Evolution and diversity of the wild rice Oryza officinalis complex, across continents genome types, and ploidy levels.
Permanent link to this recordhttp://hdl.handle.net/10754/661931
MetadataShow full item record
AbstractThe 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.
CitationShenton, 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. doi:10.1093/gbe/evaa037
SponsorsThis 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.
PublisherOxford University Press (OUP)
JournalGenome biology and evolution
RelationsIs Supplemented By:
Except where otherwise noted, this item's license is described as 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/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.