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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 #412044
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 2024: A comparative resource on plant reference genomes, pan-genomes and pathways

Author
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item KUMAR, VIVEK - Cold Spring Harbor Laboratory
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item TELLO-RUIZ, MARCELA - Cold Spring Harbor Laboratory
item WEI, SHARON - Cold Spring Harbor Laboratory
item ELSER, JUSTIN - Oregon State University
item GUPTA, PAUL - Oregon State University
item Ware, Doreen
item NAITHANI, SUSHMA - Oregon State University
item JAISWAL, PANKAJ - Oregon State University
item GEORGE, NANCY - Embl-Ebi
item PAPATHEODOROU, IRENE - Embl-Ebi
item Gladman, Nicholas
item NAAMATI, GUY - Embl-Ebi
item DYER, SARAH - 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: 2/29/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Gramene, established in 2002 (https://www.gramene.org), is a pivotal open-source plant genome database facilitating agricultural research. Focused on functional genomics in both crops and model plants, it boasts 150 plant reference genomes on the main site and 100+ crop-specific genomes on subsites (e.g., https://maize-pangenome.gramene.org with 37 maize genomes). This extensive resource enables maize researchers to seamlessly transition from genes in other species to their maize counterparts, evaluating expression, identifying variants, visualizing genomic context, and exploring metabolic pathways. Collaborations and adherence to FAIR principles have fueled Gramene's growth. Release 68 (December 2023) presents ~157K gene family trees, including ~2K maize-specific gene families, shedding light on eukaryotic evolution. The release incorporates tools for amino acid alignments, gene neighborhood conservation, and whole-genome DNA alignments, enhancing gene structure annotation. Genetic variants for 17 species, encompassing 50 million maize HapMap2 and Panzea 2.7 GBS SNPs, are available with detailed views and filters. Plant Reactome features curated rice pathways extended to 130 species, encompassing 270 projected maize pathways (B73 v4 and v5). Integration of EBI Atlas provides gene expression data for 26 species, including maize, offering insights across tissues and conditions. Recent enhancements include eFP Browsers for advanced gene expression visualizations and the CLIMtools portal for interactive views of environmental data and genome-wide associations in Arabidopsis and rice. The platform supports gene queries through text-based searches and sequence-based BLAST. Gramene's funding, from diverse sources including USDA-ARS, Wellcome Trust, BBSRC/NSF, and EMBL member states, underscores its sustainability. The integrated gene search interface now includes curated papers, enriching gene function understanding by linking well-annotated homologs with gene models from other species.