title: Rapid diversification of five Oryza AA genomes associated with rice adaptation.
abstract: 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.
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of the Chinese Academy of Sciences, Beijing 100039, China;
authors.forename: Qun-Jie
authors.initials: QJ
authors.lastname: Zhang
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of the Chinese Academy of Sciences, Beijing 100039, China;
authors.forename: Ting
authors.initials: T
authors.lastname: Zhu
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of the Chinese Academy of Sciences, Beijing 100039, China;
authors.forename: En-Hua
authors.initials: EH
authors.lastname: Xia
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of the Chinese Academy of Sciences, Beijing 100039, China;
authors.forename: Chao
authors.initials: C
authors.lastname: Shi
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
authors.forename: Yun-Long
authors.initials: YL
authors.lastname: Liu
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
authors.forename: Yun
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of the Chinese Academy of Sciences, Beijing 100039, China;
authors.forename: Yuan
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
authors.forename: Wen-Kai
authors.initials: WK
authors.lastname: Jiang
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
authors.forename: You-Jie
authors.initials: YJ
authors.lastname: Zhao
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
authors.forename: Shu-Yan
authors.initials: SY
authors.lastname: Mao
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
authors.forename: Li-Ping
authors.initials: LP
authors.lastname: Zhang
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
authors.forename: Hui
authors.initials: H
authors.lastname: Huang
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
authors.forename: Jun-Ying
authors.initials: JY
authors.lastname: Jiao
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
authors.forename: Ping-Zhen
authors.initials: PZ
authors.lastname: Xu
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of the Chinese Academy of Sciences, Beijing 100039, China;
authors.forename: Qiu-Yang
authors.initials: QY
authors.lastname: Yao
authors.affiliation: Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China;
authors.forename: Fan-Chun
authors.initials: FC
authors.lastname: Zeng
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
authors.forename: Li-Li
authors.initials: LL
authors.lastname: Yang
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China;
authors.forename: Ju
authors.initials: J
authors.lastname: Gao
authors.affiliation: Institute of Cereal Crop Sciences, Yunnan Academy of Agricultural Sciences, Kunming 650205, China;
authors.forename: Da-Yun
authors.initials: DY
authors.lastname: Tao
authors.affiliation: Department of Natural Sciences, Northeastern State University, Broken Arrow, OK 74014; and.
authors.forename: Yue-Ju
authors.initials: YJ
authors.lastname: Wang
authors.affiliation: Department of Genetics, University of Georgia, Athens, GA 30602-7223 lgao@mail.kib.ac.cn maize@uga.edu.
authors.forename: Jeffrey L
authors.initials: JL
authors.lastname: Bennetzen
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; lgao@mail.kib.ac.cn maize@uga.edu.
authors.forename: Li-Zhi
authors.initials: LZ
authors.lastname: Gao
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000349:Africa; D000595:Amino Acid Sequence; D001208:Asia; D001315:Australia; D001483:Base Sequence; D004171:Diploidy; D019143:Evolution, Molecular; D018628:Gene Dosage; D059647:Gene-Environment Interaction; D017343:Genes, Plant; D014644:Genetic Variation; D018745:Genome, Plant; D035683:MicroRNAs / Q000235:genetics; D008969:Molecular Sequence Data; D005810:Multigene Family; D012275:Oryza / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D012641:Selection, Genetic; D016415:Sequence Alignment; D017385:Sequence Homology; D013020:South America; D013045:Species Specificity
chemical_list: D035683:MicroRNAs; D010940:Plant Proteins; D018749:RNA, Plant
keywords: Oryza; comparative genomics; full-genome sequencing; genomic variation; positive selection