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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.

Background Bakanae disease, caused by seed-borne Fusarium species, mainly F. fujikuroi, is a rice disease whose importance is considerably increasing in several rice growing countries, leading to incremental production losses.ResultsA germplasm collection of japonica rice was screened for F. fujikuroi resistance, allowing the identification of accessions with high-to-moderate levels of resistance to bakanae. A GWAS approach uncovered two genomic regions highly associated with the observed phenotypic variation for response to bakanae infection on the short arm of chromosome 1 (named as qBK1_628091) and on the long arm of chromosome 4 (named as qBK4_31750955). High levels of phenotypic resistance to bakanae were associated to the cumulated presence of the resistant alleles at the two resistance loci, suggesting that they can provide useful levels of disease protection in resistance breeding. A fine comparison with the genomic positions of qBK1_628091 and qBK4_31750955 with respect to the QTLs for bakanae resistance reported in the literature suggests that the resistant loci here described represent new genomic regions associated to F. fujikuroi resistance. A search for candidate genes with a putative role in bakanae resistance was conducted considering all the annotated genes and F. fujikuroi-related DEGs included in the two genomic regions highlighting several gene functions that could be involved in resistance, thus paving the way to the functional characterization of the resistance loci.ConclusionsNew effective sources for bakanae resistance were identified on rice chromosomes 1 and 4 and tools for resistance breeding are provided.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-017-0168-z) contains supplementary material, which is available to authorized users.

The heterothallic ascomycete Fusarium fujikuroi (teleomorph: Gibberella fujikuroi) is the causal agent of bakanae of rice, a disease of increasing economic importance in the major rice‐producing areas in the world and a serious threat for Italian rice cultivation. A few studies have characterized F. fujikuroi isolates in America and the Philippines but no data are available on the genetic structure of Italian pathogen populations. Microsatellite SSRs are useful tools to study the intraspecific diversity at population level. In this study, 19 polymorphic SSRs have been identified and applied to characterize the genetic variation of 334 isolates of F. fujikuroi coming from eight Italian rice‐growing areas. A high degree of diversity at haplotype level has emerged: in the eight populations, 107 unique haplotypes were scored. Analysis of molecular variance (amova) showed that 98% of genetic variability occurred within F. fujikuroi Italian populations, as confirmed by the allelic Shannon index ranging from 0.56 to 1.06. The presence of a 1:1 ratio of mating type alleles in six out of eight of the Italian fungal populations suggests a potential for sexual reproduction in the field. However, the high fraction of clonality (43%), confirmed by neighbour‐joining clustering analysis, and the high level of linkage disequilibrium observed, indicates that reproduction of F. fujikuroi is mostly clonal in Italy. All data suggest that the observed genetic variability was probably mediated by human activity and transmission by rice seeds.

Many fungal plant pathogens secrete an array of cell wall degrading enzymes mainly involved in the pathogenesis. In this work, a cDNA clone encoding an extracellular endo-1,4-β-glucanase (named PlEGL1) from the causal agent of the Corky Root Rot of tomato, Pyrenochaeta lycopersici, was isolated and characterized, in order to understand its putative role in the pathogenesis and its mechanism of action. Multiple alignment of the deduced amino acidic sequence shows a high homology with other endoglucanases from different phytopathogenic fungi and detects a well-defined conserved domain of the Glycosyl Hydrolase family 61 (GH61). In vitro, Plegl1 gene transcription is correlated to a cellulolytic activity of the fungus, regulated, in its turn, by the presence of sugar and/or cellulose in the culture medium. In the infected plants, expression level of Plegl1 is positively correlated to the development of the disease. PlEGL1 was heterologously expressed in Escherichia coli and the recombinant protein was purified and tested for its cellulolytic ability, showing a very weak activity, in agreement with all the endoglucanases belonging to GH61 family. The finding in this paper will provide the basis for further determination of biochemical properties of the PlEGL1 protein and its possible involvement in the host-pathogen interaction.