Abstract
Speciation from Oryza rufipogon, the most closely related wild relatives, to cultivated species of rice Oryza sativa, is known multi-lineage. However, exact status of divergence and evolutionary process of O.rufipogon is not yet explored in detail. To have a concept about evolutionary origins and process in the most closely related wild species O.rufipogon, illumina GAIIx short read sequencing of three typical accessions of O.rufipogon (W0106, W1921 and W1943) and an accession from each two major subspecies of O.sativa (Japonica and Indica), have been conducted for reconstructing their genomes. The comparative analysis among genome structures of five accessions based on the reference IRGSP build5 genome showed Japonica and Indica subspecies of O.sativa were descended from at least two lineages of O.rufipogon. Opposite to our expectation, however, it revealed that perennial and annual ecotypes of O.rufipogon don't necessarily share the genetic backgrounds with Japonica and Indica subspecies of O.sativa, respectively. Detail structural variations and phylogenetic relationships among them will be discussed in relation to species diversification, and evolutionary history.