Adopting graph-based pangenomics for agronomy and biodiversity: available resources and challenges

In a review published in the Peer Community Journal, a consortium of bioinformatics researchers and engineers provides an overview of the tools and methods that still need to be developed to fully exploit graph-based pangenomes in agronomy and biodiversity studies. These graphs, built from multiple complete genomes of a same species, make it possible to move away from the bias inherent to a single reference genome and open the way to the detection of complex structural variants that remain inaccessible to conventional approaches.

The article identifies a series of methodological bottlenecks that still hinder the widespread adoption of this approach: the lack of standardized metrics to assess graph quality, the shortage of visualization tools suited to graphs comprising hundreds of millions of nodes, the difficulty of unambiguously representing certain variants (repeats, inversions, polyploid regions), and the absence of a consensus file format for carrying functional annotation (genes, transposable elements) directly on the graph structure rather than on a linear genome. The authors also highlight the lack of dedicated, interoperable data repositories for sharing these graphs in line with FAIR principles.

This forward-looking publication is the result of a collaboration between the AGAP (Montpellier), DIADE (Montpellier), URGI (Versailles), IRISA (Rennes), BIOGECO (Bordeaux), MIAT (Toulouse), GDEC (Clermont-Ferrand), IGEPP (Le Rheu) and BIOGER (Palaiseau) units, and aims to mobilize the bioinformatics community to address these gaps and boost interest in graph-based pangenomes. Several contributors to this work were funded by the AgroDiv France 2030 program, reference ANR-22-PEAE-0005. This work was also carried out under the GET-A-PAN network, launched by INRAE in November 2025 to structure the community around pangenomic methodologies.

Reference: Bocs, S.; Carrette, C.; Confais, J.; Dubois, S.; Duvaux, L.; Klopp, C.; Lapalu, N.; Lasserre-Zuber, P.; Legeai, F.; Lemaitre, C.; Linard, B.; Marthe, N.; Pierre, B.; Sarah, G.; Sabot, F.; Tranchant-Dubreuil, C.; Zytnicki, M. Adopting graph-based pangenomics for agronomy and biodiversity studies: current resources and challenges. Peer Community Journal, Volume 6 (2026), article no. e86. https://doi.org/10.24072/pcjournal.781

Contact: Nicolas Lapalu, nicolas.lapalu@inrae.fr