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 journalArticle

1 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 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.

Original languageEnglish (US)
Pages (from-to)413-428
Number of pages16
JournalGenome biology and evolution
Volume12
Issue number4
DOIs
StatePublished - Apr 1 2020

Keywords

  • C genome
  • polyploid
  • reference genome
  • rice
  • transposon
  • wild rice

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

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    Shenton, M., Kobayashi, M., Terashima, S., Ohyanagi, H., Copetti, D., Hernández-Hernández, T., Zhang, J., Ohmido, N., Fujita, M., Toyoda, A., Ikawa, H., Fujiyama, A., Furuumi, H., Miyabayashi, T., Kubo, T., Kudrna, D., Wing, R., Yano, K., Nonomura, K. I., ... 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. https://doi.org/10.1093/gbe/evaa037