The 30th International Conference on Arabidopsis Research (ICAR 2019)

686 / 2019-05-01 10:08:56

Functional Comparative Analyses with Gramene

Comparative Genomics, Pathways, genetic diversity, phylogenetics, ontologies

Plenary track > Omics& New Technology

Need to find orthologs for your favorite Arabidopsis genes? How about expression or functional mutants in a staple crop like sorghum? Or perhaps you want to compare entire pathways, and visualize the Arabidopsis interactome? Gramene (http://www.gramene.org) is an integrated resource for comparative functional analysis in plants. We provide access to 61 reference genomes including A. thaliana, A. lyrata and A. halleri, and pathways for 82 plants species. Gramene’s integrated search capabilities render interactive views for gene features, gene neighborhoods, phylogenetic trees, expression profiles, pathways, and cross-references. Its phylogenetic tree collection amounts to nearly 93,000 gene families. A. thaliana is the dicot model for 60 pairwise whole-genome alignments; additional pairs with A. lyrata or A. halleri include Japonica rice, cacao or grapevine. Our synteny collection includes maps for A. thaliana with A. lyrata, Brassica rapa, Japonica rice, cacao or grape; and for A. lyrata and grapevine. We host 12.9 million Arabidopsis SNPs from the 1001 Arabidopsis Genomes Project. The Plant Reactome hosts 298 reference pathways curated in rice and projected to Arabidopsis and other species by orthology. Visualizations of EBI Expression Atlas data from almost 800 experiments are integrated in the search results view, genome and pathway browsers. Gramene is supported by an NSF grant IOS-1127112, and partially from USDA-ARS (1907-21000-030-00D).