P0344Overview of Gramene
In partnership with Ensembl Plants, we host genome browsers for 44 complete reference genomes, including updated assemblies for maize and hexaploid wheat, as well as and 2 diploid wheat progenitors, 12 Oryza and rice-related species, Brachypodium, 2 Arabidopsis species, 3 Brassica species, sorghum, barley, soybean, foxtail millet, Medicago, 2 Solanum species (tomato and potato), beet, banana, grape, cocoa, peach, red clover, poplar, Amborella trichopoda, and 7 lower plants. Each genome encompasses value-added annotations, gene-trees, and whole genome alignments. Evolutionary histories provided in phylogenetic gene trees classify orthologous and paralogous relationships as speciation and duplication events. Orthologous genes inform synteny maps that enable interspecies browsing across ancestral regions. Browsers from multiple species can be viewed simultaneously, with links showing homologous gene and whole-genome alignment mappings. SNP and structural diversity data, available for 12 species, are displayed in the context of gene annotation, showing functional consequences that can be assigned to individual accessions within the diversity panel. Functional data include phenotypic, transcriptome profiling, and methylome data. Visual displays can be downloaded as high-resolution, publication-ready, image files. A fully integrated BLAST tool enables visualization of alignments within the browser. For data mining, our BioMart tool enables complex queries of sequence, annotation, homology and variation data, and provides an additional gateway into the genome browsers.
Gramene also provides plant pathway databases and tools. The Plant Reactome (http://plantreactome.gramene.org/) hosts ~240 rice pathways (80% manually curated) and orthology-based projections of the rice reference pathways to 62 plant species. Both our pathway and genome browsers display EBI-ATLAS baseline gene expression. Gramene is supported by an NSF grant IOS-1127112, and partially from USDA-ARS (1907-21000-030-00D).