Pangenome graphs for the analysis and monitoring of fungal plant pathogen populations

SémIdeev
 31/01/2025
 12:00:00
 Nicolas Lapalu, Bioger INRAe
 IDEEV - Salle Rosalind Franklin

The assembly of whole genomes by long-read sequencing has enabled the collection of resolved telomere-to-telomere (T2T) haplotypes, encouraging genome-wide approaches to study structural variations. Unlike comparative genomics approaches based on gene content or other types of annotation (such as transposable elements), the analysis of structural variants on a genome-wide scale can now be addressed by graph-oriented approaches. Pangenome graphs (PGGs) are capable of storing the full genetic diversity of the genomes under study, theoretically achieving superior performance in read alignment, variant identification, and genotyping for population studies. Our goal is to evaluate the use of PGGs instead of linear-reference genomes for population genetics analyses of the fungal plant pathogens Zymoseptoria tritici and Pyricularia oryzae as use cases.