Journal Article

Rapid diversification of five Oryza AA genomes associated with rice adaptation

Jun-Ying Jiao, Qun-Jie Zhang, Fan-Chun Zeng, Yuan Liu, Ju Gao, Qiu-Yang Yao, Ping-Zhen Xu, Chao Shi, Li-Ping Zhang, Da-Yun Tao, Shu-Yan Mao, Li-Li Yang, Yue-Ju Wang, Ting Zhu, Yun-Long Liu, You-Jie Zhao, Li-Zhi Gao, En-Hua Xia, Wen-Kai Jiang, Hui Huang, Jeffrey L. Bennetzen, Yun Zhang

2014

Overview

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. Significance Asian rice ( Oryza sativa ) is among the world’s most important crops. The genus Oryza has become a model for the study of plant genome structure, function, and evolution. We have undertaken de novo, full-genome sequence analysis of five diploid AA-genome species that are closely related to O. sativa . These species are native to quite different environments, representing four continents, thus exhibiting very different adaptations. Our studies identify specific genetic changes, in both gene copy number and the degree of diversifying natural selection, that indicate specific genes responsible for these adaptations, particularly in genes related to defense against pathogens and reproductive diversification. This genome discovery and comparative analysis provide a powerful tool for future Oryza study and rice improvement.

• Publisher: National Academy of Sciences,National Acad Sciences
• Subject: Adaptation, Physiological - genetics / Africa / Amino Acid Sequence / Asia / Australia / Base Sequence / Biodiversity / Biological Sciences / Crop improvement / crops / Diploidy / Evolution / Evolution, Molecular / Gene Dosage / Gene-Environment Interaction / Genes / Genes, Plant / Genetic Variation / Genome, Plant / Genomes / Genomics / indigenous species / International comparisons / MicroRNAs - genetics / Molecular Sequence Data / Multigene Family / natural selection / Nonnative species / Oryza / Oryza - classification / Oryza - genetics / Oryza barthii / Oryza glaberrima / Oryza glumaepatula / Oryza meridionalis / Oryza sativa / pathogens / Phylogeny / Plant Proteins - genetics / PNAS Plus / Rice / RNA, Plant - genetics / Selection, Genetic / Sequence Alignment / sequence analysis / Sequence Homology / South America / Speciation / Species Specificity