@article{c812a999b4df4ff7b10b2324c878887e,
title = "Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species",
abstract = "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.",
author = "Kyunghee Kim and Lee, {Sang Choon} and Junki Lee and Yeisoo Yu and Kiwoung Yang and Choi, {Beom Soon} and Koh, {Hee Jong} and Waminal, {Nomar Espinosa} and Choi, {Hong Il} and Kim, {Nam Hoon} and Woojong Jang and Park, {Hyun Seung} and Jonghoon Lee and Lee, {Hyun Oh} and Joh, {Ho Jun} and Lee, {Hyeon Ju} and Park, {Jee Young} and Sampath Perumal and Murukarthick Jayakodi and Lee, {Yun Sun} and Backki Kim and Dario Copetti and Soonok Kim and Sunggil Kim and Lim, {Ki Byung} and Kim, {Young Dong} and Jungho Lee and Cho, {Kwang Su} and Park, {Beom Seok} and Wing, {Rod A.} and Yang, {Tae Jin}",
note = "Funding Information: We thank all members of the Laboratory of Functional Crop Genomics and Biotechnology, Seoul National University, Korea and Phyzen (http://www.phyzen.com/), for their technical assistance. This work was carried out with the support of “Cooperative Research Program for Agriculture Science & Technology Development (Project No. PJ01103001, PJ01100801)”, Rural Development Administration, Republic of Korea and partially supported by a grant entitled “The Genetic Evaluation of Important Biological Resources 2012, 2013” from the National Institute of Biological Resources under the Ministry of Environment, Republic of Korea. Preparation of the NGS data sets of wild Oryza species was supported by the US NSF Plant Genome Program{\textquoteright}s Oryza Genome Evolution project #1026200 to R.A.W. & Y.Y.",
year = "2015",
month = oct,
day = "28",
doi = "10.1038/srep15655",
language = "English (US)",
volume = "5",
journal = "Scientific reports",
issn = "2045-2322",
publisher = "Nature Publishing Group",
}