Browsing and Comparing Genomes Using the Gramene Ensembl Browser

This workshop will demonstrate Gramene’s genome browser and, associated annotation and visualization resources--including variation, phylogenetic trees and comparative maps (www.gramene.org).  Release 40 hosts interlinked browsers for 28 complete reference plant genomes, each displaying community annotation, whole genome alignments, and additional analyses.  Annotated protein coding genes are subjected to InterPro domain prediction, Gene Ontology assignment, and cross-referencing to third party databases such as RefSeq.  SNP and structural diversity data, available for nine reference genomes, is visualized in the context of gene annotation and each variant site is classified with respect to its predicted consequence on transcript structure (e.g. Missense variant).  For most studies users can drill-down to individual genotypes of each strain accession within the study’s diversity panel.  Evolutionary histories of protein-coding genes are provided in phylogenetic gene trees using a method that infers orthologous and paralogous relationships.  Orthology information is in turn used to build synteny maps that are presented in a graphical user interface that promotes interspecies browsing across ancestrally derived regions.  In addition, genome browsers from multiple species can be simultaneously viewed in a stacked arrangement, highlighting matching regions from DNA-level whole-genome alignments.  Virtually all visualization displays can be downloaded as high-resolution, publication-ready, image files.