Overview of Gramene's Ensembl Genome Browser

The Gramene database (http://www.gramene.org) is an integrated resource for comparative genomics and pathways in plants. In partnership with Ensembl Plants, we host genome browsers for 44 complete reference genomes, including cereals, crops, and model species. Each genome encompasses value-added annotations, gene trees, and whole-genome alignments. Evolutionary histories provided in phylogenetic 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 11 species, is displayed in the context of gene annotation, showing functional consequences assigned to individual accessions within a diversity panel. Functional data include phenotypic, transcriptome profiling, and methylome data. Visual displays can be downloaded as high-resolution, publication-ready, image files. Fully integrated BLAST enables visualization of alignments within the browser, an assembly converter tool for transforming genomic coordinates across assemblies, and for data mining, the BioMart tool enables complex queries of sequence, annotation, homology, and variation data, and provides an additional gateway into the genome browsers. Both our genome and pathway browsers display baseline gene expression from the Expression Atlas. Our integrated search database and modern user interface leverage these diverse annotations to allow scientists finding genes by selecting auto-suggested filters with results shown interactively in aggregate and gene-context views. Gramene is supported by NSF grant IOS-1127112, and partially from USDA-ARS 1907-21000-030-00D.