GrameneOryza: A Comprehensive Resource for Oryza Genomes, Genetic Variation, and Functional Data

Authors: WEI, SHARON - Cold Spring Harbor Laboratory; CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory; OLSON, ANDREW - Cold Spring Harbor Laboratory; LU, ZHENYUAN - Cold Spring Harbor Laboratory; TELLO-RUIZ, MARCELA - Cold Spring Harbor Laboratory; KUMAR, VIVEK - Cold Spring Harbor Laboratory; KUMARI, SUNITA - Cold Spring Harbor Laboratory; ZHANG, LIFANG - Cold Spring Harbor Laboratory; OLSON, AUDRA - Cold Spring Harbor Laboratory; Ware, Doreen; KIM, CATHERINE - Cold Spring Harbor Laboratory; Gladman, Nicholas

Submitted to: Database: The Journal of Biological Databases and Curation
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/1/2025
Publication Date: 4/5/2025
Citation: Wei, S., Chougule, K., Olson, A., Lu, Z., Tello-Ruiz, M.K., Kumar, V., Kumari, S., Zhang, L., Olson, A., Ware, D., Kim, C., Gladman, N.P. 2025. GrameneOryza: A Comprehensive Resource for Oryza Genomes, Genetic Variation, and Functional Data. Database: The Journal of Biological Databases and Curation. 2025. https://doi.org/10.1093/database/baaf021 .
DOI: https://doi.org/10.1093/database/baaf021

Interpretive Summary: GrameneOryza (https://oryza.gramene.org) is an online resource for rice pan-genomes, adhering to FAIR (Findable, Accessible, Interoperable, and Reusable) principles of data management. It hosts a selection of high-quality Oryza genomes, genetic variation, gene function, and trait data. The paper reported on the latest release, version 8, which includes 28 Oryza genomes, covering wild rice and domesticated cultivars; 38K protein-coding gene family trees essential for identifying orthologs, paralogs, and developing pan-gene sets; 66 million single nucleotide variants (SNVs) anchored to the Os-Nipponbare-Reference-IRGSP-1.0 genome; 19 million RG3K SNVs for each of the 7 platinum-quality Asian rice genomes; 1,200 phenotypes with QTLs. The release 8 also updated SNVs with rsID from EVA release 5, a big step towards interoperability of genetic variations; and introduced Oryza CLIMtools portal which offers insights into environmental impacts on genome adaptation. The paper showcased the platform's integrated search interface with gene examples and illustrated the unique community curation function. The new search result page integrates the gene, genetic variation, population and germplasm together, making it a one stop mart for the user to shop for the potential variants and germplasms to advance their research and breeding project.

Technical Abstract: Rice is a vital staple crop, sustaining over half of the global population, and is a key model for genetic research. To support the growing need for comprehensive and accessible rice genomic data, GrameneOryza (https://oryza.gramene.org) was developed as an online resource adhering to FAIR (Findable, Accessible, Interoperable, and Reusable) principles of data management. It distinguishes itself through its comprehensive multi-species focus, encompassing a wide variety of Oryza genomes and related species, and its integration with FAIR principles to ensure data accessibility and usability. It offers a community curated selection of high-quality Oryza genomes, genetic variation, gene function, and trait data. The latest release, version 8, includes 28 Oryza genomes, covering wild rice and domesticated cultivars. These genomes, along with Leersia perrieri and seven additional outgroup species, form the basis for 38K protein-coding gene family trees, essential for identifying orthologs, paralogs, and developing pan-gene sets. GrameneOryza's genetic variation data features 66 million single nucleotide variants (SNVs) anchored to the Os-Nipponbare-Reference-IRGSP-1.0 genome, derived from various studies, including the Rice Genome 3K (RG3K) project. The RG3K sequence reads were also mapped to seven additional platinum-quality Asian rice genomes, resulting in 19 million SNVs for each genome, significantly expanding the coverage of genetic variation beyond the Nipponbare reference. Of the 66 million SNVs on IRGSP-1.0, 27 million acquired standardized reference SNP cluster identifiers (rsIDs) from the European Variation Archive release v5. Additionally, 1,200 distinct phenotypes provide a comprehensive overview of quantitative trait loci (QTL) features. The newly introduced Oryza CLIMtools portal offers insights into environmental impacts on genome adaptation. The platform's integrated search interface, along with a BLAST server and curation tools, facilitates user access to genomic, phylogenetic, gene function, and QTL data, supporting broad research applications.