A draft sequence of the rice genome (Oryza sativa L. ssp. indica).
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.
Yu
Jun
J
Beijing Genomics Institute/Center of Genomics and Bioinformatics, Chinese Academy of Sciences, Beijing 101300, China.
Hu
Songnian
S
Wang
Jun
J
Wong
Gane Ka-Shu
GK
Li
Songgang
S
Liu
Bin
B
Deng
Yajun
Y
Dai
Li
L
Zhou
Yan
Y
Zhang
Xiuqing
X
Cao
Mengliang
M
Liu
Jing
J
Sun
Jiandong
J
Tang
Jiabin
J
Chen
Yanjiong
Y
Huang
Xiaobing
X
Lin
Wei
W
Ye
Chen
C
Tong
Wei
W
Cong
Lijuan
L
Geng
Jianing
J
Han
Yujun
Y
Li
Lin
L
Li
Wei
W
Hu
Guangqiang
G
Huang
Xiangang
X
Li
Wenjie
W
Li
Jian
J
Liu
Zhanwei
Z
Li
Long
L
Liu
Jianping
J
Qi
Qiuhui
Q
Liu
Jinsong
J
Li
Li
L
Li
Tao
T
Wang
Xuegang
X
Lu
Hong
H
Wu
Tingting
T
Zhu
Miao
M
Ni
Peixiang
P
Han
Hua
H
Dong
Wei
W
Ren
Xiaoyu
X
Feng
Xiaoli
X
Cui
Peng
P
Li
Xianran
X
Wang
Hao
H
Xu
Xin
X
Zhai
Wenxue
W
Xu
Zhao
Z
Zhang
Jinsong
J
He
Sijie
S
Zhang
Jianguo
J
Xu
Jichen
J
Zhang
Kunlin
K
Zheng
Xianwu
X
Dong
Jianhai
J
Zeng
Wanyong
W
Tao
Lin
L
Ye
Jia
J
Tan
Jun
J
Ren
Xide
X
Chen
Xuewei
X
He
Jun
J
Liu
Daofeng
D
Tian
Wei
W
Tian
Chaoguang
C
Xia
Hongai
H
Bao
Qiyu
Q
Li
Gang
G
Gao
Hui
H
Cao
Ting
T
Wang
Juan
J
Zhao
Wenming
W
Li
Ping
P
Chen
Wei
W
Wang
Xudong
X
Zhang
Yong
Y
Hu
Jianfei
J
Wang
Jing
J
Liu
Song
S
Yang
Jian
J
Zhang
Guangyu
G
Xiong
Yuqing
Y
Li
Zhijie
Z
Mao
Long
L
Zhou
Chengshu
C
Zhu
Zhen
Z
Chen
Runsheng
R
Hao
Bailin
B
Zheng
Weimou
W
Chen
Shouyi
S
Guo
Wei
W
Li
Guojie
G
Liu
Siqi
S
Tao
Ming
M
Wang
Jian
J
Zhu
Lihuang
L
Yuan
Longping
L
Yang
Huanming
H
D017360:Arabidopsis / Q000235:genetics; D001482:Base Composition; D019295:Computational Biology; D020451:Contig Mapping; D004251:DNA Transposable Elements; D021901:DNA, Intergenic; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D030561:Databases, Nucleic Acid; D005091:Exons; D020440:Gene Duplication; D017343:Genes, Plant; D018745:Genome, Plant; D023281:Genomics; D007438:Introns; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics*; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics; D011110:Polymorphism, Genetic; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D013045:Species Specificity; D026801:Synteny
D004251:DNA Transposable Elements; D021901:DNA, Intergenic; D018744:DNA, Plant; D010940:Plant Proteins