Tracking evolutionary dynamics within the fungal wheat pathogen "Zymoseptoria tritici"

Plant pathogenic fungi are very widespread and can pose severe risks to global food production through single as well as mixed infection. Crop control is based on the use of synthetic chemicals and plant resistance breeding. However, fungal plant pathogens quickly overcome both strategies. During coinfections, plant pathogens can increase disease severity and change co-infecting genotypes virulence evolution. Hence, monitoring tools improving crop pathogen detection as well as understanding the impact of co-infection events on disease severity are lacking. Additionally, we still lack information on the genetic basis shaping virulence and fungicide resistance evolution over time. In this PhD thesis I focused on developing monitoring tool to track virulence and fungicide resistance evolution in the fungal wheat pathogen Zymoseptoria tritici using different molecular and genomic tools. Here I designed a microfluidics-based amplicon sequencing assay to multiplex several loci targeting virulence and fungicide resistance genes, and randomly selected genome-wide markers. More than hundred types of samples were used to assess the performance of our assay. This later allowed an accurate amplification of all designed loci and performed well regardless of the sample type. I also explored the outcomes of mixed interactions within and outside the plant host by using a large sample size to provide a deeper picture about the consequences of such interactions on disease severity as well as virulence and growth effects. I found that the growth kinetics and virulence in single interactions deviated from those seen during mixed interactions indicating competitive exclusion between conspecific strains. Additionally, the outcomes were divergent within and outside the plant host indicating that the plant immune system plays a key role in shaping the within-plant interaction outcomes and adds significant complexity. Finally, I used a data set of worldwide populations of Z. tritici to investigate transposable elements (TEs) located nearby important virulence and fungicide resistance genes allowing to retrace the evolutionary history of the pathogen worldwide as well as a better crop protection strategies. I identified a considerable number of TEs belonging to different families and superfamilies, I also detected recent insertions represented by unique insertions called singletons. Overall, this PhD thesis allows monitoring newly evolved Z. tritici genotypes and understanding the genetic basis mediating their adaptation to their hosts and environment. Besides, the thesis provides information about the consequences of mixed interactions on disease severity and how these can shape change in virulence and growth of plant pathogens.