Evolution and Diversity of the Wild Rice Oryza officinalis Complex, across Continents, Genome Types, and Ploidy Levels. (3rd March 2020)

• Record Type: Journal Article
• Authors: Shenton, Matt; Kobayashi, 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
• Editors: Slotte, Tanja
• Is Part Of: Genome biology and evolution. Volume 12:Number 4(2020)
• Page Start: 413
• Page End: 428
• Publication Date: 2020-03-03
• Subjects: rice -- C genome -- wild rice -- transposon -- polyploid -- reference genome; Genomics -- Periodicals; Genes -- Periodicals; 572.8605
• DOI: 10.1093/gbe/evaa037
• Languages: English
• ISSNs: 1759-6653

Abstract

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.