From metagenome to gene : Identification of the first Synchytrium endobioticum effector through comparative genomics

Plant pathogens can have great social and economic impact, and are a continuous threat to food security. This is clearly the case for Synchytrium endobioticum, the species causing potato wart disease. S. endobioticum is an obligate biotrophic fungus of the phylum Chytridiomycota (chytrids), which is a basal lineage in the fungal kingdom. The lack of chemical control agents, the impact of the pathogen (complete loss of tuber yields from infected field have been reported), and the production of resting spores that remain viable and infectious in infested soils for decades, led to a quarantine status for S. endobioticum in most countries world-wide. Potato wart disease has been reported from all continents where potato is cultivated, and strict phytosanitary control measures are enforced to prevent the introduction and spread of the pathogen. The use of resistant potato varieties has proven successful in achieving these goals. In chapter 1, over a century of potato wart research is reviewed to place our current knowledge in historic perspective. Observations from light microscopy and electron microscopy studies of S. endobioticum performed in the twentieth century are combined with recent molecular studies. Based on our current knowledge on molecular plant-pathogen interactions, a model is presented to describe the interaction between S. endobioticum and its host in particular with respect to plant resistance. Chapter 2 describes the independent sequencing, assembly and functionally annotation of two S. endobioticum genomes. A comparative genomics approach, in which knowledge acquired from other fungal taxa is exploited, is used to gain insights into genomic features underlying the obligate biotrophic and pathogenic lifestyle of the pathogen. Our study underlines the high diversity in chytrids compared to the well-studied Ascomycota and Basidiomycota, and reflects biological differences between the phyla. Moreover, it highlights the surprising commonalities between pla