Tracking of Diversity and Evolution in the Brown Rot Fungi Monilinia fructicola, Monilinia fructigena, and Monilinia laxa

Monilinia species are among the most devastating fungi worldwide as they cause brown rot and blossom blight on fruit trees. To understand the molecular bases of their pathogenic lifestyles, we compared the newly assembled genomes of single strains of Monilinia fructicola, M. fructigena and M. laxa, with those of Botrytis cinerea and Sclerotinia sclerotiorum, as the closest species within Sclerotiniaceae. Phylogenomic analysis of orthologous proteins and syntenic investigation suggest that M. laxa is closer to M. fructigena than M. fructicola, and is closest to the other investigated Sclerotiniaceae species. This indicates that M. laxa was the earliest result of the speciation process. Distinct evolutionary profiles were observed for transposable elements (TEs). M. fructicola and M. laxa showed older bursts of TE insertions, which were affected (mainly in M. fructicola) by repeat-induced point (RIP) mutation gene silencing mechanisms. These suggested frequent occurrence of the sexual process in M. fructicola. More recent TE expansion linked with low RIP action was observed in M. fructigena, with very little in S. sclerotiorum and B. cinerea. The detection of active non-syntenic TEs is indicative of horizontal gene transfer and has resulted in alterations in specific gene functions. Analysis of candidate effectors, biosynthetic gene clusters for secondary metabolites and carbohydrate-active enzymes, indicated that Monilinia genus has multiple virulence mechanisms to infect host plants, including toxins, cell-death elicitor, putative virulence factors and cell-wall-degrading enzymes. Some species-specific pathogenic factors might explain differences in terms of host plant and organ preferences between M. fructigena and the other two Monilinia species

Esophageal Eosinophilia and Eosinophilic Esophagitis in Celiac Children: A Ten Year Prospective Observational Study

The association between eosinophilic esophagitis and celiac disease is still controversial and its prevalence is highly variable. We aimed to investigate the prevalence of esophageal eosinophilia and eosinophilic esophagitis in a large group of children with celiac disease, prospectively followed over 11 years. Methods: Prospective observational study performed between 2008 and 2019. Celiac disease diagnosis was based on ESPGHAN criteria. At least four esophageal biopsies were sampled in patients who underwent endoscopy. The presence of at least 15 eosinophils/HPF on esophageal biopsies was considered suggestive of esophageal eosinophilia; at the same time, eosinophilic esophagitis was diagnosed according to the International Consensus Diagnostic Criteria for Eosinophilic Esophagitis. Results: A total of 465 children (M 42% mean age 7.1 years (range: 1–16)) were diagnosed with celiac disease. Three hundred and seventy patients underwent endoscopy, and esophageal biopsies were available in 313. The prevalence of esophageal eosinophilia in children with celiac disease was 1.6% (95% CI: 0.54–2.9). Only one child was diagnosed as eosinophilic esophagitis; we calculated a prevalence of 0.3% (95% CI: 0.2–0.5%). The odds ratio for an association between eosinophilic esophagitis and celiac disease was at least 6.5 times higher (95% CI: 0.89–47.7; p = 0.06) than in the general population. Conclusion: The finding of an increased number of eosinophils (>15/HPF) in celiac patients does not have a clinical implication or warrant intervention, and therefore we do not recommend routine esophageal biopsies unless clinically indicated

The Mycovirome in a Worldwide Collection of the Brown Rot Fungus Monilinia fructicola

The fungus Monilinia fructicola is responsible for brown rot on stone and pome fruit and causes heavy yield losses both pre- and post-harvest. Several mycoviruses are known to infect fungal plant pathogens. In this study, a metagenomic approach was applied to obtain a comprehensive characterization of the mycovirome in a worldwide collection of 58 M. fructicola strains. Deep sequencing of double-stranded (ds)RNA extracts revealed a great abundance and variety of mycoviruses. A total of 32 phylogenetically distinct positive-sense (+) single-stranded (ss)RNA viruses were identified. They included twelve mitoviruses, one in the proposed family Splipalmiviridae, and twelve botourmiaviruses (phylum Lenarviricota), eleven of which were novel viral species; two hypoviruses, three in the proposed family Fusariviridae, and one barnavirus (phylum Pisuviricota); as well as one novel beny-like virus (phylum Kitrinoviricota), the first one identified in Ascomycetes. A partial sequence of a new putative ssDNA mycovirus related to viruses within the Parvoviridae family was detected in a M. fructicola isolate from Serbia. The availability of genomic sequences of mycoviruses will serve as a solid basis for further research aimed at deepening the knowledge on virus–host and virus–virus interactions and to explore their potential as biocontrol agents against brown rot disease

Mating type and fungicide resistance in populations of Podosphaera xanthii in south Italy

Powdery mildew is one of the most common and severe diseases of cucurbits, causing heavy yield losses in all growing areas when not successfully controlled. Two different fungal species, Podosphaera xanthii and Golovinomyces orontii, are generally recognized as causal agents. The results of monitoring carried out in 2016 and 2018 confirmed that P. xanthii is the exclusive pathogen causing cucurbit powdery mildew (CPM) in southern Italy. P. xanthii is a bipolar heterothallic fungus; a PCR-based method for distinguishing MAT1-1 and MAT1-2 idiomorphs was applied for assessing mating type distribution in fungal populations present on cucurbits in different sites. The idiomorph MAT1-2 was prevalent over the MAT1-1 in 2016, whereas they were approximately in a 1:1 ratio in 2018; this finding corroborated the hypothesis that the MAT1-1 idiomorph was more recently introduced in the area. Cyflufenamid-resistant isolates were widespread in commercial greenhouses and field plantings even though use of this fungicide had been drastically reduced by the farmers 1 year before the monitoring due to the effectiveness losses observed in CPM control. Occurrence of cyflufenamid resistance and its impact on efficacy were evaluated in a field trial comparing different fungicide spray schedules. Cyflufenamid-resistant isolates were detected even at the first appearance of symptoms on leaves, increasing over time. Isolates resistant to cyflufenamid showed a resistance factor as high as 900. Generally, P. xanthii was better controlled when cyflufenamid was used in integrated strategies rather than in spray schedules based on the exclusive use of the fungicide

A Ready-to-Use Single- and Duplex-TaqMan-qPCR Assay to Detect and Quantify the Biocontrol Agents Trichoderma asperellum and Trichoderma gamsii

Trichoderma asperellum strain icc012 and Trichoderma gamsii strain icc080, the microbial active ingredients of RemedierTM (ISAGRO, Novara, Italy), are biocontrol agents (BCAs) employable for crop protection against a wide range of fungal pathogens, including soil-borne pathogens and fungi involved in grapevine trunk disease. In this study, single and duplex real-time quantitative PCR (qPCR) methods to detect and quantify T. asperellum and T. gamsii were developed. Primers/probe sets were designed on the T. asperellum and T. gamsii rpb2 genes and tested for specificity on a panel of microorganisms commonly associated with grape wood and soil. No differences were observed comparing single- and duplex-qPCR assays on different BCAs, 1 pg of target DNA was detected approximately at Cq = 34. R2-values and the efficiency were always equal to 0.99 and >80%, respectively. The detection limit of the duplex-qPCR assay on artificially inoculated samples was 2 × 103 and 4 × 104 conidia g-1 of grape wood tissue and soil, respectively. The methods will be useful to better schedule BCA application in the field and in grapevine nurseries, as well as for investigating the dynamic of BCA populations

qPCR and RT-qPCR assays for the quantification of Trichoderma asperellum icc012 and Trichoderma gamsii icc080 used as biocontrol agents against Phaeomoniella chlamydospora in grapevine nursery.

Trichoderma asperellum strain icc012 (TA) and Trichoderma gamsii strain icc080 (TG) (Remedier, Isagro S.p.A., Italy) are biological control agents (BCAs) proposed against esca disease on grapevine. This research was aimed at evaluating their effectiveness against esca in the nursery with particular regard to Phaeomoniella chlamydospora population and at developing a fast and reliable method to quantify the two BCAs. The effectiveness of TA and TG was evaluated on 1103 P. rootstocks, artificially inoculated at the hydration stage with conidia of the benomyl-resistant mutant C1.A43.1 of P. chlamydospora and successively treated or not with Remedier at different time combinations (end of hydration, at planting, and three times during plant growth). Eight different combination programs were compared. At uprooting of rootstocks, wood fragments were sampled at 1 cm and 2–15 cm over the crown from at least 90 rootstocks per program. The incidence of fungi, including the C1.A43.1 mutant and the BCAs, was evaluated on malt extract agar (MEA) and MEA amended with 10 mg L-1 of benomyl. Natural infections of P. chlamydospora were rarely recovered while the population of the artificially inoculated mutant C1.A43.1 was always reduced by BCAs (P≤0.05, ranging from 18% with only one application at hydration to 36% with four applications). Fomitopsis sp., Acremonium sp., and Fusarium sp. were also reduced by BCAs. qPCR and RT-qPCR detection methods based on specific primers and TaqMan probes were set up and applied to quantify singularly and in duplex the populations of TA and TG. The primers/probe sets were designed on the polymorphic region of the rpb2 gene and the method allows to specifically detect up to 10 pg of DNA and 150 pg of RNA. Further studies are in progress to evaluate the effectiveness of the BCAs and define the most appropriate usage in grapevine nursery for reducing infection of esca-associated fungi

Primary central nervous system anaplastic large cell lymphoma in children: Case presentation and systematic review of literature

Primary central nervous system lymphoma (PCNSL) is an extranodal non-Hodgkin lymphoma (NHL) originating in brain tissue, spinal cord, leptomeninges, and vitreoretinal eye, accounting for 3%–5% of all brain tumors and less than 1% of all NHLs