Reference-free identification and pangenome analysis of accessory chromosomes in a major fungal plant pathogen.

ABSTRACT: Accessory chromosomes, found in some but not all individuals of a species, play an important role in pathogenicity and host specificity in fungal plant pathogens. However, their variability complicates reference-based analysis, especially when these chromosomes are missing in the reference genome. Pangenome variation graphs offer a reference-free alternative for studying these chromosomes. Here, we constructed a pangenome variation graph for 73 diverse Fusarium oxysporum genomes, a major fungal plant pathogen with a compartmentalized genome that includes conserved core as well as variable accessory chromosomes. To obtain insights into accessory chromosome dynamics, we first constructed a chromosome similarity network using all-vs-all similarity mapping. We identified eleven core chr

SUBMITTER: van Westerhoven AC 

PROVIDER: S-EPMC11963757 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature