Population Genomics of Fungal Plant Pathogens and the Analyses of Rapidly Evolving Genome Compartments.

Genome sequencing of fungal pathogens have documented extensive variation in genome structure and composition between species and in many cases between individuals of the same species. This type of genomic variation can be adaptive for pathogens to rapidly evolve new virulence phenotypes. Analyses of genome-wide variation in fungal pathogen genomes rely on high quality assemblies and methods to detect and quantify structural variation. Population genomic studies in fungi have addressed the underlying mechanisms whereby structural variation can be rapidly generated. Transposable elements, high mutation and recombination rates as well as incorrect chromosome segregation during mitosis and meiosis contribute to extensive variation observed in many species. We here summarize key findings in the field of fungal pathogen genomics and we discuss methods to detect and characterize structural variants including an alignment-based pipeline to study variation in population genomic data.

Highly flexible infection programs in a specialized wheat pathogen.

Many filamentous plant pathogens exhibit high levels of genomic variability, yet the impact of this variation on host-pathogen interactions is largely unknown. We have addressed host specialization in the wheat pathogen Zymoseptoria tritici. Our study builds on comparative analyses of infection and gene expression phenotypes of three isolates and reveals the extent to which genomic variation translates into phenotypic variation. The isolates exhibit genetic and genomic variation but are similarly virulent. By combining confocal microscopy, disease monitoring, staining of ROS, and comparative transcriptome analyses, we conducted a detailed comparison of the infection processes of these isolates in a susceptible wheat cultivar. We characterized four core infection stages: establishment, biotrophic growth, lifestyle transition, and necrotrophic growth and asexual reproduction that are shared by the three isolates. However, we demonstrate differentiated temporal and spatial infection development and significant differences in the expression profiles of the three isolates during the infection stages. More than 20% of the genes were differentially expressed and these genes were located significantly closer to transposable elements, suggesting an impact of epigenetic regulation. Further, differentially expressed genes were enriched in effector candidates suggesting that isolate-specific strategies for manipulating host defenses are present in Z. tritici. We demonstrate that individuals of a host-specialized pathogen have highly differentiated infection programs characterized by flexible infection development and functional redundancy. This illustrates how high genetic diversity in pathogen populations results in highly differentiated infection phenotypes, which fact needs to be acknowledged to understand host-pathogen interactions and pathogen evolution.