DYNAGEN · Mechanisms of mChr-mediated genome dynamics in the cereal blast fungus Magnaporthe oryzae

Plant pathogenic fungi represent a serious threat for the productivity of agricultural systems. The blast fungus Magnaporthe oryzae is a multi-host pathogen that infects both, cultivated and wild grass species, including important agronomic crops such as rice, wheat and barley. Despite reproducing asexually, clonal lineages of the blast fungus display remarkable genomic and phenotypic plasticity. Most strikingly, these isolates contain highly variable mini-chromosomes, which can contribute to the emergence of new pathogen variants. Intriguingly, phenotypic variation is prevalent in the field but phenotypes remain stable during subculturing, suggesting increased genome plasticity during this process. However, the extent of genomic structural variation in local populations and the underlying mechanisms, particularly somatic interchromosomal recombination, remains limited.The aim of this project is to determine the molecular and regulatory mechanisms underlying genome dynamics and the phenotypic outcomes of structural genomic variation. Using two complementary and multidisciplinary approaches, that combine population genomics, experimental evolution, computational biology and molecular genetic techniques, I will investigate how environmental conditions and developmental cues influence the emergence of structural genomic variants and their phenotypic consequences. In addition, I will determine the impact of interchromosomal recombination events between mini-chromosomes and core chromosomes on local mutation rates, establishing if non-allelic recombination between core and mini-chromosomes contribute to local mutation rate biases affecting virulence effector gene divergence.Collectively, the results from DYNAGEN will advance our understanding of the molecular mechanisms underlying structural genomic variation in fungal plant pathogens. This knowledge could be used to guide surveillance of emerging pathogen variants and develop crop disease prevention strategies.