Sequence and analysis of rice chromosome 4

Qi Feng, Yujun Zhang, Pei Hao, Shengyue Wang, Gang Fu, Yucheng Huang, Ying Li, Jingjie Zhu, Yilei Liu, Xin Hu, Peixin Jia, Yu Zhang, Qiang Zhao, Kai Ying, Shuliang Yu, Yesheng Tang, Qijun Weng, Lei Zhang, Ying Lu, Jie Mu, Yiqi Lu, Lei S. Zhang, Zhen Yu, Danlin Fan, Xiaohui Liu, Tingting Lu, Can Li, Yongrui Wu, Tongguo Sun, Haiyan Lei, Tao Li, Hao Hu, Jianping Guan, Mei Wu, Runquan Zhang, Bo Zhou, Zehua Chen, Ling Chen, Zhaoqing Jin, Rong Wang, Haifeng Yin, Zhen Cai, Shuangxi Ren, Gang Lv, Wenyi Gu, Genfeng Zhu, Yuefeng Tu, Jia Jia, Yi Zhang, Jie Chen, Hui Kang, Xiaoyun Chen, Chunyan Shao, Yun Sun, Qiuping Hu, Xianglin Zhang, Wei Zhang, Lijun Wang, Chunwei Ding, Haihui Sheng, Jingli Gu, Shuting Chen, Lin Ni, Fenghua Zhu, Wei Chen, Lefu Lan, Ying Lai, Zhukuan Cheng, Minghong Gu, Jiming Jiang, Jiayang Li, Guofan Hong, Yongbiao Xue and Bin Han ()
Additional contact information
Qi Feng: Chinese Academy of Sciences
Yujun Zhang: Chinese Academy of Sciences
Pei Hao: Chinese Academy of Sciences
Shengyue Wang: Chinese National Human Genome Center at Shanghai
Gang Fu: Chinese National Human Genome Center at Shanghai
Yucheng Huang: Chinese Academy of Sciences
Ying Li: Chinese Academy of Sciences
Jingjie Zhu: Chinese Academy of Sciences
Yilei Liu: Chinese Academy of Sciences
Xin Hu: Chinese Academy of Sciences
Peixin Jia: Chinese Academy of Sciences
Yu Zhang: Chinese Academy of Sciences
Qiang Zhao: Chinese Academy of Sciences
Kai Ying: Chinese Academy of Sciences
Shuliang Yu: Chinese Academy of Sciences
Yesheng Tang: Chinese Academy of Sciences
Qijun Weng: Chinese Academy of Sciences
Lei Zhang: Chinese Academy of Sciences
Ying Lu: Chinese Academy of Sciences
Jie Mu: Chinese Academy of Sciences
Yiqi Lu: Chinese Academy of Sciences
Lei S. Zhang: Chinese Academy of Sciences
Zhen Yu: Chinese Academy of Sciences
Danlin Fan: Chinese Academy of Sciences
Xiaohui Liu: Chinese Academy of Sciences
Tingting Lu: Chinese Academy of Sciences
Can Li: Chinese Academy of Sciences
Yongrui Wu: Chinese Academy of Sciences
Tongguo Sun: Chinese Academy of Sciences
Haiyan Lei: Chinese Academy of Sciences
Tao Li: Chinese Academy of Sciences
Hao Hu: Chinese Academy of Sciences
Jianping Guan: Chinese Academy of Sciences
Mei Wu: Chinese Academy of Sciences
Runquan Zhang: Chinese Academy of Sciences
Bo Zhou: Chinese Academy of Sciences
Zehua Chen: Chinese Academy of Sciences
Ling Chen: Chinese Academy of Sciences
Zhaoqing Jin: Chinese Academy of Sciences
Rong Wang: Chinese Academy of Sciences
Haifeng Yin: Chinese National Human Genome Center at Shanghai
Zhen Cai: Chinese National Human Genome Center at Shanghai
Shuangxi Ren: Chinese National Human Genome Center at Shanghai
Gang Lv: Chinese National Human Genome Center at Shanghai
Wenyi Gu: Chinese National Human Genome Center at Shanghai
Genfeng Zhu: Chinese National Human Genome Center at Shanghai
Yuefeng Tu: Chinese National Human Genome Center at Shanghai
Jia Jia: Chinese National Human Genome Center at Shanghai
Yi Zhang: Chinese National Human Genome Center at Shanghai
Jie Chen: Chinese National Human Genome Center at Shanghai
Hui Kang: Chinese National Human Genome Center at Shanghai
Xiaoyun Chen: Chinese National Human Genome Center at Shanghai
Chunyan Shao: Chinese National Human Genome Center at Shanghai
Yun Sun: Chinese National Human Genome Center at Shanghai
Qiuping Hu: Chinese National Human Genome Center at Shanghai
Xianglin Zhang: Chinese National Human Genome Center at Shanghai
Wei Zhang: Chinese National Human Genome Center at Shanghai
Lijun Wang: Chinese National Human Genome Center at Shanghai
Chunwei Ding: Chinese National Human Genome Center at Shanghai
Haihui Sheng: Chinese National Human Genome Center at Shanghai
Jingli Gu: Chinese National Human Genome Center at Shanghai
Shuting Chen: Chinese National Human Genome Center at Shanghai
Lin Ni: Chinese National Human Genome Center at Shanghai
Fenghua Zhu: Chinese National Human Genome Center at Shanghai
Wei Chen: Chinese Academy of Sciences
Lefu Lan: Chinese Academy of Sciences
Ying Lai: Chinese Academy of Sciences
Zhukuan Cheng: Yangzhou University
Minghong Gu: Yangzhou University
Jiming Jiang: University of Wisconsin
Jiayang Li: Chinese Academy of Sciences
Guofan Hong: Chinese Academy of Sciences
Yongbiao Xue: Chinese Academy of Sciences
Bin Han: Chinese Academy of Sciences

Nature, 2002, vol. 420, issue 6913, 316-320

Abstract: Abstract Rice is the principal food for over half of the population of the world. With its genome size of 430 megabase pairs (Mb), the cultivated rice species Oryza sativa is a model plant for genome research1. Here we report the sequence analysis of chromosome 4 of O. sativa, one of the first two rice chromosomes to be sequenced completely2. The finished sequence spans 34.6 Mb and represents 97.3% of the chromosome. In addition, we report the longest known sequence for a plant centromere, a completely sequenced contig of 1.16 Mb corresponding to the centromeric region of chromosome 4. We predict 4,658 protein coding genes and 70 transfer RNA genes. A total of 1,681 predicted genes match available unique rice expressed sequence tags. Transposable elements have a pronounced bias towards the euchromatic regions, indicating a close correlation of their distributions to genes along the chromosome. Comparative genome analysis between cultivated rice subspecies shows that there is an overall syntenic relationship between the chromosomes and divergence at the level of single-nucleotide polymorphisms and insertions and deletions. By contrast, there is little conservation in gene order between rice and Arabidopsis.

Date: 2002
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DOI: 10.1038/nature01183

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