Exploring and Comparing Plant Genomes Using the Gramene/Ensembl Plants Browser

Learn the benefits of using Gramene and Ensembl Plants (www.gramene.org & www.plants.ensembl.org) to accelerate your research goals.  We host genome browsers for 39 complete reference genomes, each displaying value-added annotations, gene-trees, and whole genome alignments.  Evolutionary histories are provided in phylogenetic gene trees that 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 eleven species, are displayed in the context of gene annotation, along with the consequence of variation on transcript structure (e.g. Missense variant).  For each variant, drill-down to individual accession genotypes within the study’s diversity panel. New data include the maize methylome and RNA-seq for each of ten Oryza species.  New BLAST service displays alignment results directly onto genome browsers and karyotype views.  Privately upload your own experimental data, such as RNA-seq alignments, to view in the context of gene annotations.  All reference assemblies are synced with iPlant Genome Services giving cross-platform compatibility between your analyses and Gramene displays.  Download visual displays as high-resolution, publication-ready, image files, along with the underlying supporting data in conventional file formats.  Mine data using Gramene’s BioMart; perform complex queries of annotation, homology and variation data, then click to visualize results.  Gramene is funded by a grant from the NSF (IOS-1127112).