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Cytoplasmic chloroplast (cp) genomes and nuclear ribosomal DNA (nR) are the primary sequences used to understand plant diversity and evolution. We introduce a high-throughput method to simultaneously obtain complete cp and nR sequences using Illumina platform whole-genome sequence. We applied the method to 30 rice specimens belonging to nine  Oryza  species. Concurrent phylogenomic analysis using cp and nR of several of specimens of the same  Oryza  AA genome species provides insight into the evolution and domestication of cultivated rice, clarifying three ambiguous but important issues in the evolution of wild  Oryza  species. First, cp-based trees clearly classify each lineage but can be biased by inter-subspecies cross-hybridization events during speciation. Second,  O. glumaepatula , a South American wild rice, includes two cytoplasm types, one of which is derived from a recent interspecies hybridization with  O. longistminata . Third, the Australian  O. rufipogan -type rice is a perennial form of  O. meridionalis .

Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species