User guide for the Gramene Maize 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 Maize PanGenome. The site is available at https://maize-pangenome.gramene.org/guides.

To support the user experience, the guide takes you on a tour of the site using the lipoxygenase 9 gene model, also known as lox9 and with gene identifier Zm00001eb005920 in v5, as the exemplar model.

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 maize pangenomes installation on the Ensembl browser, including comparative analysis data such as gene family trees, whole-genome alignments, and synteny maps, as well as regulation data like epigenomics and RNA-Seq gene expression from the MaizeCODE project. Genetic and phenotypic variation will be made available in the browser in future releases.