Sequence and analysis of rice chromosome 4 (original) (raw)

• Letter
• Published: 21 November 2002
• Yujun Zhang1 na1,
• Pei Hao1 na1,
• Shengyue Wang2 na1,
• Gang Fu2,
• Yucheng Huang1,
• Ying Li1,
• Jingjie Zhu1,
• Yilei Liu1,
• Xin Hu1,
• Peixin Jia1,
• Yu Zhang1,
• Qiang Zhao1,
• Kai Ying1,
• Shuliang Yu1,
• Yesheng Tang1,
• Qijun Weng1,
• Lei Zhang1,
• Ying Lu1,
• Jie Mu1,
• Yiqi Lu1,
• Lei S. Zhang1,
• Zhen Yu1,
• Danlin Fan1,
• Xiaohui Liu1,
• Tingting Lu1,
• Can Li1,
• Yongrui Wu1,
• Tongguo Sun1,
• Haiyan Lei1,
• Tao Li1,
• Hao Hu1,
• Jianping Guan1,
• Mei Wu1,
• Runquan Zhang1,
• Bo Zhou1,
• Zehua Chen1,
• Ling Chen1,
• Zhaoqing Jin1,
• Rong Wang1,
• Haifeng Yin2,
• Zhen Cai2,
• Shuangxi Ren2,
• Gang Lv2,
• Wenyi Gu2,
• Genfeng Zhu2,
• Yuefeng Tu2,
• Jia Jia2,
• Yi Zhang2,
• Jie Chen2,
• Hui Kang2,
• Xiaoyun Chen2,
• Chunyan Shao2,
• Yun Sun2,
• Qiuping Hu2,
• Xianglin Zhang2,
• Wei Zhang2,
• Lijun Wang2,
• Chunwei Ding2,
• Haihui Sheng2,
• Jingli Gu2,
• Shuting Chen2,
• Lin Ni2,
• Fenghua Zhu2,
• Wei Chen3,
• Lefu Lan3,
• Ying Lai3,
• Zhukuan Cheng4,5 na1,
• Minghong Gu4,
• Jiming Jiang5 na1,
• Jiayang Li3,
• Guofan Hong1,
• Yongbiao Xue3 &
• …
• Bin Han1

Nature volume 420, pages 316–320 (2002)Cite this article

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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.

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Acknowledgements

We thank T. Sasaki and the RGP for rice genetic and EST markers and a PAC genomic library of rice Nipponbare; R. Wing and the CUGI for providing BAC libraries of the Nipponbare variety; Monsanto for the rice working-draft sequence data; G. Barry and J. Liu for help; R. Buell and Q. Yuan for help with the annotation and analysis of chromosome 4 sequences; X. Huang and Z. Ning for help with using the AAT and the ssaha programs, respectively; members of the National Centre for Gene Research for assistance; Z. Xu, Z. Chen, G. Wang, Q. Ma and Q. Zhang for support; and X. Lin, X. Deng, Y. Li, L. Zhou, N. Zheng, X. Liu and members of the IRGSP for discussion. This work was supported by grants from the Ministry of Science and Technology of the People's Republic of China, Chinese Academy of Sciences, and the Shanghai Municipal Commission of Science and Technology.

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Author notes

1. Qi Feng, Yujun Zhang, Pei Hao, Shengyue Wang, Zhukuan Cheng and Jiming Jiang: These authors contributed equally to this work

Authors and Affiliations

1. National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, 200233, China
   Qi Feng, Yujun Zhang, Pei Hao, 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, Guofan Hong & Bin Han
2. Chinese National Human Genome Center at Shanghai, 351 Guo Shoujing Road, Shanghai, 201203, China
   Shengyue Wang, Gang Fu, 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
3. Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, 100101, Andingmenwai, Beijing, China
   Wei Chen, Lefu Lan, Ying Lai, Jiayang Li & Yongbiao Xue
4. Yangzhou University, 27 Wenhua Road, Yangzhou, Jiangsu, 225009, China
   Zhukuan Cheng & Minghong Gu
5. Department of Horticulture, University of Wisconsin, Wisconsin, 53706, Madison, USA
   Zhukuan Cheng & Jiming Jiang

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1. Qi Feng
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2. Yujun Zhang
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63. Lin Ni
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Correspondence toBin Han.

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Feng, Q., Zhang, Y., Hao, P. et al. Sequence and analysis of rice chromosome 4.Nature 420, 316–320 (2002). https://doi.org/10.1038/nature01183

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• Received: 04 April 2002
• Accepted: 16 September 2002
• Issue Date: 21 November 2002
• DOI: https://doi.org/10.1038/nature01183

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