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4 results on '"Zhongbin Shi"'

1. De novo assembly of human genomes with massively parallel short read sequencing

Author

Xiaodong Fang, Wubin Qian, Jing Wang, Hongmei Zhu, Gao Shan, Songgang Li, Jue Ruan, Yingrui Li, Karsten Kristiansen, Jun Wang, Shengting Li, Huanming Yang, Zhongbin Shi, and Ruiqiang Li

Subjects
Genetics, Resource, Asian Continental Ancestry Group, Contig, Assembly software, Genome, Human, Sequence assembly, Black People, Hybrid genome assembly, Computational biology, Sequence Analysis, DNA, Biology, Genome, DNA sequencing, Asian People, Human Genome Project, Humans, Human genome, Sequence Alignment, Genetics (clinical), Paired-end tag, African Continental Ancestry Group, Oligonucleotide Array Sequence Analysis
Abstract

Next-generation massively parallel DNA sequencing technologies provide ultrahigh throughput at a substantially lower unit data cost; however, the data are very short read length sequences, making de novo assembly extremely challenging. Here, we describe a novel method for de novo assembly of large genomes from short read sequences. We successfully assembled both the Asian and African human genome sequences, achieving an N50 contig size of 7.4 and 5.9 kilobases (kb) and scaffold of 446.3 and 61.9 kb, respectively. The development of this de novo short read assembly method creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost-effective way.

Published
2010

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

Author

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

3. The genome of the cucumber, Cucumis sativus L

Author

Jian Wu, Jie Guo, Xiaowu Wang, Yuhong Yang, Guangcun Li, Lijia Ma, Zhang Baoxi, Zhouchao Cheng, Shifang Liu, Jianwen Li, Shenhao Wang, Shuang Yang, Lars Bolund, Kui Lin, Shiqiang Liu, Li Li, Hongmei Zhu, Wei Fan, Jing Wang, Lin Fang, Qiuxiang Shi, Zhuo Li, Yang Wu, Xuefeng Li, Ying Li, Ruiqiang Li, Mingwei Wang, Yao Lu, Yingrui Li, Bingyan Xie, Won Kyong Cho, Jue Ruan, Hongkun Zheng, Wubin Qian, Jack E. Staub, Jing Zhao, Bo Li, Xiaodong Fang, Ming Wen, Zhaoling Xuan, Han Miao, Xingfang Gu, Weiwei Jin, Zhigang Wu, Zhentao Yang, Hui Liu, Shengping Zhang, Man Li, Zhangjun Fei, Shaochuan Li, Quanfei Huang, Jae-Yean Kim, Bowen Zhao, Guohua Yang, Zhonghua Zhang, Geng Tian, Dongyuan Liu, Jianjun Cao, Nan Qin, Jun He, Xiaoli Ren, Yi Ren, Huiqing Liang, Min Jian, Zhiqi Jia, Yong Xu, Houxiang Kang, Peixiang Ni, Guojie Zhang, Katarzyna Heller-Uszynska, Guoqing Li, Huanming Yang, Rifei Sun, Sanwen Huang, William J. Lucas, Qingle Cai, Hancheng Zheng, Yuanyuan Ren, Jun Li, Yong Zhang, Yongchen Du, Hailong Yang, Jun Wang, Karsten Kristiansen, Rui Chen, Andrzej Kilian, Shuzhi Jiang, Juanbin Zhang, Songgang Li, Yan Zhou, Asan, Edwin A. G. van der Vossen, Yinqi Bai, Xiuqing Zhang, Yonghua Han, and Zhongbin Shi

Subjects
DNA, Plant, Molecular Sequence Data, arabidopsis-thaliana, Biology, Plant disease resistance, Genes, Plant, Genome, Synteny, phloem, diversity, resistance, PRI Biodiversiteit en Veredeling, Gene Duplication, Botany, expression, Genetics, Arabidopsis thaliana, gene, Gene, Plant Diseases, Repetitive Sequences, Nucleic Acid, Whole genome sequencing, plants, Nucleic acid sequence, food and beverages, ethylene biosynthesis, sequence, biology.organism_classification, Immunity, Innate, PRI Biodiversity and Breeding, DNA Transposable Elements, EPS, Cucumis sativus, Cucumis, rice genome, Genome, Plant
Abstract

Udgivelsesdato: 2009-Dec Cucumber is an economically important crop as well as a model system for sex determination studies and plant vascular biology. Here we report the draft genome sequence of Cucumis sativus var. sativus L., assembled using a novel combination of traditional Sanger and next-generation Illumina GA sequencing technologies to obtain 72.2-fold genome coverage. The absence of recent whole-genome duplication, along with the presence of few tandem duplications, explains the small number of genes in the cucumber. Our study establishes that five of the cucumber's seven chromosomes arose from fusions of ten ancestral chromosomes after divergence from Cucumis melo. The sequenced cucumber genome affords insight into traits such as its sex expression, disease resistance, biosynthesis of cucurbitacin and 'fresh green' odor. We also identify 686 gene clusters related to phloem function. The cucumber genome provides a valuable resource for developing elite cultivars and for studying the evolution and function of the plant vascular system.

Published
2009

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

Author

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

Subjects
Genetics, Multidisciplinary, biology, Species name, biology.animal, Correct name, Ailuropoda, Sequence assembly, biology.organism_classification, Genome, Ailuropoda melanoleuca, Sequence (medicine)
Abstract

Nature 463, 311–317 (2010) In this Article, the Latin species name of the giant panda was written incorrectly as Ailuropoda melanoleura. The correct name is Ailuropoda melanoleuca.

Published
2010

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