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

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cg.contributor.affiliationNational Institute of Genetics, Japan
cg.contributor.affiliationMeiji University
cg.contributor.affiliationKing Abdullah University of Science and Technology
cg.contributor.affiliationUniversity of Arizona
cg.contributor.affiliationInternational Rice Research Institute
cg.contributor.affiliationKobe University
cg.identifier.doihttps://doi.org/10.1093/gbe/evaa037
cg.issn1759-6653
cg.journalGenome Biology and Evolution
dc.contributor.authorShenton, Matt
dc.contributor.authorKobayashi, Masaaki
dc.contributor.authorTerashima, Shin
dc.contributor.authorOhyanagi, Hajime
dc.contributor.authorCopetti, Dario
dc.contributor.authorHernández-Hernández, Tania
dc.contributor.authorZhang, Jianwei
dc.contributor.authorOhmido, Nobuko
dc.contributor.authorFujita, Masahiro
dc.contributor.authorToyoda, Atsushi
dc.contributor.authorIkawa, Hiroshi
dc.contributor.authorFujiyama, Asao
dc.contributor.authorFuruumi, Hiroyasu
dc.contributor.authorMiyabayashi, Toshie
dc.contributor.authorKubo, Takahiko
dc.contributor.authorKudrna, David
dc.contributor.authorWing, Rod
dc.contributor.authorYano, Kentaro
dc.contributor.authorNonomura, Ken-ichi
dc.contributor.authorSato, Yutaka
dc.contributor.authorKurata, Nori
dc.date.accessioned2024-12-19T12:54:00Zen
dc.date.available2024-12-19T12:54:00Zen
dc.identifier.urihttps://hdl.handle.net/10568/164535
dc.titleEvolution and diversity of the wild rice Oryza officinalis Complex, across continents, genome types, and ploidy levelsen
dcterms.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.en
dcterms.accessRightsOpen Access
dcterms.available2020-03-03
dcterms.bibliographicCitationKurata, Nori. 2020. Evolution and diversity of the wild rice Oryza officinalis Complex, across continents, genome types, and ploidy levels. Genome Bioloy and Evolution, Volume 12, no. 4; pages 413-428.en
dcterms.issued2020-03-03
dcterms.languageen
dcterms.licenseCC-BY-NC-4.0
dcterms.publisherOxford University Press
dcterms.subjectecologyen
dcterms.subjectevolutionen
dcterms.subjectbehavior and systematics geneticsen
dcterms.typeJournal Article

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