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 journalArticle

74 Citations (Scopus)

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.

Original languageEnglish (US)
Article number15655
JournalScientific Reports
Volume5
DOIs
StatePublished - Oct 28 2015

Fingerprint

Chloroplasts
Genome
Ribosomal DNA
Chloroplast Genome
Oryza
Cytoplasm

ASJC Scopus subject areas

  • General

Cite this

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

In: Scientific Reports, Vol. 5, 15655, 28.10.2015.

Research output: Contribution to journalArticle

Kim, K, Lee, SC, Lee, J, Yu, Y, Yang, K, Choi, BS, Koh, HJ, Waminal, NE, Choi, HI, Kim, NH, Jang, W, Park, HS, Lee, J, Lee, HO, Joh, HJ, Lee, HJ, Park, JY, Perumal, S, Jayakodi, M, Lee, YS, Kim, B, Copetti, D, Kim, S, Kim, S, Lim, KB, Kim, YD, Lee, J, Cho, KS, Park, BS, Wing, RA & Yang, TJ 2015, 'Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species', Scientific Reports, vol. 5, 15655. https://doi.org/10.1038/srep15655
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. / Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species. In: Scientific Reports. 2015 ; Vol. 5.
@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}",
year = "2015",
month = "10",
day = "28",
doi = "10.1038/srep15655",
language = "English (US)",
volume = "5",
journal = "Scientific Reports",
issn = "2045-2322",
publisher = "Nature Publishing Group",

}

TY - JOUR

T1 - Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species

AU - Kim, Kyunghee

AU - Lee, Sang Choon

AU - Lee, Junki

AU - Yu, Yeisoo

AU - Yang, Kiwoung

AU - Choi, Beom Soon

AU - Koh, Hee Jong

AU - Waminal, Nomar Espinosa

AU - Choi, Hong Il

AU - Kim, Nam Hoon

AU - Jang, Woojong

AU - Park, Hyun Seung

AU - Lee, Jonghoon

AU - Lee, Hyun Oh

AU - Joh, Ho Jun

AU - Lee, Hyeon Ju

AU - Park, Jee Young

AU - Perumal, Sampath

AU - Jayakodi, Murukarthick

AU - Lee, Yun Sun

AU - Kim, Backki

AU - Copetti, Dario

AU - Kim, Soonok

AU - Kim, Sunggil

AU - Lim, Ki Byung

AU - Kim, Young Dong

AU - Lee, Jungho

AU - Cho, Kwang Su

AU - Park, Beom Seok

AU - Wing, Rod A

AU - Yang, Tae Jin

PY - 2015/10/28

Y1 - 2015/10/28

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84945971151&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84945971151&partnerID=8YFLogxK

U2 - 10.1038/srep15655

DO - 10.1038/srep15655

M3 - Article

C2 - 26506948

AN - SCOPUS:84945971151

VL - 5

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

M1 - 15655

ER -