Open Access Research article

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

Maria Aragona1, Andrea Minio2, Alberto Ferrarini2, Maria Teresa Valente1, Paolo Bagnaresi3, Luigi Orrù3, Paola Tononi2, Gianpiero Zamperin2, Alessandro Infantino1, Giampiero Valè34, Luigi Cattivelli3 and Massimo Delledonne2*

Author Affiliations

1 Consiglio per la ricerca e la sperimentazione in agricoltura, Centro di Ricerca per la Patologia vegetale, Via C. G. Bertero 22, 00156 Roma, Italy

2 Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada le Grazie, 15, 37134 Verona, Italy

3 Consiglio per la ricerca e la sperimentazione in agricoltura, Centro di Ricerca per la Genomica e la post genomica animale e vegetale, Via S. Protaso 302, 29017 Fiorenzuola d’Arda (PC), Italy

4 Consiglio per la ricerca e la sperimentazione in agricoltura, Unità di Ricerca per la Risicoltura, S.S. 11 per Torino Km 2,5, 13100 Vercelli, Italy

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BMC Genomics 2014, 15:313  doi:10.1186/1471-2164-15-313

Published: 27 April 2014



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.


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).


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.

Pyrenochaeta lycopersici; Pathogenicity; Genome assembly; Next Generation Sequencing technologies (NGS)