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

Kyunghee Kim, Sang Choon Lee, Junki Lee, Yeisoo Yu, Kiwoung Yang, Beom Soon Choi, Hee Jong Koh, Nomar Espinosa Waminal, Hong Il Choi, Nam Hoon Kim, Woojong Jang, Hyun Seung Park, Jonghoon Lee, Hyun Oh Lee, Ho Jun Joh, Hyeon Ju Lee, Jee Young Park, Sampath Perumal, Murukarthick Jayakodi, Yun Sun LeeBackki Kim, Dario Copetti, Soonok Kim, Sunggil Kim, Ki Byung Lim, Young Dong Kim, Jungho Lee, Kwang Su Cho, Beom Seok Park, Rod A. Wing, Tae Jin Yang

Research output: Contribution to journalArticlepeer-review

153 Scopus citations


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.

Original languageEnglish (US)
Article number15655
JournalScientific reports
StatePublished - Oct 28 2015

ASJC Scopus subject areas

  • General


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