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Rapid diversification of five Oryza AA genomes associated with rice adaptation
Zhang, Qun-Jie1,2; Zhu, Ting1,2; Xia, En-Hua1,2; Shi, Chao1,2; Liu, Yun-Long1; Zhang, Yun1; Liu, Yuan1,2; Jiang, Wen-Kai1; Zhao, You-Jie1; Mao, Shu-Yan1; Zhang, Li-Ping1; Huang, Hui1; Jiao, Jun-Ying1; Xu, Ping-Zhen1; Yao, Qiu-Yang1,2; Zeng, Fan-Chun3; Yang, Li-Li1; Gao, Ju1,3; Tao, Da-Yun4; Wang, Yue-Ju5; 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
Source PublicationPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
ISSN0027-8424
Volume111Issue:46Pages:E4954-E4962
AbstractComparative 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.
KeywordComparative Genomics Full-genome Sequencing Genomic Variation Positive Selection Oryza
Subject AreaMultidisciplinary Sciences
DOI10.1073/pnas.1418307111
Indexed BySCI
Language英语
WOS IDWOS:000345153300010
Citation statistics
Cited Times:92[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.kib.ac.cn/handle/151853/18510
Collection中国西南野生生物种质资源库
Corresponding AuthorBennetzen,JL (reprint author),Univ Georgia,Dept Genet,Athens,GA 30602 USA.; maize@uga.edu; lgao@mail.kib.ac.cn
Affiliation1.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
Recommended Citation
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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