_Vitis vinifera _PanGenome
This user guide refers to the contents of the first public release (August 2021) of the Grape PanGenome. Currently, the PanGenome hosts 18 genomes including 20 Vitis vinifera genomes, 2 versions of the Vitis vinifera ssp. vinifera PN40024 reference* (Jaillon et al, 2007; Vitulo et al, 2014; Canaguier et al, 2017; Rustenholz et al, manuscript in preparation), and 7 outgroups (Arabidopsis thaliana, _Oryza sativa _Japonica, Sorghum bicolor, Vitis vinifera ssp. vinifera PN40024, Selaginella moellendorffii, Chlamydomonas reinhardtii, and Drosophila melanogaster).
At present, most data types are only available for the _PN40024 _reference version 3, so this guide will focus on the phytochrome B gene model (PHYB), using its v3 gene identifier: VIT_05s0077g00940.
Let’s begin!
Go to http://vitis.gramene.org/
Locate the search box at the top left corner of the page. Type a search term (gene, species, pathway, ontology term, protein domain, etc.). For the exercises below, we will focus on searching for the grape PHYB gene or VIT_05s0077g00940.
PanGenome Search Interface
Querying a_ _Gene
Let’s start by typing “PHYB” in the search box and observe the auto-completion suggestions that pop-up as you type, as well as the various data categories in which the potential results are organized.