Browsing and Comparing 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 currently host browsers for 38 complete reference genomes, each displaying value-added annotations, gene-trees, and whole genome alignments.  In the last year we added the basal angiosperm, Amborella trichopoda, the crops Brassica oleracea, Prunus persica, and Theobroma cacao, five rice-related species in the Oryza and Leersia genera, and the unicellular alga Ostreococcus lucimarinus.  These build upon a foundation that includes rice, maize, sorghum, diploid and hexaploid wheats, barley, Brachypodium, and banana.  As well, we host soybean, Arabidopsis, Brassicas, potato, tomato, grapevine, and several lower plants.  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.  In addition, genome 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 most studies users can drill-down to individual genotypes of each accession within the study’s diversity panel. Learn how visual displays can be downloaded as high-resolution, publication-ready, image files, along with the underlying supporting data in conventional cross-compatible formats.  Complementing these resources is our BioMart data-mining interface, which enables complex queries of annotation, homology and variation data, and serves as an additional gateway into the genome browsers.