Evolution and Diversity of the Wild Rice Oryza officinalis Complex, across Continents, Genome Types, and Ploidy Levels
Author
Shenton, MattKobayashi, Masaaki
Terashima, Shin
Ohyanagi, Hajime
Copetti, Dario
Hernández-Hernández, Tania
Zhang, Jianwei

Ohmido, Nobuko
Fujita, Masahiro
Toyoda, Atsushi
Ikawa, Hiroshi
Fujiyama, Asao
Furuumi, Hiroyasu
Miyabayashi, Toshie
Kubo, Takahiko
Kudrna, David
Wing, Rod
Yano, Kentaro
Nonomura, Ken-Ichi
Sato, Yutaka
Kurata, Nori
Affiliation
Univ Arizona, Arizona Genom Inst, BIO5 InstUniv Arizona, Sch Plant Sci
Issue Date
2020-03-03
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OXFORD UNIV PRESSCitation
Shenton, M., Kobayashi, M., Terashima, S., Ohyanagi, H., Copetti, D., Hernández-Hernández, T., ... & Kurata, N. (2020). Evolution and Diversity of the Wild Rice Oryza officinalis Complex, across Continents, Genome Types, and Ploidy Levels. Genome biology and evolution, 12(4), 413-428.Journal
GENOME BIOLOGY AND EVOLUTIONRights
© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/).Collection Information
This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.Abstract
The Oryza officinalis complex is the largest species group in Oryza, with more than nine species from four continents, and is a tertiary gene pool that can be exploited in breeding programs for the improvement of cultivated rice. Most diploid and tetraploid members of this group have a C genome. Using a new reference C genome for the diploid species O. officinalis, and draft genomes for two other C genome diploid species Oryza eichingeri and Oryza rhizomatis, we examine the influence of transposable elements on genome structure and provide a detailed phylogeny and evolutionary history of the Oryza C genomes. The O. officinalis genome is 1.6 times larger than the A genome of cultivated Oryza sativa, mostly due to proliferation of Gypsy type long-terminal repeat transposable elements, but overall syntenic relationships are maintained with other Oryza genomes (A, B, and F). Draft genome assemblies of the two other C genome diploid species, Oryza eichingeri and Oryza rhizomatis, and short-read resequencing of a series of other C genome species and accessions reveal that after the divergence of the C genome progenitor, there was still a substantial degree of variation within the C genome species through proliferation and loss of both DNA and long-terminal repeat transposable elements. We provide a detailed phylogeny and evolutionary history of the Oryza C genomes and a genomic resource for the exploitation of the Oryza tertiary gene pool.Note
Open access journalISSN
1759-6653PubMed ID
32125373Version
Final published versionae974a485f413a2113503eed53cd6c53
10.1093/gbe/evaa037
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Except where otherwise noted, this item's license is described as © The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/).
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