Change, exchange and adaptation: Accessory genome evolution in the plant pathogen Fusarium oxysporum

Fungal plant pathogens pose a major threat to global food security. The interaction between plants and pathogens is characterized by a dynamic co-evolutionary arms race, during which plants evolve mechanisms to detect and defend against pathogens, while pathogens adapt to evade or suppress the plant immune responses. Many fungal pathogens have developed a powerful strategy to facilitate rapid adaptation; rapidly changing genomic regions that can be exchanged between individuals, known as accessory regions. Fusarium oxysporum is a major fungal plant pathogen that causes wilting diseases in many economically important crops. This plant pathogen is well known for having a compartmentalized genome with accessory regions ranging from small regions embedded in otherwise conserved core chromosomes to entire accessory chromosomes. It is known that these accessory regions are crucial in determining pathogenicity in a few F. oxysporum strains, however, in many F. oxysporum strains accessory chromosomes have not yet been identified, and it is thus unknown how accessory regions in F. oxysporum evolved. In this thesis, we analyze the accessory genome of F. oxysporum, with a specific focus on strains that infect banana. We describe the spread of these strains, which threatens banana-production and food security in tropical- and sub-tropical regions. We identified various accessory regions associated with pathogenicity and describe their evolutionary dynamics. Our findings show that these accessory regions expand through segmental duplications and can undergo large intrachromosomal duplications. Furthermore, we find that these accessory regions evolve through recombination and horizontal transfer. Through this research, we gained important insights into how fungal plant pathogens evolve and adapt. This knowledge can help to improve breeding strategies and aid crop protection.