ArticleNature genetics2018
Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.
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Article in Nature genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 293 papers, 1 of them a synthesis that pooled it.
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293citing papers in PubMed, 1 pooled it
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Who cites it
293 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome.Journal of proteome research · 2024Pooled it
- Genome-wide prediction of cloned disease resistance homologues across the Oryza genus.The plant genome · 2026Article
- Divergent roles of ent-kaurene oxidase paralogs in rice momilactone biosynthesis.Journal of integrative plant biology · 2026Article
- A CDC20 allelic series reveals stage-specific control of metaphase-to-anaphase transitions during mitosis and meiosis in rice.Science China. Life sciences · 2026Article
- Natural variation inScience advances · 2026Article
- Genomic Footprints of Historical Introgression Between Ancient Lineages of Wild Oryza AA-Genome Species With Widely Separated Contemporary Distributions.Genome biology and evolution · 2026Article
- A Rare Allele of ST5 From Wild Rice Enhances Salt Tolerance in Rice.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Engineered diazotrophs with host-inducible nitrogen supply systems: Transforming rice farming through innovative nitrogen biofertilizers.Journal of integrative plant biology · 2026Review
- Alternatively spliced killer-protector system confers S19-mediated hybrid male sterility in rice.Nature communications · 2026Article
- Rapid GC content evolution in rice through GC-biased gene conversion and selection for translation efficiency.Nature communications · 2026Article
- Exploring wild rices for photosynthetic efficiency improvement in rice.Physiology and molecular biology of plants : an international journal of functional plant biology · 2026Article
- Telomere-to-telomere genome assembly of Oryza australiensis reveals transposon-driven centromere repositioning and shared EE-DD ancestry.Nature communications · 2026Article
- Harnessing salt tolerance and CScientific reports · 2026Article
- Centromeric retrotransposons shape chromosomal evolution beyond pericentromeric regions.Mobile DNA · 2026Article
- Microbiome eco-evolution of cultivated and wild rice species across the genus Oryza and its importance in supporting rice growth.Microbiome · 2026Article
- Pan-genome of wild and cultivated rice uncovers genetic diversity, lost and selected sequences during rice domestication.Rice (New York, N.Y.) · 2026Article
- Key Genomic Regions of Rice Cultivar GuiHeFeng and Its Derivatives Revealed by Genome-Wide Analysis.Plants (Basel, Switzerland) · 2026Article
- Transcriptomic basis underlying the evolution of female horn plasticity in scarab beetles.Frontiers in zoology · 2026Article
- Gametocidal genes: biological mechanisms owing to hybrid dysgenesis in crop breeding, challenges and innovation.Annals of botany · 2026Review
- Independent Origin of Phenol Non-responsive Phenotype Caused By Phr1 Variation During Domestication of Asian and African Rice.Rice (New York, N.Y.) · 2026Article
233 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
65 authors.
Joshua C SteinCold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Yeisoo YuArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
Dario CopettiArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
Derrick J ZwicklDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
Li ZhangDepartment of Ecology and Evolution, University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0000-0002-0698-0754
Chengjun ZhangDepartment of Ecology and Evolution, University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0000-0001-9759-4906
Kapeel ChouguleCold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Dongying GaoCenter for Applied Genetic Technologies, University of Georgia, Athens, GA, USA.
Aiko IwataCenter for Applied Genetic Technologies, University of Georgia, Athens, GA, USA.
Jose Luis GoicoecheaArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
Sharon WeiCold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Jun WangDepartment of Biological Sciences, Wayne State University, Detroit, MI, USA.
Yi LiaoState Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
Muhua WangArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
Julie JacqueminArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
Claude BeckerMax Planck Institute for Developmental Biology, Tübingen, Germany.ORCID http://orcid.org/0000-0003-3406-4670
Dave KudrnaArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
Jianwei ZhangArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
Carlos E M LondonoArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
Xiang SongArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
Seunghee LeeArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
Paul SanchezArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
Andrea ZuccoloArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.ORCID http://orcid.org/0000-0001-7574-0714
Jetty S S AmmirajuArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
Jayson TalagArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
Ann DanowitzArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
Luis F RiveraArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
Andrea R GschwendDepartment of Ecology and Evolution, University of Chicago, Chicago, IL, USA.
Christos NoutsosCold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Cheng-Chieh WuInstitute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
Shu-Min KaoInstitute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
Jhih-Wun ZengInstitute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
Fu-Jin WeiInstitute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
Qiang ZhaoNational Center for Gene Research, Chinese Academy of Sciences, Shanghai, China.
Qi FengNational Center for Gene Research, Chinese Academy of Sciences, Shanghai, China.ORCID http://orcid.org/0000-0001-5450-1343
Moaine El BaidouriLaboratoire Génome et Développement des Plantes, UMR 5096 UPVD/CNRS, Université de Perpignan Via Domitia, Perpignan, France.
Marie-Christine CarpentierLaboratoire Génome et Développement des Plantes, UMR 5096 UPVD/CNRS, Université de Perpignan Via Domitia, Perpignan, France.
Eric LasserreLaboratoire Génome et Développement des Plantes, UMR 5096 UPVD/CNRS, Université de Perpignan Via Domitia, Perpignan, France.ORCID http://orcid.org/0000-0002-1408-2612
Richard CookeLaboratoire Génome et Développement des Plantes, UMR 5096 UPVD/CNRS, Université de Perpignan Via Domitia, Perpignan, France.
Daniel da Rosa FariasPlant Genomics and Breeding Center, Universidade Federal de Pelotas, Pelotas, Brazil.
Luciano Carlos da MaiaPlant Genomics and Breeding Center, Universidade Federal de Pelotas, Pelotas, Brazil.
Railson S Dos SantosPlant Genomics and Breeding Center, Universidade Federal de Pelotas, Pelotas, Brazil.
Kevin G NybergDepartment of Biology, University of Maryland, College Park, MD, USA.
Kenneth L McNallyInternational Rice Research Institute, Los Baños, Philippines.
Ramil MauleonInternational Rice Research Institute, Los Baños, Philippines.
Nickolai AlexandrovInternational Rice Research Institute, Los Baños, Philippines.
Jeremy SchmutzHudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
Dave FlowersHudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
Chuanzhu FanDepartment of Biological Sciences, Wayne State University, Detroit, MI, USA.
Detlef WeigelMax Planck Institute for Developmental Biology, Tübingen, Germany.
Kshirod K JenaInternational Rice Research Institute, Los Baños, Philippines.
Thomas WickerInstitute of Plant Biology, University of Zurich, Zurich, Switzerland.
Mingsheng ChenState Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
Bin HanNational Center for Gene Research, Chinese Academy of Sciences, Shanghai, China.
Robert HenryQueensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia.ORCID http://orcid.org/0000-0002-4060-0292
Yue-Ie C HsingInstitute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
Nori KurataNational Institute of Genetics, Mishima, Japan.
Antonio Costa de OliveiraPlant Genomics and Breeding Center, Universidade Federal de Pelotas, Pelotas, Brazil.
Olivier PanaudLaboratoire Génome et Développement des Plantes, UMR 5096 UPVD/CNRS, Université de Perpignan Via Domitia, Perpignan, France.ORCID http://orcid.org/0000-0002-9292-503X
Scott A JacksonCenter for Applied Genetic Technologies, University of Georgia, Athens, GA, USA.ORCID http://orcid.org/0000-0002-3172-1607
Carlos A MachadoDepartment of Biology, University of Maryland, College Park, MD, USA.
Michael J SandersonDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
Manyuan LongDepartment of Ecology and Evolution, University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0000-0002-6755-197X
Doreen WareCold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.ORCID http://orcid.org/0000-0002-8125-3821
Rod A WingArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA. rwing@email.arizona.edu.ORCID http://orcid.org/0000-0001-6633-6226
Funding
No grant is acknowledged in the PubMed record.
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.
Indexed as
Evolution, MolecularGenetic VariationConserved SequenceCrops, AgriculturalDomesticationGenetic SpeciationGenome, PlantOryzaPhylogeny
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