Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus

<jats:title>Abstract</jats:title> <jats:sec> <jats:title>Background</jats:title> <jats:p> <jats:italic>Penicillium digitatum</jats:italic> is a fungal necrotroph causing a common citrus postharvest disease known as green mold. In order to gain insight into the genetic bases of its virulence mechanisms and its high degree of host-specificity, the genomes of two <jats:italic>P. digitatum</jats:italic> strains that differ in their antifungal resistance traits have been sequenced and compared with those of 28 other Pezizomycotina.</jats:p> </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p>The two sequenced genomes are highly similar, but important differences between them include the presence of a unique gene cluster in the resistant strain, and mutations previously shown to confer fungicide resistance. The two strains, which were isolated in Spain, and another isolated in China have identical mitochondrial genome sequences suggesting a recent worldwide expansion of the species. Comparison with the closely-related but non-phytopathogenic <jats:italic>P. chrysogenum</jats:italic> reveals a much smaller gene content in <jats:italic>P. digitatum</jats:italic>, consistent with a more specialized lifestyle. We show that large regions of the <jats:italic>P. chrysogenum</jats:italic> genome, including entire supercontigs, are absent from <jats:italic>P. digitatum</jats:italic>, and that this is the result of large gene family expansions rather than acquisition through horizontal gene transfer<jats:italic>.</jats:italic> Our analysis of the <jats:italic>P. digitatum</jats:italic> genome is indicative of heterothallic sexual reproduction and reveals the molecular basis for the inability of this species to assimilate nitrate or produce the metabolites patulin and penicillin. Finally, we identify the predicted secretome, which provides a first approximation to the protein repertoire used during invasive growth.</jats:p> </jats:sec> <jats:sec> <jats:title>Conclusions</jats:title> <jats:p>The complete genome of <jats:italic>P. digitatum</jats:italic>, the first of a phytopathogenic <jats:italic>Penicillium</jats:italic> species, is a valuable tool for understanding the virulence mechanisms and host-specificity of this economically important pest.</jats:p> </jats:sec>