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 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.
Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.|Phyzen Genome Institute, 501-1, Gwanak Century Tower, Kwanak-gu, Seoul, 151-836, Republic of Korea.
Kyunghee
K
Kim
Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
Sang-Choon
SC
Lee
Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
Junki
J
Lee
Phyzen Genome Institute, 501-1, Gwanak Century Tower, Kwanak-gu, Seoul, 151-836, Republic of Korea.|Arizona Genomics Institute, School of Plant Sciences, The University of Arizona, Tucson, Arizona, 85721, USA.
Yeisoo
Y
Yu
Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.|Department of Horticulture, Sunchon National University, Suncheon, 540-950, Republic of Korea.
Kiwoung
K
Yang
Phyzen Genome Institute, 501-1, Gwanak Century Tower, Kwanak-gu, Seoul, 151-836, Republic of Korea.
Beom-Soon
BS
Choi
Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
Hee-Jong
HJ
Koh
Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
Nomar Espinosa
NE
Waminal
Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
Hong-Il
HI
Choi
Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
Nam-Hoon
NH
Kim
Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
Woojong
W
Jang
Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
Hyun-Seung
HS
Park
Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
Jonghoon
J
Lee
Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.|Phyzen Genome Institute, 501-1, Gwanak Century Tower, Kwanak-gu, Seoul, 151-836, Republic of Korea.
Hyun Oh
HO
Lee
Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
Ho Jun
HJ
Joh
Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
Hyeon Ju
HJ
Lee
Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
Jee Young
JY
Park
Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
Sampath
S
Perumal
Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
Murukarthick
M
Jayakodi
Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
Yun Sun
YS
Lee
Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
Backki
B
Kim
Arizona Genomics Institute, School of Plant Sciences, The University of Arizona, Tucson, Arizona, 85721, USA.
Dario
D
Copetti
Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 404-170, Republic of Korea.
Soonok
S
Kim
Department of Plant Biotechnology, Biotechnology Research Institute, Chonnam National University, Gwangju, 500-757, Republic of Korea.
Sunggil
S
Kim
Department of Horticultural Science, Kyungpook National University, Daegu, 702-701, Republic of Korea.
Ki-Byung
KB
Lim
Department of Life Science, Hallym University, Chuncheon, Kangwon-do, 200-702, Republic of Korea.
Young-Dong
YD
Kim
Green Plant Institute, #2-202 Biovalley, 89 Seoho-ro, Kwonseon-gu, Suwon, Republic of Korea.
Jungho
J
Lee
Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang-gun, Kangwon-do, 232-955, Republic of Korea.
Kwang-Su
KS
Cho
Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju, 560-500, Republic of Korea.
Beom-Seok
BS
Park
Arizona Genomics Institute, School of Plant Sciences, The University of Arizona, Tucson, Arizona, 85721, USA.
Rod A
RA
Wing
Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
Tae-Jin
TJ
Yang
D001315:Australia; D002736:Chloroplasts / Q000235:genetics*; D003593:Cytoplasm / Q000235:genetics; D019143:Evolution, Molecular; D014644:Genetic Variation / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D012275:Oryza / Q000235:genetics*; D010802:Phylogeny; D012270:Ribosomes / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods