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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 #433496
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: Advancing Plant Pan-Genome Resources and Community Standards

Author
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item WEI, XUEHONG - Cold Spring Harbor Laboratory
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item VAN BUREN, PETER - Cold Spring Harbor Laboratory
item OLSON, AUDRA - Cold Spring Harbor Laboratory
item KIM, SUYUN - Cold Spring Harbor Laboratory
item BRAYNEN, JANEEN - Cold Spring Harbor Laboratory
item Ware, Doreen
item ZHANG, LIFANG - Cold Spring Harbor Laboratory
item Gladman, Nicholas

Submitted to: CONFERENCE ON THE BIOLOGY OF GENOMES
Publication Type: Abstract Only
Publication Acceptance Date: 5/5/2026
Publication Date: 5/5/2026
Citation: Olson, A., Kumari, S., Wei, X., Chougule, K., Lu, Z., Van Buren, P., Olson, A., Kim, S., Braynen, J., Ware, D., Zhang, L., Gladman, N.P. 2026. Gramene: Advancing Plant Pan-Genome Resources and Community Standards . CONFERENCE ON THE BIOLOGY OF GENOMES. Conference on the Biology of Genomes.

Interpretive Summary:

Technical Abstract: Since 2001, Gramene has served as a major resource for comparative plant genomics, supporting research in genetics, breeding, systems biology, and evolution. With over 1,500 citations and a global user base spanning more than 100 countries, Gramene provides integrated access to genome annotations, genetic variation, pathways, regulatory networks, environment–variant associations, and gene expression data through coordinated platforms including Ensembl, Plant Reactome, CLIMtools, EMBL-EBI Expression Atlas, and BAR. Rebranded as Gramene Plants to reflect its expanded taxonomic scope, Release 69 includes 233 reference genomes, curated pathways for 139 species, expression data from 1,026 studies across 27 species, and variation data mapped to 27 genomes representing 19 species. Recent updates include integrated expression visualization tools, a literature-curated catalog of gene functions, and a Germplasm tab linking accessions with loss-of-function alleles to public seed repositories. A major recent focus has been the expansion of crop pan-genome resources, including GrameneMaize, GrameneOryza, GrameneGrapevine, and SorghumBase. These portals enable exploration of structural variation, gene presence/absence variation, gene expression and gene family evolution across diverse germplasm. Integration of standard reference SNP identifiers (rsIDs) further enhances reproducibility, interoperability, and alignment with FAIR data principles. In addition to data integration, Gramene actively supports the research community through workshops, webinars, and training initiatives in FAIR data practices, biocuration, and data management. Together, Gramene Plants and its crop-specific pan-genome portals provide a scalable, community-driven infrastructure for advancing plant genomics research.