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The sequence and denovo assembly of thegiant panda genome Ruiqiang LiWei FanGeng Tian2009 год

The sequence and de novo assembly of the giant panda genome
статья из журнала

Полный текстСтраница публикацииПубликация в OpenAlex
Аннотация: 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. The genome of the giant panda — specifically of the female Beijing Olympics mascot Jingjing — has been determined using short-read sequencing technology, a first for such a complex genome. It consists of some 2.4 billion DNA base pairs, compared to 3 billion in humans, and contains around 21,000 protein-encoding genes, similar to the human genome. Genomic diversity reflected in the sequence is high, raising hopes that despite a population of only about 2,500, conservation efforts can keep the species from extinction. Intriguingly, the panda appears to have all the genes needed for a carnivorous digestive system but lacks digestive cellulase genes. It may therefore depend on its gut microbiome to handle its famously limited bamboo diet. Taste may be a diet-limiting factor: loss of function of the T1R1 gene means that pandas may not experience the umami taste associated with high-protein foods. Technical aspects of this work pave the way for the use of next-generation sequencing for rapid de novo assembly of large eukaryotic genomes. Here, a draft sequence of the giant panda genome is assembled using next-generation sequencing technology alone. Genome analysis reveals a low divergence rate in comparison with dog and human genomes and insights into panda-specific traits; for example, the giant panda's bamboo diet may be more dependent on its gut microbiome than its own genetic composition.
Год издания: 2009
Авторы: Ruiqiang Li, Wei Fan, Geng Tian, Hongmei Zhu, Lin He, Jing Cai, Quanfei Huang, Qingle Cai, Bo Li, Yinqi Bai, Zhihe Zhang, Ya‐Ping 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, Ming‐Wei Wang, Zhongbin Shi, Ming Wen, Binghang Liu, Xiaoli Ren, Huisong Zheng, Dong Dong, Kathleen Cook, Shan Gao, Hao Zhang, Carolin Kosiol, Xueying Xie, Zuhong Lu, Hancheng Zheng, Yingrui Li, Cynthia 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, Tomáš Vinař, 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 V. Olson, Xiuqing Zhang, Songgang Li, Huanming Yang, Jian Wang, Jun Wang
Издательство: Nature Portfolio
Источник: Nature
Ключевые слова: Genomics and Phylogenetic Studies, RNA and protein synthesis mechanisms, Biochemical Analysis and Sensing Techniques
Другие ссылки: Nature (PDF)
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Europe PMC (PubMed Central) (PDF)
Europe PMC (PubMed Central) (HTML)
PubMed Central (HTML)
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