Evolution and diversity of the wild rice Oryza officinalis complex, across continents genome types, and ploidy levels.

Matt Shenton, Masaaki Kobayashi, Shin Terashima, Hajime Ohyanagi, Dario Copetti, Tania Hernández-Hernández, Jianwei Zhang, Nobuko Ohmido, Masahiro Fujita, Atsushi Toyoda, Hiroshi Ikawa, Asao Fujiyama, Hiroyasu Furuumi, Toshie Miyabayashi, Takahiko Kubo, David Kudrna, Rod Wing, Kentaro Yano, Ken-Ichi Nonomura, Yutaka SatoNori Kurata

Research output: Contribution to journalArticlepeer-review

21 Scopus citations

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 Oryza officinalis, and draft genomes for two other C genome diploid species O. eichingeri and O. 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 O. sativa, mostly due to proliferation of Gypsy type long-terminal repeat (LTR) 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, O. eichingeri and O. 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 LTR 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.
Original languageEnglish (US)
Pages (from-to)413-428
Number of pages16
JournalGenome biology and evolution
Volume12
Issue number4
DOIs
StatePublished - Mar 4 2020

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: This work was supported by the NBRP Genome Information Upgrading Program (NBRP MEXT, Japan) for NK; the National Bioresource Project (NBRP AMED, Japan) for YS; and the Systems Functional Genetics Project of the Transdisciplinary Research Integration Center, ROIS, Japan for NK.

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  • Oryza officinalis complex gene and repeat annotations

    Shenton, M. (Creator), Kobayashi, M. (Creator), Terashima, S. (Creator), Ohyanagi, H. (Creator), Copetti, D. (Creator), Hernández-Hernández, T. (Creator), Zhang, J. (Creator), Ohmido, N. (Creator), Fujita, M. (Creator), Toyoda, A. (Creator), Ikawa, H. (Creator), Fujiyama, A. (Creator), Furuumi, H. (Creator), Miyabayashi, T. (Creator), Kubo, T. (Creator), Kudrna, D. (Creator), wing, R. (Creator), Yano, K. (Creator), Nonomura, K. (Creator), Sato, Y. (Creator), Kurata, N. (Creator), Shenton, M. (Creator), Kobayashi, M. (Creator), Terashima, S. (Creator), Copetti, D. (Creator), Hernández-Hernández, T. (Creator), Zhang, J. (Creator), Ohmido, N. (Creator), Fujita, M. (Creator), Toyoda, A. (Creator), Ikawa, H. (Creator), Fujiyama, A. (Creator), Furuumi, H. (Creator), Miyabayashi, T. (Creator), Kubo, T. (Creator), Kudrna, D. (Creator), wing, R. (Creator), Yano, K. (Creator), Nonomura, K. (Creator), Sato, Y. (Creator), Kurata, N. (Creator), Shenton, M. (Creator), Kobayashi, M. (Creator), Terashima, S. (Creator), Copetti, D. (Creator), Hernández-Hernández, T. (Creator), Zhang, J. (Creator), Ohmido, N. (Creator), Fujita, M. (Creator), Toyoda, A. (Creator), Ikawa, H. (Creator), Fujiyama, A. (Creator), Furuumi, H. (Creator), Miyabayashi, T. (Creator), Kubo, T. (Creator), Kudrna, D. (Creator), wing, R. (Creator), Yano, K. (Creator), Nonomura, K. (Creator), Sato, Y. (Creator) & Kurata, N. (Creator), CyVerse Data Commons, 2019

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