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Chinese Science Bulletin

, 46:1937 | Cite as

A draft sequence of the rice (Oryza sativa ssp.indica) genome

  • Jun Yu
  • Songnian Hu
  • Jun Wang
  • Songgang Li
  • Ka-Shu Gane Wong
  • Bin Liu
  • Yajun Deng
  • Li Dai
  • Yan Zhou
  • Xiuqing Zhang
  • Mengliang Cao
  • Jing Liu
  • Jiandong Sun
  • Jiabin Tang
  • Yanjiong Chen
  • Xiaobing Huang
  • Wei Lin
  • Chen Ye
  • Wei Tong
  • Lijuan Cong
  • Jianing Geng
  • Yujun Han
  • Lin Li
  • Wei Li
  • Guangqiang Hu
  • Xiangang Huang
  • Wenjie Li
  • Jian Li
  • Zhanwei Liu
  • Long Li
  • Jianping Liu
  • Qiuhui Qi
  • Jinsong Liu
  • Li Li
  • Xuegang Wang
  • Hong Lu
  • Tingting Wu
  • Miao Zhu
  • Peixiang Ni
  • Hua Han
  • Wei Dong
  • Xiaoyu Ren
  • Xiaoli Feng
  • Peng Cui
  • Xianran Li
  • Hao Wang
  • Xin Xu
  • Wenxue Zhai
  • Zhao Xu
  • Jinsong Zhang
  • Sijie He
  • Jianguo Zhang
  • Jichen Xu
  • Kunlin Zhang
  • Xianwu Zheng
  • Jianhai Dong
  • Wanyong Zeng
  • Lin Tao
  • Xuewei Chen
  • Jun He
  • Daofeng Liu
  • Wei Tian
  • Chaoguang Tian
  • Hongai Xia
  • Gang Li
  • Hui Gao
  • Ping Li
  • Wei Chen
  • Xudong Wang
  • Yong Zhang
  • Jianfei Hu
  • Jing Wang
  • Song Liu
  • Jian Yang
  • Guangyu Zhang
  • Yuqing Xiong
  • Zhijie Li
  • Long Mao
  • Chengshu Zhou
  • Zhen Zhu
  • Runsheng Chen
  • Bailin Hao
  • Weimou Zheng
  • Shouyi Chen
  • Wei Guo
  • Guojie Li
  • Siqi Liu
  • Guyang Huang
  • Ming Tao
  • Jian Wang
  • Lihuang Zhu
  • Longping Yuan
  • Huanming Yang
Papers

Abstract

The sequence of the rice genome holds fundamental information for its biology, including physiology, genetics, development, and evolution, as well as information on many beneficial phenotypes of economic significance. Using a “whole genome shotgun” approach, we have produced a draft rice genome sequence ofOryza sativa ssp.indica, the major crop rice subspecies in China and many other regions of Asia. The draft genome sequence is constructed from over 4.3 million successful sequencing traces with an accumulative total length of 2214.9 Mb. The initial assembly of the non-redundant sequences reached 409.76 Mb in length, based on 3.30 million successful sequencing traces with a total length of 1797.4 Mb from anindica variant cultivar93-11, giving an estimated coverage of 95.29% of the rice genome with an average base accuracy of higher than 99%. The coverage of the draft sequence, the randomness of the sequence distribution, and the consistency of BIG-ASSEMBLER, a custom-designed software package used for the initial assembly, were verified rigorously by comparisons against finished BAC clone sequences from bothindica andjapanica strains, available from the public databases. Over all, 96.3% of full-length cDNAs, 96.4% of STS, STR, RFLP markers, 94.0% of ESTs and 94.9% unigene clusters were identified from the draft sequence. Our preliminary analysis on the data set shows that our rice draft sequence is consistent with the comman standard accepted by the genome sequencing community. The unconditional release of the draft to the public also undoubtedly provides a fundamental resource to the international scientific communities to facilitate genomic and genetic studies on rice biology.

Keywords

rice genome draft sequences 

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Copyright information

© Science in China Press 2001

Authors and Affiliations

  • Jun Yu
    • 1
    • 2
  • Songnian Hu
    • 1
  • Jun Wang
    • 1
    • 2
    • 6
  • Songgang Li
    • 1
    • 6
  • Ka-Shu Gane Wong
    • 1
    • 2
  • Bin Liu
    • 1
  • Yajun Deng
    • 1
    • 10
  • Li Dai
    • 1
  • Yan Zhou
    • 2
  • Xiuqing Zhang
    • 1
    • 3
  • Mengliang Cao
    • 1
  • Jing Liu
    • 2
  • Jiandong Sun
    • 1
  • Jiabin Tang
    • 1
    • 3
  • Yanjiong Chen
    • 1
    • 10
  • Xiaobing Huang
    • 1
  • Wei Lin
    • 2
  • Chen Ye
    • 1
  • Wei Tong
    • 1
  • Lijuan Cong
    • 1
  • Jianing Geng
    • 1
  • Yujun Han
    • 1
  • Lin Li
    • 1
  • Wei Li
    • 1
    • 5
  • Guangqiang Hu
    • 1
  • Xiangang Huang
    • 1
  • Wenjie Li
    • 1
  • Jian Li
    • 1
  • Zhanwei Liu
    • 1
  • Long Li
    • 1
  • Jianping Liu
    • 1
  • Qiuhui Qi
    • 1
  • Jinsong Liu
    • 1
  • Li Li
    • 1
  • Xuegang Wang
    • 1
  • Hong Lu
    • 1
  • Tingting Wu
    • 1
  • Miao Zhu
    • 1
  • Peixiang Ni
    • 1
  • Hua Han
    • 1
  • Wei Dong
    • 1
    • 3
  • Xiaoyu Ren
    • 1
  • Xiaoli Feng
    • 1
    • 3
  • Peng Cui
    • 1
  • Xianran Li
    • 1
  • Hao Wang
    • 1
  • Xin Xu
    • 1
  • Wenxue Zhai
    • 3
  • Zhao Xu
    • 1
  • Jinsong Zhang
    • 3
  • Sijie He
    • 3
  • Jianguo Zhang
    • 1
  • Jichen Xu
    • 3
  • Kunlin Zhang
    • 1
    • 6
  • Xianwu Zheng
    • 3
  • Jianhai Dong
    • 2
  • Wanyong Zeng
    • 3
  • Lin Tao
    • 2
  • Xuewei Chen
    • 3
  • Jun He
    • 2
  • Daofeng Liu
    • 3
  • Wei Tian
    • 2
    • 10
  • Chaoguang Tian
    • 1
  • Hongai Xia
    • 1
  • Gang Li
    • 1
  • Hui Gao
    • 1
  • Ping Li
    • 3
  • Wei Chen
    • 3
  • Xudong Wang
    • 3
  • Yong Zhang
    • 1
    • 6
  • Jianfei Hu
    • 1
    • 6
  • Jing Wang
    • 1
    • 6
  • Song Liu
    • 1
  • Jian Yang
    • 1
  • Guangyu Zhang
    • 1
  • Yuqing Xiong
    • 1
  • Zhijie Li
    • 1
  • Long Mao
    • 3
  • Chengshu Zhou
    • 4
  • Zhen Zhu
    • 3
  • Runsheng Chen
    • 1
    • 5
  • Bailin Hao
    • 2
    • 7
  • Weimou Zheng
    • 1
    • 7
  • Shouyi Chen
    • 3
  • Wei Guo
    • 8
  • Guojie Li
    • 9
  • Siqi Liu
    • 1
    • 2
  • Guyang Huang
    • 1
    • 2
  • Ming Tao
    • 1
    • 2
  • Jian Wang
    • 1
    • 2
  • Lihuang Zhu
    • 3
  • Longping Yuan
    • 4
  • Huanming Yang
    • 1
    • 2
    • 3
  1. 1.Beijing Genomics Institute/Center of Genomics & BioinformaticsChinese Academy of SciencesBeijingChina
  2. 2.Hangzhou Genomics Institute/Institute of Bioinformatics of Zhejiang University/Key Laboratory of Bioinformatics of Zhejiang ProvinceHangzhouChina
  3. 3.Institute of GeneticsChinese Academy of SciencesBeijingChina
  4. 4.National Hybrid Rice R & D CenterChangshaChina
  5. 5.Laboratory of Bioinformatics, Institute of BiophysicsChinese Academy of SciencesBeijingChina
  6. 6.College of Life SciencesPeking UniversityBeijingChina
  7. 7.Institute of Theoretical PhysicsChinese Academy of SciencesBeijingChina
  8. 8.Digital China Ltd.BeijingChina
  9. 9.Institute of Computing TechnologyChinese Academy of SciencesBeijingChina
  10. 10.Medical CollegeXi’an Jiaotong UniversityXi’anChina

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