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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 #414843
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: A comparative resource on plant reference genomes, pan-genomes and pathways

Author
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item Gladman, Nicholas
item KUMAR, VIVEK - Cold Spring Harbor Laboratory
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item TELLO-RUIZ, MARCELA - Cold Spring Harbor Laboratory
item WEI, SHARON - Cold Spring Harbor Laboratory
item ELSER, JUSTIN - Cold Spring Harbor Laboratory
item Ware, Doreen
item GUPTA, PARUL - Oregon State University
item NAITHANI, SUSHMA - Oregon State University
item JAISWAL, PANKAJ - Oregon State University
item GEORGE, NANCY - Embl-Ebi
item NAAMATI, GUY - Embl-Ebi
item PAPATHEODOROU, IRENE - Embl-Ebi
item DYER, SARA - Embl-Ebi
item PASHA, ASHER - University Of Toronto
item PROVART, NICHOLAS - University Of Toronto

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 5/7/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Gramene (https://www.gramene.org) was founded in 2002 as the first plant comparative genomic database. Since then it has grown into a curated, open-source, integrated data resource for crops and model plant species that supports agricultural researchers worldwide. It currently hosts 150 plant reference genomes and four crop-focused pan-genome websites (sorghumbase.org, maize-pangenome.gramene.org, oryza.gramene.org, and vitis.gramene.org) with over 100 additional species-specific genomes. Genomic databases for the reference genomes are built in collaboration with EnsemblPlants. Each crop-focused pan-genome site includes an integrated search interface, a genome browser, FTP site, BLAST interface, and APIs for programmatic access. Plant Reactome provides curated rice pathways and projects them via orthology to 130 other species. Baseline gene expression data from EBI Atlas for 30 plant species are integrated into the site, providing insights on multiple tissues and conditions for a single gene, across a set of paralogs, or for all genes in a pathway. The site recently integrated eFP Browsers from the Bio-Analytical Resource for Plant Biology (BAR), offering additional visualizations of gene expression in developmental and stress profiles. The resource also hosts genetic variation data for 17 species. SNPs are easily viewed and filtered based on their predicted functional effect (missense, stop-gained, etc.) and impact (SIFT scores). The CLIMtools portal brings interactive web-based views of environmental data, RiboSNitch prediction, and associations between local climate variables and genotypes in Arabidopsis and rice. Finally, the integrated gene search includes curated papers describing gene function and leverages gene family trees to pair well annotated homologs with gene models from other species. Gramene is funded by USDA ARS 8062-21000-041-00D. Ensembl Plants is primarily funded by Wellcome Trust Grant 222155/Z/20/Z, BBSRC/NSF grant BB/T015608/1 and the European Molecular Biology Laboratory (EMBL). EBI Atlas is funded by the EMBL member states and Wellcome Trust Grant 221401/Z/20/Z.