The Genomes of Oryza sativa: a history of duplications.
We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000-40,000. Only 2%-3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.
Yu
Jun
J
Beijing Institute of Genomics of the Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics Institute, China. junyu@genomics.org.cn <junyu@genomics.org.cn>
Wang
Jun
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Lin
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Songgang
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Hu
Songnian
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Zeng
Changqing
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Jianguo
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Yong
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Ruiqiang
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Xu
Zuyuan
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Shengting
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Xianran
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Zheng
Hongkun
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Cong
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Yin
Jianning
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Geng
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Guangyuan
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Shi
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Lv
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Qingfa
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Dawei
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Yunze
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Xiangang
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Zhixi
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Tong
Zongzhong
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Shuangli
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Jia
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Lishun
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Lei
Tingting
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Chen
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C
Chen
Huan
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Xu
Zhao
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Li
Haihong
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Huang
Haiyan
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Zhang
Feng
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Xu
Huayong
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Li
Na
N
Zhao
Caifeng
C
Li
Shuting
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Dong
Lijun
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Huang
Yanqing
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Li
Long
L
Xi
Yan
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Qi
Qiuhui
Q
Li
Wenjie
W
Zhang
Bo
B
Hu
Wei
W
Zhang
Yanling
Y
Tian
Xiangjun
X
Jiao
Yongzhi
Y
Liang
Xiaohu
X
Jin
Jiao
J
Gao
Lei
L
Zheng
Weimou
W
Hao
Bailin
B
Liu
Siqi
S
Wang
Wen
W
Yuan
Longping
L
Cao
Mengliang
M
McDermott
Jason
J
Samudrala
Ram
R
Wang
Jian
J
Wong
Gane Ka-Shu
GK
Yang
Huanming
H
D001483:Base Sequence; D002681:China; D002874:Chromosome Mapping; D020440:Gene Duplication; D017343:Genes, Plant; D018745:Genome, Plant; D012275:Oryza / Q000235:genetics*