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

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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.
Funding Information
  • United States Department of Agriculture
  • USDA (8062-21000-051-000D)
  • USDA (0201-88888-003-000D)
  • USDA (0201-88888-002-000D)
  • National Science Foundation (2122358)
  • National Science Foundation (2122357)
  • National Science Foundation (2029854)
  • National Aeronautics and Space Administration (80NSSC22K0891)
  • National Aeronautics and Space Administration (80NSSC22K0855)
  • Defense Advanced Research Projects Agency (HR0011-23-9-0054)
  • National Institutes of Health (S10OD028632-01)
  • NHRGI (U24 HG012198)
  • Natural Sciences and Engineering Research Council of Canada
  • Wellcome Trust (WT222155/Z/20/Z)
  • Wellcome Trust (221401/Z/20/Z)
  • European Molecular Biology Laboratory
  • Oregon State University

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