The Genomes of Oryza sativa: A history of duplications

doi:10.1371/journal.pbio.0030038

CORC > 计算技术研究所 > 中国科学院计算技术研究所 > 中国科学院计算技术研究所期刊论文 > 英文

	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
刊名	PLOS BIOLOGY
	2005-02-01
卷号	3 期号:2 页码:266-281
ISSN号	1545-7885
DOI	10.1371/journal.pbio.0030038
英文摘要	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.
WOS研究方向	Biochemistry & Molecular Biology ; Life Sciences & Biomedicine - Other Topics
语种	英语
出版者	PUBLIC LIBRARY SCIENCE
WOS记录号	WOS:000227404100011
内容类型	期刊论文
源URL	[http://119.78.100.204/handle/2XEOYT63/10261]
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.Univ Washington, UW Genome Ctr, Dept Med, Seattle, WA 98195 USA 3.Univ Washington, Dept Microbiol, Computat Genom Grp, Seattle, WA 98195 USA 4.Natl Hybrid Rice R&D Ctr, Changsha, Peoples R China 5.Chinese Acad Sci, Kunming Inst Zool, Kunming, Peoples R China 6.Beijing Normal Univ, Coll MAth Sci, Dept Stat & Financial Math, Beijing, Peoples R China 7.Chinese Acad Sci, Bioinformat Lab, Comp Technol Inst, Beijing, Peoples R China 8.Beijing N Computat Ctr, Beijing, Peoples R China 9.Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China 10.Peking Univ, Coll Life Sci, Beijing 100871, Peoples R China
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.