De novo genome assembly and comparative genomics of the newly important barley pathogen Ramularia collo-cygni.

Background: Ramularia collo-cygni is a newly important foliar pathogen of barley responsible for the disease Ramularia leaf spot. The fungus exhibits a prolonged endophytic growth stage before switching life habit to become an aggressive necrotrophic pathogen that causes significant losses to both grain yield and quality. Results: The 30.3 Mb R. collo-cygni genome was sequenced using a combination of Illumina and 454 technologies and a draft assembly containing 11625 predicted gene models was produced which was estimated to be 94% complete. Phylogenetic analysis confirmed the classification of R. collo-cygni within the Mycosphaerellaceae. A predicted secretome of 1054 proteins was identified including genes involved in hydrolysis of proteins and carbohydrates and redox functions. Low levels of plant cell wall degrading enzymes, associated with the stealth pathogenesis of plant pathogens from the Mycosphaerellaceae, were also observed in the R. collo-cygni genome. A large number of genes associated with secondary metabolite production including homologs of genes involved in toxin production by other Dothideomycete plant pathogens were identified. Conclusions: The genome sequence of R. collo-cygni provides a framework for understanding the genetic basis of and will help inform the biological processes responsible for this fungus becoming an important pathogen. Low carbohydrate modifying enzyme content supports the prolonged endophytic growth habit of this fungus. Further understanding of R. collo-cygni gene regulation during host interactions will be used in future to determine the genetic factors that results in this fungus switching from endophytic growth to aggressive necrotrophy.