Letters to Nature
Nature 420, 316-320 (21 November 2002) | doi:10.1038/nature01183; Received 4 April 2002; Accepted 16 September 2002
Sequence and analysis of rice chromosome 4
Qi Feng1,2, Yujun Zhang1,2, Pei Hao1,2, Shengyue Wang2,3, Gang Fu3, 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 Yin3, Zhen Cai3, Shuangxi Ren3, Gang Lv3, Wenyi Gu3, Genfeng Zhu3, Yuefeng Tu3, Jia Jia3, Yi Zhang3, Jie Chen3, Hui Kang3, Xiaoyun Chen3, Chunyan Shao3, Yun Sun3, Qiuping Hu3, Xianglin Zhang3, Wei Zhang3, Lijun Wang3, Chunwei Ding3, Haihui Sheng3, Jingli Gu3, Shuting Chen3, Lin Ni3, Fenghua Zhu3, Wei Chen4, Lefu Lan4, Ying Lai4, Zhukuan Cheng5,6, Minghong Gu5, Jiming Jiang6, Jiayang Li4, Guofan Hong1, Yongbiao Xue4 & Bin Han1
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China
- Chinese National Human Genome Center at Shanghai, 351 Guo Shoujing Road, Shanghai 201203, China
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, Andingmenwai, Beijing 100101, China
- Yangzhou University, 27 Wenhua Road, Yangzhou, Jiangsu 225009, China
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA
- These authors contributed equally to this work
Correspondence to: Bin Han1 Correspondence and requests for materials should be addressed to B.H. (e-mail: Email: bhan@ncgr.ac.cn).
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.
