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Background   Pyrenochaeta lycopersici  is a soil-dwelling ascomycete pathogen that causes corky root rot disease in tomato ( Solanum lycopersicum ) and other  Solanaceous  crops, reducing fruit yields by up to 75%. Fungal pathogens that infect roots receive less attention than those infecting the aerial parts of crops despite their significant impact on plant growth and fruit production.    Results  We assembled a 54.9Mb  P. lycopersici  draft genome sequence based on Illumina short reads, and annotated approximately 17,000 genes. The  P. lycopersici  genome is closely related to hemibiotrophs and necrotrophs, in agreement with the phenotypic characteristics of the fungus and its lifestyle. Several gene families related to host–pathogen interactions are strongly represented, including those responsible for nutrient absorption, the detoxification of fungicides and plant cell wall degradation, the latter confirming that much of the genome is devoted to the pathogenic activity of the fungus. We did not find a MAT gene, which is consistent with the classification of  P. lycopersici  as an imperfect fungus, but we observed a significant expansion of the gene families associated with heterokaryon incompatibility (HI).    Conclusions  The  P. lycopersici  draft genome sequence provided insight into the molecular and genetic basis of the fungal lifestyle, characterizing previously unknown pathogenic behaviors and defining strategies that allow this asexual fungus to increase genetic diversity and to acquire new pathogenic traits.

De novo genome assembly of the soil-borne fungus and tomato pathogen Pyrenochaeta lycopersici