Rapid diversification of five Oryza AA genomes associated with rice adaptation

doi:10.1073/pnas.1418307111

	Rapid diversification of five Oryza AA genomes associated with rice adaptation
	Zhang, Qun-Jie 1,2; Zhu, Ting 1,2; Xia, En-Hua1,2 ; Shi, Chao 1,2; Liu, Yun-Long 1; Zhang, Yun 1; Liu, Yuan1,2 ; Jiang, Wen-Kai 1; Zhao, You-Jie 1; Mao, Shu-Yan 1; Zhang, Li-Ping 1; Huang, Hui 1; Jiao, Jun-Ying 1; Xu, Ping-Zhen 1; Yao, Qiu-Yang 1,2; Zeng, Fan-Chun 3; Yang, Li-Li 1; Gao, Ju 1,3; Tao, Da-Yun 4; Wang, Yue-Ju 5; Bennetzen, Jeffrey L.6; Gao, Li-Zhi1 ; Bennetzen,JL (reprint author),Univ Georgia,Dept Genet,Athens,GA 30602 USA.; maize@uga.edu ; lgao@mail.kib.ac.cn
	2014-11-18
发表期刊	PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
ISSN	0027-8424
卷号	111 期号:46 页码:E4954-E4962
摘要	Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia. Extensive variation in noncoding RNA gene numbers, function enrichment, and rates of sequence divergence might also help account for the different genetic adaptations of these rice species. Collectively, these resources provide new opportunities for evolutionary genomics, numerous insights into recent speciation, a valuable database of functional variation for crop improvement, and tools for efficient conservation of wild rice germplasm.
关键词	Comparative Genomics Full-genome Sequencing Genomic Variation Positive Selection Oryza
学科领域	Multidisciplinary Sciences
DOI	10.1073/pnas.1418307111
收录类别	SCI
语种	英语
WOS记录号	WOS:000345153300010
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/18510
专题	中国西南野生生物种质资源库
通讯作者	Bennetzen,JL (reprint author),Univ Georgia,Dept Genet,Athens,GA 30602 USA.; maize@uga.edu; lgao@mail.kib.ac.cn
作者单位	1.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species Southwest China, Plant Germplasm & Genom Ctr, Kunming 650201, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100039, Peoples R China 3.Kunming Univ Sci & Technol, Fac Life Sci & Technol, Kunming 650500, Peoples R China 4.Yunnan Acad Agr Sci, Inst Cereal Crop Sci, Kunming 650205, Peoples R China 5.Northeastern State Univ, Dept Nat Sci, Broken Arrow, OK 74014 USA 6.Univ Georgia, Dept Genet, Athens, GA 30602 USA
推荐引用方式 GB/T 7714	Zhang, Qun-Jie,Zhu, Ting,Xia, En-Hua,et al. Rapid diversification of five Oryza AA genomes associated with rice adaptation[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA,2014,111(46):E4954-E4962.
APA	Zhang, Qun-Jie.,Zhu, Ting.,Xia, En-Hua.,Shi, Chao.,Liu, Yun-Long.,...&lgao@mail.kib.ac.cn.(2014).Rapid diversification of five Oryza AA genomes associated with rice adaptation.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA,111(46),E4954-E4962.
MLA	Zhang, Qun-Jie,et al."Rapid diversification of five Oryza AA genomes associated with rice adaptation".PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 111.46(2014):E4954-E4962.

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