Drivers of genome evolution in a fungal pathogen of wheat

Chromosome rearrangements involve duplication, deletions, inversions and translocations. Breakpoints of chromosome rearrangements are frequently in close proximity to transposable elements (TEs). TEs are known to mediate chromosome rearrangements through their own activity or through ectopic recombination. During this PhD we aimed to better understand the causes and consequences of chromosome rearrangements in Zymoseptoria tritici, an important pathogen of wheat. To study the origins of chromosome rearrangements the first chapter focusses on the de-repression of TEs, which is stress induced during a wheat infection cycle as well as in nutrient limited media. Stress was shown to drive epigenetic changes and trigger TE de-repression in multiple organisms. We find that TEs respond differently to stresses. Furthermore, effector genes in close proximity to TEs show a de-repression during early infection suggesting that TEs and effectors may be under the same epigenetic control. De-repressed TEs can place a mutational burden on the genome. Therefore, in the second chapter we aimed to quantify the number of chromosome rearrangements occurring in all 21 chromosomes in hundreds of progeny through a single round of meiosis. We find that the fidelity with which chromosomes go through meiosis differs between chromosomes. Chromosomes with a higher repeat content and lower synteny were less stable. In the final chapter we focused on a single rearranged chromosome that was generated by a self-fusion. We hypothesized that such a fused chromosome would go through degenerative breakage-fusion-bridge (BFB) cycles. Here we show the exact process whereby the highly unstable fused chromosome was created through ectopic recombination between a specific repeat family. We trace the fate of the novel chromosome through five rounds of meiosis and show that degenerative cycles occur through repeated ectopic recombination and non-disjunction. The ability of Z. tritici to tolerate chromosome duplications, losses and rearrangements makes this species a great model to observe and investigate the interplay between TE dynamics and chromosome rearrangements