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

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 me...

Full description

Saved in:

Bibliographic Details
Published in:	Scientific reports Vol. 5; no. 1; p. 15655
Main Authors:	Kim, Kyunghee, Lee, Sang-Choon, Lee, Junki, Yu, Yeisoo, Yang, Kiwoung, Choi, Beom-Soon, Koh, Hee-Jong, Waminal, Nomar Espinosa, Choi, Hong-Il, Kim, Nam-Hoon, Jang, Woojong, Park, Hyun-Seung, Lee, Jonghoon, Lee, Hyun Oh, Joh, Ho Jun, Lee, Hyeon Ju, Park, Jee Young, Perumal, Sampath, Jayakodi, Murukarthick, Lee, Yun Sun, Kim, Backki, Copetti, Dario, Kim, Soonok, Kim, Sunggil, Lim, Ki-Byung, Kim, Young-Dong, Lee, Jungho, Cho, Kwang-Su, Park, Beom-Seok, Wing, Rod A., Yang, Tae-Jin
Format:	Journal Article
Language:	English
Published:	London Nature Publishing Group UK 28-10-2015 Nature Publishing Group
Subjects:	45/22 45/23 45/77 631/114/1386 631/449/2669 Australia Chloroplasts - genetics Cytoplasm - genetics Evolution, Molecular Genetic Variation - genetics Genome, Plant - genetics Humanities and Social Sciences multidisciplinary Oryza - genetics Phylogeny Ribosomes - genetics Science Sequence Analysis, DNA - methods Australia
Online Access:	Get full text
Tags:	Add Tag No Tags, Be the first to tag this record!

Description
Summary:	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 .
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Present address: Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea. These authors contributed equally to this work.
ISSN:	2045-2322 2045-2322
DOI:	10.1038/srep15655