Crop pan-genomics involves sequencing, comparing, and integrating multiple genomes from the same crop species. Exploiting the information encoded in these pan-genomes can facilitate the development of new cultivars that are more resilient to future challenges like increased drought and heat stress.

While sequencing quality is no longer a major concern, accurately assessing the completeness of genome assemblies and subsequent gene annotations remains challenging. Although there are ongoing efforts to visualise and browse pan-genomes, such as through graph-based representations, easy access to gene Presence Absence Variation (PAV) data or structural rearrangements is still lacking, limiting knowledge extraction.
 

E-PAN aims to streamline the efforts of various research groups within the ELIXIR Plant Community. The initiative focuses on developing standards, computational pipelines, and tutorials to evaluate the quality of pan-genomes and address identified challenges. Additionally, the project will assess and integrate diverse approaches for data visualisation and browsing, which will be utilised by partners sharing pan-genomics results.
 

This study involves the collaboration of four ELIXIR Nodes: ELIXIR Germany, ELIXIR Belgium (Klaas Vandepoele, Michiel Van Bel), ELIXIR Portugal and ELIXIR Slovenia.