GET-A-PAN

The GET-A-PAN network, created in 2025, aims to bring together INRAE researchers and engineers involved in the methodological aspects of pangenomic analyses. Its goal is to foster exchanges and collaborative projects to accelerate the transition from genomics to pangenomics within the institute. A sustainable and multidisciplinary framework, leveraging all available expertise, is essential for effectively utilizing pangenomic data and addressing the associated computational and bioinformatics challenges.

The standard method for genetic variation analysis involves comparing new genomes to a reference genome to identify structural variations, but this approach is biased. This issue is particularly pronounced in cultivated species: rustic or wild varieties, which carry variants of interest (such as drought or disease resistance), often lose these traits during domestication, making them absent from the reference. Pangenome graphs provide a solution by integrating all this genetic diversity and facilitating the analysis of the most complex variations.

Network members collectively contributed to an opinion paper focusing on the challenges and expectations for the development of pangenome graph usage in agronomy: https://hal.inrae.fr/hal-05357866.

They also participated in creating a tutorial for establishing and using pangenome graphs : https://genotoul-bioinfo.pages.mia.inra.fr/pangenome_hackathon/.

Network website: https://pangenomes.mathnum.inrae.fr.

Network coordinators:

10 INRAE staff members from 6 scientific departments (BAP, EcoDiv, GA, MathNum, MICA, SPE) :

• Johann Confais (BAP)
• Ludovic Duvaux (ECODIV)
• Thomas Faraut (GA)
• Christine Gaspin (MathNum)
• Guillaume Gautreau (MICA)
• Christophe Klopp (MathNum)
• Nicolas Lapalu (SPE - BIOGER)
• Fabrice Legeai (SPE)
• Benjamin Linard (MathNum)
• Matthias Zytnicki (MathNum)