Genomic analysis of Botrytis cinerea: an essential tool for better understanding a complex pathogen

The fungus Botrytis cinerea is an important pre- and post-harvest pathogen, causing very significant economic damage in dozens of crops worldwide. Despite extensive chemical control, and the development of biological control agents, yield and quality losses remain substantial. Some quantitative resistance loci have been identified in tomato and Arabidopsis, but the genes and mechanisms contributing to resistance remain to be characterized. In order to design a rational disease control strategy, it is crucial to increase our understanding of mechanisms that B. cinerea exploits to infect host plants. Obtaining a properly annotated genome sequence is instrumental to this understanding. The genomes of two B. cinerea strains, B05.10 and T4, were published (Amselem et al., 2011), but the coverage was low and the data contained errors. A second version was recently published (Staats and van Kan, 2012), for which the coverage and data quality were markedly higher. An effort to further improve the assembly and annotation is ongoing. I will present an overview of the current status of B. cinerea genome sequencing and illustrate how genome information can be exploited to study fungal gene expression in different developmental stages and during host infection. Furthermore I will present preliminary results of an effort to sequence the genomes of ten other Botrytis species, all of which are specialized necrotrophic pathogens, specific for a single host species.