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Science 5 April 2002:
Vol. 296. no. 5565, pp. 79 - 92
DOI: 10.1126/science.1068037
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Research Articles

A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica)

Jun Yu,1234* Songnian Hu,1* Jun Wang,125* Gane Ka-Shu Wong,124* Songgang Li,15 Bin Liu,1 Yajun Deng,16 Li Dai,1 Yan Zhou,27 Xiuqing Zhang,13 Mengliang Cao,8 Jing Liu,2 Jiandong Sun,1 Jiabin Tang,13 Yanjiong Chen,16 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,19 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 Tao Li,1 Xuegang Wang,1 Hong Lu,1 Tingting Wu,1 Miao Zhu,1 Peixiang Ni,1 Hua Han,1 Wei Dong,13 Xiaoyu Ren,1 Xiaoli Feng,13 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,15 Xianwu Zheng,3 Jianhai Dong,2 Wanyong Zeng,3 Lin Tao,2 Jia Ye,2 Jun Tan,2 Xide Ren,1 Xuewei Chen,3 Jun He,2 Daofeng Liu,3 Wei Tian,26 Chaoguang Tian,1 Hongai Xia,1 Qiyu Bao,1 Gang Li,1 Hui Gao,1 Ting Cao,1 Juan Wang,1 Wenming Zhao,1 Ping Li,3 Wei Chen,1 Xudong Wang,3 Yong Zhang,15 Jianfei Hu,15 Jing Wang,15 Song Liu,1 Jian Yang,1 Guangyu Zhang,1 Yuqing Xiong,1 Zhijie Li,1 Long Mao,3 Chengshu Zhou,8 Zhen Zhu,3 Runsheng Chen,19 Bailin Hao,210 Weimou Zheng,110 Shouyi Chen,3 Wei Guo,11 Guojie Li,12 Siqi Liu,12 Ming Tao,12 Jian Wang,12 Lihuang Zhu,3dagger Longping Yuan,8dagger Huanming Yang123dagger

We have produced a draft sequence of the rice genome for the most widely cultivated subspecies in China, Oryza sativa L. ssp. indica, by whole-genome shotgun sequencing. The genome was 466 megabases in size, with an estimated 46,022 to 55,615 genes. Functional coverage in the assembled sequences was 92.0%. About 42.2% of the genome was in exact 20-nucleotide oligomer repeats, and most of the transposons were in the intergenic regions between genes. Although 80.6% of predicted Arabidopsis thaliana genes had a homolog in rice, only 49.4% of predicted rice genes had a homolog in A. thaliana. The large proportion of rice genes with no recognizable homologs is due to a gradient in the GC content of rice coding sequences.

1 Beijing Genomics Institute/Center of Genomics and Bioinformatics, Chinese Academy of Sciences, Beijing 101300, China.
2 Hangzhou Genomics Institute-Institute of Bioinformatics of Zhejiang University-Key Laboratory of Bioinformatics of Zhejiang Province, Hangzhou 310007, China.
3 Institute of Genetics, Chinese Academy of Sciences, Beijing 100101, China.
4 University of Washington Genome Center, Department of Medicine, Seattle, WA 98195, USA.
5 College of Life Sciences, Peking University, Beijing 100871, China.
6 Medical College, Xi'an Jiaotong University, Xi'an 710061, China.
7 Fudan University, Shanghai 200433, China.
8 National Hybrid Rice R&D Center, Changsha 410125, China.
9 Laboratory of Bioinformatics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
10 Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100080, China.
11 Digital China Ltd., Beijing 100080, China.
12 Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China.
*   These authors contributed equally to this work.

dagger    To whom correspondence should be addressed. E-mail: hyang{at}genomics.org.cn.

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