Evolution and diversity of the wild rice Oryza officinalis complex, across continents genome types, and ploidy levels.
dc.contributor.author | Shenton, Matt | |
dc.contributor.author | Kobayashi, Masaaki | |
dc.contributor.author | Terashima, Shin | |
dc.contributor.author | Ohyanagi, Hajime | |
dc.contributor.author | Copetti, Dario | |
dc.contributor.author | Hernández-Hernández, Tania | |
dc.contributor.author | Zhang, Jianwei | |
dc.contributor.author | Ohmido, Nobuko | |
dc.contributor.author | Fujita, Masahiro | |
dc.contributor.author | Toyoda, Atsushi | |
dc.contributor.author | Ikawa, Hiroshi | |
dc.contributor.author | Fujiyama, Asao | |
dc.contributor.author | Furuumi, Hiroyasu | |
dc.contributor.author | Miyabayashi, Toshie | |
dc.contributor.author | Kubo, Takahiko | |
dc.contributor.author | Kudrna, David | |
dc.contributor.author | Wing, Rod | |
dc.contributor.author | Yano, Kentaro | |
dc.contributor.author | Nonomura, Ken-Ichi | |
dc.contributor.author | Sato, Yutaka | |
dc.contributor.author | Kurata, Nori | |
dc.date.accessioned | 2020-03-08T11:41:15Z | |
dc.date.available | 2020-03-08T11:41:15Z | |
dc.date.issued | 2020-03-03 | |
dc.date.submitted | 2019-07-28 | |
dc.identifier.citation | Shenton, 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.doi | 10.1093/gbe/evaa037 | |
dc.identifier.uri | http://hdl.handle.net/10754/661931 | |
dc.description.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 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.sponsorship | This 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.publisher | Oxford University Press (OUP) | |
dc.relation.url | https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evaa037/5775507 | |
dc.rights | 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. | |
dc.rights.uri | http://creativecommons.org/licenses/by-nc/4.0/ | |
dc.title | Evolution and diversity of the wild rice Oryza officinalis complex, across continents genome types, and ploidy levels. | |
dc.type | Article | |
dc.contributor.department | Biological and Environmental Sciences and Engineering (BESE) Division | |
dc.identifier.journal | Genome biology and evolution | |
dc.eprint.version | Publisher's Version/PDF | |
dc.contributor.institution | National Institute of Genetics, Japan. | |
dc.contributor.institution | School of Agriculture, Meiji University, Japan. | |
dc.contributor.institution | Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, USA. | |
dc.contributor.institution | Division of the Living Environment, Kobe University, Japan. | |
kaust.person | Ohyanagi, Hajime | |
dc.date.accepted | 2020-02-18 | |
dc.relation.issupplementedby | DOI:10.25739/awh3-dm39 | |
refterms.dateFOA | 2020-03-08T11:42:35Z | |
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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