Functional dissection of the meiotic drive of female-inherited accessory chromosomes in Zymoseptoria tritici

Accessory chromosomes are non-essential genetic elements that occur in the genomes of many eukaryotes. These chromosomes show presence/absence polymorphisms and are often lost and unpaired during meiosis. In some fungal species, these chromosomes confer fitness advantages, often in the form of increased virulence. However, in some species, they have a negative fitness effect, for instance, in Zymoseptoria tritici, a fungal wheat pathogen. Accessory chromosomes are likely maintained in populations of this pathogen despite their negative fitness cost via a meiotic drive that is restricted to female-inherited and unpaired accessory chromosomes. The mechanism of this meiotic drive is unclear, but it likely involves the additional replication of female-inherited and unpaired accessory chromosomes. The main focus of this thesis was to improve our understanding of the mechanism of meiotic drive of accessory chromosomes and to gain deeper insight into genetic changes associated with meiosis (namely recombination, gene conversion and de novo mutations) in Z. tritici. In Chapter I, I give an overview of the structural and functional features of fungal accessory chromosomes that might be affecting their segregation patterns and discuss mechanisms that could explain meiotic drives of fungal accessory chromosomes. In Chapter II, I calculate higher recombination and gene conversion rates on accessory chromosomes and detect signatures of repeat-induced point mutation (RIP) in duplications and transposable elements (TEs). In Chapter III, I observe how disomic chromosomes undergo meiosis and distinguish the stage of meiosis at which re-replication of accessory chromosomes under meiotic drive occurs. In conclusion, I show how genetic changes during meiosis shape the Z. tritici genome and provide novel insights into the mechanism of meiotic drive of accessory chromosomes in this important plant pathogen