Evolution and Diversity of the Wild Rice Oryza officinalis Complex, across Continents, Genome Types, and Ploidy Levels
| Autor: | Shin Terashima, Hiroyasu Furuumi, Rod A. Wing, Matt Shenton, Nobuko Ohmido, Dario Copetti, David Kudrna, Hiroshi Ikawa, Tania Hernández-Hernández, Jianwei Zhang, Masaaki Kobayashi, Ken Ichi Nonomura, Atsushi Toyoda, Toshie Miyabayashi, Nori Kurata, Kentaro Yano, Asao Fujiyama, Takahiko Kubo, Hajime Ohyanagi, Masahiro Fujita, Yutaka Sato |
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| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
Transposable element transposon Oryza 010603 evolutionary biology 01 natural sciences Genome Evolution Molecular C genome 03 medical and health sciences Polyploid Rice Wild rice Transposon Reference genome Genetics Humans wild rice Ecology Evolution Behavior and Systematics Phylogeny reference genome 030304 developmental biology Synteny 0303 health sciences Oryza sativa Ploidies biology rice Terminal Repeat Sequences polyploid food and beverages Genetic Variation biology.organism_classification Evolutionary biology DNA Transposable Elements Gene pool Genome Plant Research Article |
| Zdroj: | Genome Biology and Evolution Genome Biology and Evolution, 12 (4) |
| ISSN: | 1759-6653 |
| Popis: | 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. Genome Biology and Evolution, 12 (4) ISSN:1759-6653 |
| Databáze: | OpenAIRE |
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