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

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

Submitted to: Arabidopsis Research International Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 7/15/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Gramene (https://www.gramene.org) is a powerful, open-source, integrated data resource designed for comparative functional genomics in crops and model plant species, making it an essential tool for agricultural researchers worldwide. Arabidopsis researchers will find Gramene particularly valuable for several reasons. The site hosts over 150 plant reference genomes, including three key Arabidopsis accessions: thaliana, lyrata, and halleri, integrated within the same platform for seamless comparative studies. Detailed comparative genomics tools in collaboration with EMBL-EBI Ensembl Plants, including integrated search interfaces and genome browsers, enable exploration of Arabidopsis genomes alongside other species, uncovering evolutionary relationships and functional annotations. Gramene integrates baseline gene expression data from the EBI Atlas for 30 plant species, including Arabidopsis, offering insights into gene expression across multiple tissues and conditions. Additionally, eFP Browsers from the BAR provide intuitive visualizations of gene expression in developmental and stress profiles for Arabidopsis, maize, soybean and sorghum, enhancing understanding of gene function and regulation. Gramene contains 26 eFP images based on published studies of Arabidopsis, categorized based on biological aspect and condition, chemical treatment, development or on the tissue type. The Plant Reactome feature offers curated rice pathways projected to 130 other species through orthology, facilitating the exploration of conserved biological pathways and their functional contexts in Arabidopsis. The site includes genetic variation data for 17 species, with tools to view and filter SNPs based on functional impact, allowing researchers to study genetic variation and its effects on gene function and phenotype. The CLIMtools portal, now in its third year, presents interactive web-based views of environmental data, RiboSNitch prediction, and genome-wide associations between local climate variables and genotypes, specifically useful for studying Arabidopsis associated wtih environmental variables. Furthermore, the integrated gene search interface now features curated papers describing gene function, leveraging gene family trees to pair well-annotated homologs with gene models from other species, supporting comprehensive functional annotation and hypothesis generation. Supported by USDA-ARS (USDA-ARS 8062-21000-041-00D), Gramene is continuously evolving to provide stewardship of plant genomic resources and tools, making it an indispensable platform for advancing Arabidopsis research and agricultural genomics.