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Abstract

Many pathogens evolved compartmentalized genomes with conserved core and variable accessory regions which carry effector genes mediating virulence. The fungal plant pathogen Fusarium oxysporum has such accessory regions, often spanning entire chromosomes, yet understanding of their evolution in strains that infect the same host remains limited. Here, we define the pan-genome of 69 diverse Fusarium strains that cause Fusarium wilt of banana, a significant constraint to global banana production, and demonstrate that segmental duplications drive the evolution of accessory regions. Accessory regions are highly variable and encode distinct gene repertories, with evolutionarily less constrained, younger genes and in planta- induced effectors, which differ between strains infecting the same banana cultivars. We show that recent segmental duplications and aneuploidy of accessory chromosomes cause the expansion of accessory regions in some Fusarium species. Taken together we conclude that extensive recent duplications drive the evolution of accessory regions in Fusarium, which contribute to the evolution of virulence.