Wei, Sharon, Chougule, Kapeel, Olson, Andrew, Lu, Zhenyuan, Tello-Ruiz, Marcela K, Kumar, Vivek, Kumari, Sunita, Zhang, Lifang, Olson, Audra, Kim, Catherine, Gladman, Nick, Ware, Doreen (April 2025) GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data. Database : the journal of biological databases and curation, 2025. ISSN 1758-0463 (Public Dataset)
![[thumbnail of 10.1093.database.baaf021.pdf]](https://repository.cshl.edu/style/images/fileicons/application_pdf.png) |
PDF
10.1093.database.baaf021.pdf - Published Version Available under License Creative Commons Public Domain Dedication. Download (27MB) |
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 multispecies 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 38 K 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 3 K (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, 1200 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. Database URL: https://oryza.gramene.org.
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics bioinformatics > genomics and proteomics > databases bioinformatics > genomics and proteomics organism description > plant > Oryza organism description > plant |
| CSHL Authors: | |
| Communities: | CSHL labs > Ware lab CSHL labs > Wigler lab |
| SWORD Depositor: | CSHL Elements |
| Depositing User: | CSHL Elements |
| Date: | 4 April 2025 |
| Date Deposited: | 14 Apr 2025 12:27 |
| Last Modified: | 14 Apr 2025 12:27 |
| PMCID: | PMC11986821 |
| Related URLs: | |
| Dataset ID: |
|
| URI: | https://repository.cshl.edu/id/eprint/41847 |
Actions (login required)
 |
Administrator's edit/view item |
