The Genomes of Oryza sativa: A history of duplications

doi:10.1371/journal.pbio.0030038

	The Genomes of Oryza sativa: A history of duplications
	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 ; Wang, 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 ; Li, ST ; Dong, LJ ; Huang, YQ ; Li, L ; Xi, Y ; Qi, QH ; Li, WJ ; Zhang, B ; 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 ; Wang, J ; Wong, GKS ; Yang, HM
	2005-02-01
发表期刊	PLOS BIOLOGY
ISSN	1545-7885
卷号	3 期号:2 页码:266-281
摘要	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 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.
DOI	10.1371/journal.pbio.0030038
收录类别	SCI
语种	英语
WOS研究方向	Biochemistry & Molecular Biology ; Life Sciences & Biomedicine - Other Topics
WOS类目	Biochemistry & Molecular Biology ; Biology
WOS记录号	WOS:000227404100011
出版者	PUBLIC LIBRARY SCIENCE
引用统计	被引频次：1210[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/10262
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Yu, J
作者单位	1.Chinese Acad Sci, Beijing Genom Inst, Beijing Proteom Inst, Beijing Inst Genom, Beijing, Peoples R China 2.Zhejiang Univ, James D Watson Inst Genome Sci, Hangzhou Genom Inst, Key Lab Genom Bioinformat Zhehiang Prov, Hangzhou 310027, Peoples R China 3.Peking Univ, Coll Life Sci, Beijing 100871, Peoples R China 4.Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China 5.Beijing N Computat Ctr, Beijing, Peoples R China 6.Chinese Acad Sci, Bioinformat Lab, Comp Technol Inst, Beijing, Peoples R China 7.Beijing Normal Univ, Coll MAth Sci, Dept Stat & Financial Math, Beijing, Peoples R China 8.Chinese Acad Sci, Kunming Inst Zool, Kunming, Peoples R China 9.Natl Hybrid Rice R&D Ctr, Changsha, Peoples R China 10.Univ Washington, Dept Microbiol, Computat Genom Grp, Seattle, WA 98195 USA 11.Univ Washington, UW Genome Ctr, Dept Med, Seattle, WA 98195 USA
推荐引用方式 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.,...&Yang, HM.(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.