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

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

in 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

2015

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

2015

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

2015

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Journal Article

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

Lee, Jonghoon,

Joh, Ho Jun,

Yu, Yeisoo,

Lee, Jungho,

Cho, Kwang-Su,

Choi, Hong-Il,

Copetti, Dario,

Choi, Beom-Soon,

Waminal, Nomar Espinosa,

Lee, Hyun Oh,

Yang, Kiwoung,

Koh, Hee-Jong,

Kim, Nam-Hoon,

Park, Jee Young,

Jayakodi, Murukarthick,

Lee, Sang-Choon,

Yang, Tae-Jin,

Lee, Hyeon Ju,

Kim, Soonok,

Perumal, Sampath,

Kim, Backki,

Kim, Young-Dong,

Jang, Woojong,

Wing, Rod A.,

Park, Hyun-Seung,

Kim, Kyunghee,

Lee, Yun Sun,

Lim, Ki-Byung,

Lee, Junki,

Kim, Sunggil,

Park, Beom-Seok

2015

Overview

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 .

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Publisher

Nature Publishing Group UK,Nature Publishing Group

Subject

45/22

/ 45/23

/ 45/77

/ 631/114/1386

/ 631/449/2669

/ Australia

/ Chloroplasts - genetics