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PMID: 11935017 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

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

Science (New York, N.Y.) ·Vol. 296 ·No. 5565 ·2002-04-05 ·Pages 79-92

Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H

Abstract

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.

MeSH Terms
Arabidopsis/genetics Base Composition Computational Biology Contig Mapping DNA Transposable Elements DNA, Intergenic DNA, Plant/chemistry,genetics Databases, Nucleic Acid Exons Gene Duplication Genes, Plant Genome, Plant Genomics Introns Molecular Sequence Data Oryza/genetics Plant Proteins/chemistry,genetics Polymorphism, Genetic Repetitive Sequences, Nucleic Acid Sequence Analysis, DNA Sequence Homology, Nucleic Acid Software Species Specificity Synteny
Chemicals
DNA Transposable Elements DNA, Intergenic DNA, Plant Plant Proteins
Authors & Affiliations
100 authors, click to expand affiliations / ORCID
Yu Jun
Beijing Genomics Institute/Center of Genomics and Bioinformatics, Chinese Academy of Sciences, Beijing 101300, China.
Hu Songnian
Wang Jun
Wong Gane Ka-Shu
Li Songgang
Liu Bin
Deng Yajun
Dai Li
Zhou Yan
Zhang Xiuqing
Cao Mengliang
Liu Jing
Sun Jiandong
Tang Jiabin
Chen Yanjiong
Huang Xiaobing
Lin Wei
Ye Chen
Tong Wei
Cong Lijuan
Geng Jianing
Han Yujun
Li Lin
Li Wei
Hu Guangqiang
Huang Xiangang
Li Wenjie
Li Jian
Liu Zhanwei
Li Long
Liu Jianping
Qi Qiuhui
Liu Jinsong
Li Li
Li Tao
Wang Xuegang
Lu Hong
Wu Tingting
Zhu Miao
Ni Peixiang
Han Hua
Dong Wei
Ren Xiaoyu
Feng Xiaoli
Cui Peng
Li Xianran
Wang Hao
Xu Xin
Zhai Wenxue
Xu Zhao
Zhang Jinsong
He Sijie
Zhang Jianguo
Xu Jichen
Zhang Kunlin
Zheng Xianwu
Dong Jianhai
Zeng Wanyong
Tao Lin
Ye Jia
Tan Jun
Ren Xide
Chen Xuewei
He Jun
Liu Daofeng
Tian Wei
Tian Chaoguang
Xia Hongai
Bao Qiyu
Li Gang
Gao Hui
Cao Ting
Wang Juan
Zhao Wenming
Li Ping
Chen Wei
Wang Xudong
Zhang Yong
Hu Jianfei
Wang Jing
Liu Song
Yang Jian
Zhang Guangyu
Xiong Yuqing
Li Zhijie
Mao Long
Zhou Chengshu
Zhu Zhen
Chen Runsheng
Hao Bailin
Zheng Weimou
Chen Shouyi
Guo Wei
Li Guojie
Liu Siqi
Tao Ming
Wang Jian
Zhu Lihuang
Yuan Longping
Yang Huanming
Article Info
Journal
Science (New York, N.Y.)
Abbr.
Science
ISSN
1095-9203
Published
2002-04-05
Pages
79-92
Language
English
Region
United States
NLM ID
0404511
Subset
IM
Grants
NIEHS NIH HHS · 1 RO1 ES09909 · United States
Corrections
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