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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.accessioned2020-03-08T11:41:15Z
dc.date.available2020-03-08T11:41:15Z
dc.date.issued2020-03-03
dc.date.submitted2019-07-28
dc.identifier.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
dc.identifier.doi10.1093/gbe/evaa037
dc.identifier.urihttp://hdl.handle.net/10754/661931
dc.description.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.
dc.description.sponsorshipThis 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.
dc.publisherOxford University Press (OUP)
dc.relation.urlhttps://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evaa037/5775507
dc.rightsThis 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.
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/
dc.titleEvolution and diversity of the wild rice Oryza officinalis complex, across continents genome types, and ploidy levels.
dc.typeArticle
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.identifier.journalGenome biology and evolution
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionNational Institute of Genetics, Japan.
dc.contributor.institutionSchool of Agriculture, Meiji University, Japan.
dc.contributor.institutionArizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, USA.
dc.contributor.institutionDivision of the Living Environment, Kobe University, Japan.
kaust.personOhyanagi, Hajime
dc.date.accepted2020-02-18
dc.relation.issupplementedbyDOI:10.25739/awh3-dm39
refterms.dateFOA2020-03-08T11:42:35Z
display.relations<b>Is Supplemented By:</b><br/> <ul><li><i>[Dataset]</i> <br/> Shenton, M. (2019). <i>Oryza officinalis complex gene and repeat annotations</i> [Data set]. CyVerse Data Commons. https://doi.org/10.25739/AWH3-DM39. DOI: <a href="https://doi.org/10.25739/awh3-dm39" >10.25739/awh3-dm39</a> Handle: <a href="http://hdl.handle.net/10754/667917" >10754/667917</a></a></li></ul>


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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.
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.