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Computational Biology & Bioinformatics

(500-08) Gramene 2023: A comparative resource on plant reference genomes, pan genomes and plant reactome pathways

Posters
Location: Exhibit Hall
Body of Abstract: Gramene (http://www.gramene.org) was founded in 2002 as the first comparative database of plant genomes. It currently hosts 128 plant reference genomes and four crop-focused pan-genome websites (sorghumbase.org, maize-pangenome.gramene.org, oryza.gramene.org, and vitis.gramene.org). The Gramene knowledgebase is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species that supports agricultural researchers worldwide. The reference genome databases are a mirror of EMBL-EBI Ensembl Plants and were built in collaboration with Expression Atlas and UniProt. Each crop-focused pan-genome site includes a genome browser for each accession, FTP site, BLAST interface, and programmatic access via the Ensembl REST API and Gramene Gene Search API. Expression information is available for multiple tissues and conditions, and these link to EBI-Atlas for more detailed information on each experiment. Where genetic variation data is available, SNPs are easily viewed and filtered based on their predicted functional effect (missense, stop-gained, etc.) and impact (SIFT scores). Additionally, these data are downloadable as images and tables. Genes can be queried via text-based searches and sequence-based BLAST. The Plant Reactome pathway knowledgebase hosts curated rice pathways and gene-orthology based projections for 120 species. The CLIMtools portal brings interactive web-based views of environment x genome associations, RiboSNitch prediction, and correlations between the local environment and a pool of curated phenotypes in Arabidopsis. The Plant Reactome database is produced in collaboration with the NIH-funded human Reactome project. Gramene is funded by USDA ARS 8062-21000-041-00D.