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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #428855
Research Project: Championing Improvement of Sorghum and Other Agriculturally Important Species through Data Stewardship and Functional Dissection of Complex Traits

Location: Plant, Soil and Nutrition Research

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

Author
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item WEI, SHARON - Cold Spring Harbor Laboratory
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item TELLO-RUIZ, MARCELA - Cold Spring Harbor Laboratory
item KUMAR, VIVEK - Cold Spring Harbor Laboratory
item VAN BUREN, PETER - Cold Spring Harbor Laboratory
item OLSON, AUDRA - Cold Spring Harbor Laboratory
item KIM, CATHERINE - Cold Spring Harbor Laboratory
item BRAYNEN, JANEEN - Cold Spring Harbor Laboratory
item ZHANG, LIFANG - Cold Spring Harbor Laboratory
item DYER, SARAH - Embl-Ebi
item ALVAREZ-JARETTA, JORGE - Embl-Ebi
item SARAF, SHRANDA - Embl-Ebi
item CONTRERAS-MOREIRA, BRUNO - University Of Zaragoza
item NAAMATI, GUY - Embl-Ebi
item ERNST, CHRISTINA - Embl-Ebi
item PAPATHEODOROU, IRENE - Embl-Ebi
item GEORGE, NANCY - Syngenta - United Kingdom
item PANKAJ, JAISWAL - Oregon State University
item NAITHANI, SUSHMA - Oregon State University
item GUPTA, PARUL - Oregon State University
item ELSER, JUSTIN - Oregon State University
item D'EUSTACHIO, PETER - New York University
item ASSMANN, SARAH - Pennsylvania State University
item FERRERO-SERRANO, ANGEL - Pennsylvania State University
item PROVART, NICHOLAS - University Of Toronto
item PASHA, ASHER - University Of Toronto
item Gladman, Nicholas
item Ware, Doreen

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/14/2025
Publication Date: 12/3/2025
Citation: Olson, A., Kumari, S., Wei, S., Chougule, K., Lu, Z., Tello-Ruiz, M.K., Kumar, V., Van Buren, P., Olson, A., Kim, C., Braynen, J., Zhang, L., Dyer, S., Alvarez-Jaretta, J., Saraf, S., Contreras-Moreira, B., Naamati, G., Ernst, C., Papatheodorou, I., George, N., Pankaj, J., Naithani, S., Gupta, P., Elser, J., D'Eustachio, P., Assmann, S., Ferrero-Serrano, A., Provart, N., Pasha, A., Gladman, N.P., Ware, D. 2025. Gramene 2025: expanded comparative genomics resources, integrated search, and pan-genome portals for crop research. Nucleic Acids Research. 54(D1):D1720-D1732. https://doi.org/10.1093/nar/gkaf1260.
DOI: https://doi.org/10.1093/nar/gkaf1260

Interpretive Summary: Gramene (gramene.org) is a free online resource that helps scientists compare plant genomes and understand how genes work. The updated site, now called Gramene Plants, brings together information from over 230 plant genomes, hundreds of biological pathways, and large collections of gene expression and genetic variation data. It also includes new integrated tools for exploring how genes function, drawing on both published research and related genes that are not yet well studied. Crop-focused portals are now available for maize, sorghum, rice, and grapevine, each offering multiple genomes for side-by-side comparison. These sites highlight important genetic differences, such as loss-of-function mutations, and connect directly to seed banks where researchers can request plant material. Altogether, Gramene makes it easier for plant scientists to explore genetic diversity, trace the evolution of important traits, and apply this knowledge to agriculture.

Technical 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 1,026 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 (BAR) 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.