Gramene 2025: expanded comparative genomics and pathway resources, integrated search, and pan-genome portals for crop research
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.
Authors
- Sarah Dyer (ORCID: https://orcid.org/0000-0001-5690-9633)
- Nicholas P. Gladman (ORCID: https://orcid.org/0000-0002-9000-8377)
- Vivek Kumar (ORCID: https://orcid.org/0000-0003-1988-2536)
- Christina Ernst (ORCID: https://orcid.org/0000-0002-3569-2209)
- Catherine Kim (ORCID: https://orcid.org/0000-0002-3513-3992)
- Irene Papatheodorou (ORCID: https://orcid.org/0000-0001-7270-5470)
- Guy Naamati (ORCID: https://orcid.org/0000-0002-0523-4071)
- Sushma Naithani (ORCID: https://orcid.org/0000-0001-7819-4552)
- Sunita Kumari (ORCID: https://orcid.org/0000-0002-6605-6985)
- Xuehong Wei (ORCID: https://orcid.org/0000-0002-4585-3264)
- Justin Elser (ORCID: https://orcid.org/0000-0003-0921-1982)
- Sarah M. Assmann (ORCID: https://orcid.org/0000-0003-4541-1594)
- Pankaj Jaiswal (ORCID: https://orcid.org/0000-0002-1005-8383)
- Kapeel M. Chougule (ORCID: https://orcid.org/0000-0002-1967-4246)
- Parul Gupta (ORCID: https://orcid.org/0000-0002-0190-8753)
- Shradha Saraf (ORCID: https://orcid.org/0000-0002-6433-8356)
- Asher Pasha (ORCID: https://orcid.org/0000-0002-9315-0520)
- Ángel Ferrero‐Serrano (ORCID: https://orcid.org/0000-0002-7714-3013)
- Jorge Álvarez-Jarreta (ORCID: https://orcid.org/0000-0002-0946-0957)
- Peter D’Eustachio (ORCID: https://orcid.org/0000-0002-5494-626X)
- Marcela K Tello-Ruiz (ORCID: https://orcid.org/0000-0002-7499-5368)
- Doreen Ware (ORCID: https://orcid.org/0000-0002-8125-3821)
- Janeen Braynen (ORCID: https://orcid.org/0000-0002-0670-2148)
- Zhenyuan Lu (ORCID: https://orcid.org/0000-0003-1758-2636)
- Nancy George
- Nicholas J. Provart (ORCID: https://orcid.org/0000-0001-5551-7232)
- Andrew Olson
- Bruno Contreras‐Moreira (ORCID: https://orcid.org/0000-0002-5462-907X)
- Lifang Zhang (ORCID: https://orcid.org/0000-0002-4482-3223)
- Peter Van Buren (ORCID: https://orcid.org/0009-0004-8408-7912)
Institutions
- European Bioinformatics Institute (GB)
- Pennsylvania State University (US)
- Oregon State University (US)
- University of Toronto (CA)
- Cold Spring Harbor Laboratory (US)
- Norwich Research Park (GB)
- Syngenta (United Kingdom) (GB)
- Earlham Institute (GB)
- Bioinformatics Institute (RU)
- Robert W. Holley Center for Agriculture & Health (US)
- Estación Experimental de Aula Dei (ES)
- New York University (US)
- Syngenta (Switzerland) (CH)
Publication Details
- Journal
- Nucleic Acids Research
- Published
- 2025-12-03
- DOI
- https://doi.org/10.1093/nar/gkaf1260
- Citations
- 2
- Primary Topic
- Genetic Mapping and Diversity in Plants and Animals
- Type
- article
- Field-Weighted Citation Impact
- 3.63
Funders
- National Science Foundation
- National Aeronautics and Space Administration
- U.S. Department of Agriculture
- Oregon State University
- Wellcome Trust
- European Molecular Biology Laboratory
- Cold Spring Harbor Laboratory
- Nuclear Safety and Security Commission
- National Institutes of Health
- Defense Advanced Research Projects Agency
- Agricultural Research Service
- Advanced Research Projects Agency
- Natural Sciences and Engineering Research Council of Canada