User guide for the Gramene Vitis PanGenome site available

Is it sometimes hard to know where to start? If you are an old or new user of Gramene resources, we recommend you review our new quick user guide for exploring the Vitis PanGenome. The site is available at https://vitis.gramene.org/guides.

To support the user experience, the guide takes you on a tour of the site using the phytochrome B gene (gene symbol: PHYB), as the exemplar model, using its v3 gene identifier: VIT_05s0077g00940.

The guide demonstrates how to search for a gene in the site’s search interface and describes various views of the gene structure and associated data, such as gene family trees with color-coded protein domains, amino acid alignments across a tree, and gene neighborhood views. Other data cross-linked from collaborators are Plant Reactome pathways and EBI-Atlas gene expression. In addition, users are taken through the vitis pangenomes installation on the Ensembl browser, including gene and transcript pages, protein domains view, mRNA and protein alignments, comparative analysis data such as gene family trees, whole-genome alignments, and synteny maps, as well as relevant literature references. Genetic and phenotypic variation will be made available in the browser in future releases.