Sequence and analysis of rice chromosome 4.
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 research. Here we report the sequence analysis of chromosome 4 of O. sativa, one of the first two rice chromosomes to be sequenced completely. 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.
Feng
Qi
Q
National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China.
Zhang
Yujun
Y
Hao
Pei
P
Wang
Shengyue
S
Fu
Gang
G
Huang
Yucheng
Y
Li
Ying
Y
Zhu
Jingjie
J
Liu
Yilei
Y
Hu
Xin
X
Jia
Peixin
P
Zhang
Yu
Y
Zhao
Qiang
Q
Ying
Kai
K
Yu
Shuliang
S
Tang
Yesheng
Y
Weng
Qijun
Q
Zhang
Lei
L
Lu
Ying
Y
Mu
Jie
J
Lu
Yiqi
Y
Zhang
Lei S
LS
Yu
Zhen
Z
Fan
Danlin
D
Liu
Xiaohui
X
Lu
Tingting
T
Li
Can
C
Wu
Yongrui
Y
Sun
Tongguo
T
Lei
Haiyan
H
Li
Tao
T
Hu
Hao
H
Guan
Jianping
J
Wu
Mei
M
Zhang
Runquan
R
Zhou
Bo
B
Chen
Zehua
Z
Chen
Ling
L
Jin
Zhaoqing
Z
Wang
Rong
R
Yin
Haifeng
H
Cai
Zhen
Z
Ren
Shuangxi
S
Lv
Gang
G
Gu
Wenyi
W
Zhu
Genfeng
G
Tu
Yuefeng
Y
Jia
Jia
J
Zhang
Yi
Y
Chen
Jie
J
Kang
Hui
H
Chen
Xiaoyun
X
Shao
Chunyan
C
Sun
Yun
Y
Hu
Qiuping
Q
Zhang
Xianglin
X
Zhang
Wei
W
Wang
Lijun
L
Ding
Chunwei
C
Sheng
Haihui
H
Gu
Jingli
J
Chen
Shuting
S
Ni
Lin
L
Zhu
Fenghua
F
Chen
Wei
W
Lan
Lefu
L
Lai
Ying
Y
Cheng
Zhukuan
Z
Gu
Minghong
M
Jiang
Jiming
J
Li
Jiayang
J
Hong
Guofan
G
Xue
Yongbiao
Y
Han
Bin
B
D017360:Arabidopsis / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics*; D019295:Computational Biology; D020451:Contig Mapping; D004251:DNA Transposable Elements / Q000235:genetics; D020224:Expressed Sequence Tags; D023061:Gene Order / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D005819:Genetic Markers / Q000235:genetics; D018745:Genome, Plant; D005810:Multigene Family / Q000235:genetics; D009154:Mutation / Q000235:genetics; D012275:Oryza / Q000145:classification / Q000235:genetics*; D020161:Physical Chromosome Mapping; D010940:Plant Proteins / Q000145:classification / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D012680:Sensitivity and Specificity; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D026801:Synteny / Q000235:genetics
D004251:DNA Transposable Elements; D005819:Genetic Markers; D010940:Plant Proteins