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New insights into Oryza genome evolution: high gene colinearity and differential retrotransposon amplification

Zhang, Shibo, Gu, Yong Qiang, Singh, Jaswinder, Coleman-Derr, Devin, Brar, Darshan S., Jiang, Ning, Lemaux, Peggy G.
Plant molecular biology 2007 v.64 no.5 pp. 589-600
DNA, Oryza brachyantha, RNA, bacterial artificial chromosomes, cold stress, evolution, gene expression, genes, genetic variation, genomics, retrotransposons, transposons, wild rice
An ∼247-kb genomic region from FF genome of wild rice Oryza brachyantha, possessing the smallest Oryza genome, was compared to the orthologous ∼450-kb region from AA genome, O. sativa L. ssp. japonica. 37 of 38 genes in the orthologous regions are shared between japonica and O. brachyantha. Analyses of nucleotide substitution in coding regions suggest the two genomes diverged ∼10 million years ago. Comparisons of transposable elements (TEs) reveal that the density of DNA TEs in O. brachyantha is comparable to O. sativa; however, the density of RNA TEs is dramatically lower. The genomic fraction of RNA TEs in japonica is two times greater than in O. brachyantha. Differences, particularly in RNA TEs, in this region and in BAC end sequences from five wild and two cultivated Oryza species explain major genome size differences between sativa and brachyantha. Gene expression analyses of three ObDREB1 genes in the sequenced region indicate orthologous genes retain similar expression patterns following cold stress. Our results demonstrate that size and number of RNA TEs play a major role in genomic differentiation and evolution in Oryza. Additionally, distantly related O. brachyantha shares colinearity with O. sativa, offering opportunities to use comparative genomics to explore the genetic diversity of wild species to improve cultivated rice.