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Yu, J; Wang, J; Lin, W; Li, SG; Li, H; Zhou, J; Ni, PX; Dong, W; Hu, SN; Zeng, CQ; Zhang, JG; Zhang, Y; Li, RQ; Xu, ZY; Li, ST; Li, XR; Zheng, HK; Cong, LJ; Lin, L; Yin, JN; Geng, JN; Li, GY; Shi, JP; Liu, J; Lv, H; Li, J; Deng, YJ; Ran, LH; Shi, XL; Wang, XY; Wu, QF; Li, CF; Ren, XY; Wang, JQ; Wang, XL; Li, DW; Liu, DY; Zhang, XW; Ji, ZD; Zhao, WM; Sun, YQ; Zhang, ZP; Bao, JY; Han, YJ; Dong, LL; Ji, J; Chen, P; Wu, SM; Liu, JS; Xiao, Y; Bu, DB; Tan, JL; Yang, L; Ye, C; Zhang, JF; Xu, JY; Zhou, Y; Yu, YP; Zhang, B; Zhuang, SL; Wei, HB; Liu, B; Lei, M; Yu, H; Li, YZ; Xu, H; Wei, SL; He, XM; Fang, LJ; Zhang, ZJ; Zhang, YZ; Huang, XG; Su, ZX; Tong, W; Li, JH; Tong, ZZ; Li, SL; Ye, J; Wang, LS; Fang, L; Lei, TT; Chen, C; Chen, H; Xu, Z; Li, HH; Huang, HY; Zhang, F; Xu, HY; Li, N; Zhao, CF; Dong, LJ; Huang, YQ; Li, L; Xi, Y; Qi, QH; Li, WJ; Hu, W; Zhang, YL; Tian, XJ; Jiao, YZ; Liang, XH; Jin, JA; Gao, L; Zheng, WM; Hao, BL; Liu, SQ; Wang, W; Yuan, LP; Cao, ML; McDermott, J; Samudrala, R; Wong, GKS; Yang, HM; Yu, J , Chinese Acad Sci, Beijing Genom Inst, Beijing Proteom Inst, Beijing Inst Genom, Beijing, Peoples R China.
The Genomes of Oryza sativa: A history of duplications
Source PublicationPLOS BIOLOGY
KeywordRice Genome Arabidopsis-thaliana Sequence-analysis Protein Networks Draft Sequence Plant Genomes Genes Evolution Dna Annotation
AbstractWe 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 superscaffolds 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.
2005
ISSN1544-9173
Volume3Issue:2Pages:266-281
Subject AreaPhysics
Indexed BySCI
Citation statistics
Document Type期刊论文
Identifierhttp://ir.itp.ac.cn/handle/311006/13892
Collection理论物理所科研产出_SCI论文
Corresponding AuthorYu, J , Chinese Acad Sci, Beijing Genom Inst, Beijing Proteom Inst, Beijing Inst Genom, Beijing, Peoples R China.
Recommended Citation
GB/T 7714
Yu, J,Wang, J,Lin, W,et al. The Genomes of Oryza sativa: A history of duplications[J]. PLOS BIOLOGY,2005,3(2):266-281.
APA Yu, J.,Wang, J.,Lin, W.,Li, SG.,Li, H.,...&Yu, J , Chinese Acad Sci, Beijing Genom Inst, Beijing Proteom Inst, Beijing Inst Genom, Beijing, Peoples R China..(2005).The Genomes of Oryza sativa: A history of duplications.PLOS BIOLOGY,3(2),266-281.
MLA Yu, J,et al."The Genomes of Oryza sativa: A history of duplications".PLOS BIOLOGY 3.2(2005):266-281.
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