Gramene 2025: expanded comparative genomics and pathway resources, integrated search, and pan-genome portals for crop research

Olson, Andrew, Kumari, Sunita, Wei, Xuehong, Chougule, Kapeel, Lu, Zhenyuan, Tello-Ruiz, Marcela Karey, Kumar, Vivek, Van Buren, Peter, Olson, Audra, Kim, Catherine, Braynen, Janeen, Zhang, Lifang, Dyer, Sarah, Alvarez-Jarreta, Jorge, Saraf, Shradha, Contreras-Moreira, Bruno, Naamati, Guy, Ernst, Christina, Papatheodorou, Irene, George, Nancy, Jaiswal, Pankaj, Naithani, Sushma, Gupta, Parul, Elser, Justin, D'Eustachio, Peter, Assmann, Sarah M, Ferrero-Serrano, Ángel, Pasha, Asher, Provart, Nicholas, Gladman, Nicholas, Ware, Doreen (December 2025) Gramene 2025: expanded comparative genomics and pathway resources, integrated search, and pan-genome portals for crop research. Nucleic Acids Research (NAR). ISSN 0305-1048

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Abstract

Gramene (gramene.org) is a comprehensive reference database for comparative plant genomics and pathway analysis, integrating functional annotations, evidence-based curated pathways and their projections, and multi-omics datasets. Since our last report, Gramene has added crop-specific pan-genome portals for maize, sorghum, rice, and grapevine. These pan-genome portals host population-scale datasets and multiple assembled genomes per species, all anchored by shared reference genomes. Importantly, these portals now adopt standardized rsIDs for genetic variants, advancing FAIR data principles and enabling cross-database interoperability. The main site is now Gramene Plants, emphasizing its broad genome coverage. Release 69 features 233 reference genomes, curated pathways for 139 species, expression data from 1026 studies across 27 species, and genetic variation data mapped to 27 genomes from 19 species. Key updates to the integrated search functionality include embedded expression viewers from the Bio-Analytic Resource for Plant Biology and EMBL-EBI Expression Atlas, a literature-curated catalog of gene functions, and a new Germplasm tab linking accessions with loss-of-function alleles to seed repositories. These advances reinforce Gramene as a comprehensive platform for exploring plant genomic diversity, gene function, and evolutionary conservation across the Green Tree of Life and within key agricultural species.

Item Type: Paper
Subjects: bioinformatics
bioinformatics > genomics and proteomics > databases
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > databases > databases > Gramene
bioinformatics > genomics and proteomics > databases > databases
CSHL Authors:
Communities: CSHL labs > Ware lab
CSHL Post Doctoral Fellows
SWORD Depositor: CSHL Elements
Depositing User: CSHL Elements
Date: 3 December 2025
Date Deposited: 04 Dec 2025 14:04
Last Modified: 04 Dec 2025 14:04
Related URLs:
URI: https://repository.cshl.edu/id/eprint/42024

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