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Published (Version of record)CC BY V4.0, Open Access
Published (Version of record)CC BY V4.0, Open
Journal article
Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza
Nature Genetics, Vol.50(2), pp.285-296
02/2018
PMID: 29358651
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Source: InCites
Abstract
The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young 'AA' subclade containing the two domesticated species. This study highlights the prevalence of functionally coupled disease resistance genes and identifies many new haplotypes of potential use for future crop protection. Finally, this study marks a milestone in modern rice research with the release of a complete long-read assembly of IR 8 'Miracle Rice', which relieved famine and drove the Green Revolution in Asia 50 years ago.
Details
- Title
- Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza
- Creators
- Joshua C Stein - Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USAYeisoo Yu - Phyzen Genomics Institute, Phyzen, Inc., Seoul, South KoreaDario Copetti - University of ArizonaDerrick J Zwickl - Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USALi Zhang - Department of Ecology and Evolution, University of Chicago, Chicago, IL, USAChengjun Zhang - Department of Ecology and Evolution, University of Chicago, Chicago, IL, USAKapeel Chougule - Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USADongying Gao - Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USAAiko Iwata - Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USAJose Luis Goicoechea - Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USASharon Wei - Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USAJun Wang - Department of Biological Sciences, Wayne State University, Detroit, MI, USAYi Liao - State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, ChinaMuhua Wang - Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, GermanyJulie Jacquemin - Crop Biodiversity and Breeding Informatics Group, Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, GermanyClaude Becker - Max Planck Institute for Developmental Biology, Tübingen, GermanyDave Kudrna - University of ArizonaJianwei Zhang - Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USACarlos E M Londono - Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USAXiang Song - Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USASeunghee Lee - University of ArizonaPaul Sanchez - Rice Experiment Station, Biggs, CA, USAAndrea Zuccolo - Sant'Anna School of Advanced StudiesJetty S S Ammiraju - DuPont-Pioneer, Johnston, IA, USAJayson Talag - University of ArizonaAnn Danowitz - Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USALuis F Rivera - BIOS-Parque Los Yarumos, Manizales, ColombiaAndrea R Gschwend - Department of Ecology and Evolution, University of Chicago, Chicago, IL, USAChristos Noutsos - Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USACheng-Chieh Wu - Institute of Botany, National Taiwan University, Taipei, TaiwanShu-Min Kao - Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, BelgiumJhih-Wun Zeng - Institute of Plant and Microbial Biology, Academia Sinica, Taipei, TaiwanFu-Jin Wei - Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Tsukuba, JapanQiang Zhao - National Center for Gene Research, Chinese Academy of Sciences, Shanghai, ChinaQi Feng - National Center for Gene Research, Chinese Academy of Sciences, Shanghai, ChinaMoaine El Baidouri - Laboratoire Génome et Développement des Plantes, UMR 5096 UPVD/CNRS, Université de Perpignan Via Domitia, Perpignan, FranceMarie-Christine Carpentier - Laboratoire Génome et Développement des Plantes, UMR 5096 UPVD/CNRS, Université de Perpignan Via Domitia, Perpignan, FranceEric Lasserre - Laboratoire Génome et Développement des Plantes, UMR 5096 UPVD/CNRS, Université de Perpignan Via Domitia, Perpignan, FranceRichard Cooke - Laboratoire Génome et Développement des Plantes, UMR 5096 UPVD/CNRS, Université de Perpignan Via Domitia, Perpignan, FranceDaniel da Rosa Farias - Plant Genomics and Breeding Center, Universidade Federal de Pelotas, Pelotas, BrazilLuciano Carlos da Maia - Plant Genomics and Breeding Center, Universidade Federal de Pelotas, Pelotas, BrazilRailson S Dos Santos - Plant Genomics and Breeding Center, Universidade Federal de Pelotas, Pelotas, BrazilKevin G Nyberg - Department of Biology, University of Maryland, College Park, MD, USAKenneth L McNally - International Rice Research Institute (Phillipines)Ramil Mauleon - International Rice Research Institute (Phillipines)Nickolai Alexandrov - International Rice Research Institute (Phillipines)Jeremy Schmutz - DOE Joint Bioenergy Institute, Lawrence Berkeley National LaboratoryDave Flowers - HudsonAlpha Institute for Biotechnology, Huntsville, AL, USAChuanzhu Fan - Department of Biological Sciences, Wayne State University, Detroit, MI, USADetlef Weigel - Max Planck Institute for Developmental BiologyKshirod K Jena - International Rice Research Institute, Los Baños, PhilippinesThomas Wicker - Institute of Plant Biology, University of Zurich, Zurich, SwitzerlandMingsheng Chen - Shanghai Jiao Tong UniversityBin Han - National Center for Gene Research, Chinese Academy of Sciences, Shanghai, ChinaRobert Henry - University of QueenslandYue-Ie C Hsing - Institute of Plant and Microbial Biology, Academia Sinica, Taipei, TaiwanNori Kurata - National Institute of Genetics, Mishima, JapanAntonio Costa de Oliveira - Plant Genomics and Breeding Center, Universidade Federal de Pelotas, Pelotas, BrazilOlivier Panaud - Laboratoire Génome et Développement des Plantes, UMR 5096 UPVD/CNRS, Université de Perpignan Via Domitia, Perpignan, FranceScott A Jackson - Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USACarlos A Machado - Department of Biology, University of Maryland, College Park, MD, USAMichael J Sanderson - Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USAManyuan Long - Department of Ecology and Evolution, University of Chicago, Chicago, IL, USADoreen Ware - Robert W. Holley Center for Agriculture and Health, US Department of Agriculture, Agricultural Research Service, Ithaca, NY, USARod A Wing - University of ArizonaLawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
- Publication Details
- Nature Genetics, Vol.50(2), pp.285-296
- Publisher
- Nature Publishing Group
- Grant note
- This material is based on work supported by the US National Science Foundation under grants 0321678, 0638541, 0822284 and 1026200 to S.A.J., C.A.M., M.J.S., M.L., D. Ware and R.A.W., the Bud Antle Endowed Chair of Excellence in Agriculture and Life Sciences, the Alexander von Humboldt Research Award and the AXA Chair in Genome Biology and Evolutionary Genomics to R.A.W., DFG SFB 1101 to C.B. and D. Weigel, a University of Perpignan BQR grant to M.-C.C., E.L. and O.P., a Senior Chair from Institut Universitaire de France to O.P. and a CNPq grant to A.C.d.O. D. Ware was also funded by US National Science Foundation grant 1127112 and USDA–ARS 1907-21000-030-00D.
- Identifiers
- 991012978826902368
- Copyright
- © 2018 Nature America Inc., part of Springer Nature. All rights reserved. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
- Academic Unit
- Faculty of Science and Engineering; Science
- Language
- English
- Resource Type
- Journal article