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

Abstract

BackgroundPyrenochaeta 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.ResultsWe 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).ConclusionsThe 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.

Genetic structure of Italian populations of Pyrenochaeta lycopersici, the causal agent of corky root rot of tomato

“…Moreover, the LD analysis is complemented by STRUC-TURE (at K = 3, K = 7), which detected clear geographic structuring and provided phylogenetic signals. All of this is consistent with P. lycopersici being a soilborne pathogen with limited natural dispersion as it cannot produce reproductive and vegetative structures on infected tissues in the field, and with the sexual stage of this fungus not being known, and the genome analysis that revealed the absence of the mating type genes (Aragona et al, 2014).…”

“…The genome of P. lycopersici has been recently sequenced (Aragona et al, 2014). The information acquired on the composition and organization of the approximately 17 000 genes characterized will allow light to be shed on the taxonomy, pathogenicity and lifestyle of this species.…”

“…Recently, the analysis of the P. lycopersici genome sequence has shown that the MAT genes are apparently lacking, as the homologies in GenBank were less than 40%. Moreover, significant expansion of the gene families associated with heterokaryon incompatibility has been observed compared to other pathogenic and non-pathogenic fungal species (Aragona et al, 2014).…”

Genomic Features of Cladobotryum dendroides, Which Causes Cobweb Disease in Edible Mushrooms, and Identification of Genes Related to Pathogenicity and Mycoparasitism

“…NACHT domains are predicted NTPases, which play a role in programmed cell death (PCD); PCD might be ancient, preceding the radiation of animals and fungi [53,54]. The ankyrin proteins modulate protein-protein interactions among HET proteins [55]. HET and related genes are essential for genetic information transfer in Pyrenochaeta lycopersici [55].…”

Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota)

“…The assembly completeness was also analyzed with Benchmarking Universal Single Copy Orthologs (BUSCO 3.0.1; Waterhouse et al 2017). In addition, 238 whole-genome assemblies of other Dothideomycetes were downloaded from NCBI Gen-Bank and the JGI Genome portal (Additional file 1: Table S1; Galagan et al 2005;Fedorova et al 2008;Sharpton et al 2009;Ellwood et al 2010;Desjardins et al 2011;Goodwin et al 2011;Rouxel et al 2011;Stukenbrock et al 2011;Chan et al 2012;Hu et al 2012;Joardar et al 2012;Ng et al 2012;Ohm et al 2012;Spatafora et al 2012;Blanco-Ulate et al 2013;Condon et al 2013;Lenassi et al 2013;Yew et al 2013;Aragona et al 2014;Bihon et al 2014;Chan et al 2014;Cooke et al 2014;Gao et al 2014;Gostinčar et al, 2014;Han et al 2014;Soliai et al 2014;Sterflinger et al 2014;van der Nest et al 2014;Yang et al 2014;Franco et al 2015;Grandaubert et al 2015;Kuan et al 2015;Morales-Cruz et al 2015;Orner et al 2015;Shaw et al 2015;Shiller et al 2015;…”