Browsing and Comparing Genomes Using the Gramene Ensembl Browser

This workshop will demonstrate Gramene’s genome, phylogenetic tree, and synteny browsers, as well as associated annotation and visualization resources.  Gramene hosts interlinked browsers for 14 complete and 8 partial 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.  Evolutionary histories of annotated 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.  SNP diversity data, available for several 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. non-synonymous coding).  Virtually all visualization displays can be downloaded as high-resolution, publication-ready, image files.  Release 34 of Gramene includes browsers for Oryza sativa ssp. japonica, O. sativa ssp. indica, O. glaberrima, Sorghum bicolor, Brachypodium distachyon, Zea mays, Arabidopsis thaliana, A. lyrata, Glycine max, Vitis vinifera, Populus trichocarpus, Selaginella moellendorfii, Physcomitrella patens, and Chlamydomonas reinhardtii.  Browsers are also available for partial genomes of non-cultivated species in the Oryza genus.