ArticlePlant & cell physiology2016
OryzaGenome: Genome Diversity Database of Wild Oryza Species.
Article in Plant & cell physiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Genomic Footprints of Historical Introgression Between Ancient Lineages of Wild Oryza AA-Genome Species With Widely Separated Contemporary Distributions.Genome biology and evolution · 2026Article
- Seed abortion caused by the combination of two duplicate genes in the progeny from the cross betweenBreeding science · 2024Article
- Detection of locally adapted genomic regions in wild rice (Oryza rufipogon) using environmental association analysis.G3 (Bethesda, Md.) · 2023Article
- New Hybrid Spikelet Sterility Gene Found in Interspecific Cross betweenPlants (Basel, Switzerland) · 2022Article
- Genomics and transcriptomics to protect rice (Frontiers in plant science · 2022Review
- Collection, preservation and distribution ofBreeding science · 2021Article
- OryzaGenome2.1: Database of Diverse Genotypes in Wild Oryza Species.Rice (New York, N.Y.) · 2021Article
- Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management.Frontiers in plant science · 2021Review
- Light-induced chloroplast movements in Oryza species.Journal of plant research · 2020Article
- Rice Stress-Resistant SNP Database.Rice (New York, N.Y.) · 2019Article
- The indica nitrate reductase gene OsNR2 allele enhances rice yield potential and nitrogen use efficiency.Nature communications · 2019Article
- Infrastructures of systems biology that facilitate functional genomic study in rice.Rice (New York, N.Y.) · 2019Review
- Ideal Cereals With Lower Arsenic and Cadmium by Accurately Enhancing Vacuolar Sequestration Capacity.Frontiers in genetics · 2019Review
- RiceRelativesGD: a genomic database of rice relatives for rice research.Database : the journal of biological databases and curation · 2019Article
- Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- Selective sweep with significant positive selection serves as the driving force for the differentiation of japonica and indica rice cultivars.BMC genomics · 2017Article
- A Conserved Basal Transcription Factor Is Required for the Function of Diverse TAL Effectors in Multiple Plant Hosts.Frontiers in plant science · 2017Article
- Gigwa-Genotype investigator for genome-wide analyses.GigaScience · 2016Article
Corrections and comments
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of next-generation sequencing (NGS) technology, a flood of Oryza species reference genomes and genomic variation information has become available in recent years. This genomic information, combined with the comprehensive phenotypic information that we are accumulating in our Oryzabase, can serve as an excellent genotype-phenotype association resource for analyzing rice functional and structural evolution, and the associated diversity of the Oryza genus. Here we integrate our previous and future phenotypic/habitat information and newly determined genotype information into a united repository, named OryzaGenome, providing the variant information with hyperlinks to Oryzabase. The current version of OryzaGenome includes genotype information of 446 O. rufipogon accessions derived by imputation and of 17 accessions derived by imputation-free deep sequencing. Two variant viewers are implemented: SNP Viewer as a conventional genome browser interface and Variant Table as a text-based browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tab-delimited file download is also available. Following these SNP (single nucleotide polymorphism) data, reference pseudomolecules/scaffolds/contigs and genome-wide variation information for almost all of the closely and distantly related wild Oryza species from the NIG Wild Rice Collection will be available in future releases. All of the resources can be accessed through http://viewer.shigen.info/oryzagenome/.
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