Adopting graph-based pangenomics for agronomy and biodiversity studies: current resources and challenges
Abstract
Pangenomics is transforming the way genomics is done. By using assemblies of multiple complete genomes for the same species, it is possible to depart from a biased, reference-centric, point of view. Represented as graphs, these pangenomes open new paths for genome understanding and improvement of species of agricultural interest. They have, for instance, been used to discover new structural variants linked with traits of interest, and increased the heritability prediction. However, transitioning to a graph-based approach is not straightforward, and many tools are still needed for this shift. While numerous papers present both methodological and applied approaches on pangenomics, and many reviews present advantages of these methods, very few resources outline what remains to be done. In this paper, we would like to list methods that are still required to fully exploit pangenomes, and favor the widespread adoption of this approach.
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BibTeX
@article{bocs2026adopting,
title = {{Adopting graph-based pangenomics for agronomy and biodiversity studies: current resources and challenges}},
author = {Stéphanie Bocs and Camille Carrette and Johann Confais and Siegfried Dubois and Ludovic Duvaux and Christophe Klopp and Nicolas Lapalu and Pauline Lasserre-Zuber and Fabrice Legeai and Claire Lemaitre and Benjamin Linard and Nina Marthe and Baptiste Pierre and Gautier Sarah and François Sabot and Christine Tranchant-Dubreuil and Matthias Zytnicki},
journal = {Peer Community Journal},
year = {2026},
month = sep,
doi = {10.24072/pcjournal.781},
url = {https://hal.inrae.fr/hal-05357866v7},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Adopting graph-based pangenomics for agronomy and biodiversity studies: current resources and challenges
AU - Stéphanie Bocs
AU - Camille Carrette
AU - Johann Confais
AU - Siegfried Dubois
AU - Ludovic Duvaux
AU - Christophe Klopp
AU - Nicolas Lapalu
AU - Pauline Lasserre-Zuber
AU - Fabrice Legeai
AU - Claire Lemaitre
AU - Benjamin Linard
AU - Nina Marthe
AU - Baptiste Pierre
AU - Gautier Sarah
AU - François Sabot
AU - Christine Tranchant-Dubreuil
AU - Matthias Zytnicki
PY - 2026
DA - 2026/09/07
JO - Peer Community Journal
DO - 10.24072/pcjournal.781
UR - https://hal.inrae.fr/hal-05357866v7
AB - Pangenomics is transforming the way genomics is done. By using assemblies of multiple complete genomes for the same species, it is possible to depart from a biased, reference-centric, point of view. Represented as graphs, these pangenomes open new paths for genome understanding and improvement of species of agricultural interest. They have, for instance, been used to discover new structural variants linked with traits of interest, and increased the heritability prediction. However, transitioning to a graph-based approach is not straightforward, and many tools are still needed for this shift. While numerous papers present both methodological and applied approaches on pangenomics, and many reviews present advantages of these methods, very few resources outline what remains to be done. In this paper, we would like to list methods that are still required to fully exploit pangenomes, and favor the widespread adoption of this approach.
SN - 2804-3871
SN - 2804-3871
ER -