coupled - genetics ,Genomics ,Biology ,Genome ,Polymorphism, Single Nucleotide ,Synteny ,Article ,Receptors, G-Protein-Coupled ,Evolution, Molecular ,Contig Mapping ,Dogs ,Tandem repeat ,biology.animal ,Animals ,Humans ,Diet - veterinary ,Ursidae - classification - genetics - physiology ,Conserved Sequence ,Ailuropoda melanoleuca ,Genetics ,Multidisciplinary ,Contig ,Sequence Analysis, DNA ,Genome - genetics ,Polymorphism, Single Nucleotide - genetics ,Diet ,Fertility ,Multigene Family ,Multigene Family - genetics ,Fertility - genetics - physiology ,Synteny - genetics ,Female ,Sequence Alignment ,Ursidae ,Algorithms ,Reference genome ,Conserved Sequence - genetics - 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. © 2010 Macmillan Publishers Limited. All rights reserved., link_to_OA_fulltext
- Published
- 2009
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