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Septoria pistaciarum, a causal agent of Septoria leaf spot disease of pistachio, is a fungal pathogen that causes substantial losses in the cultivation, worldwide. This study describes the first pan-genome-based survey of this phytopathogen—comprising a total of 27 isolates, with 9 isolates each from 3 regional units of Greece (Pieria, Larissa and Fthiotida). The reference isolate (SPF8) assembled into a total of 43.1 Mb, with 38.6% contained within AT-rich regions of approximately 37.5% G:C. The genomes of the 27 isolates exhibited on average 42% gene-coding and 20% repetitive regions. The genomes of isolates from the southern Fthiotida region appeared to more diverged from each other than the other regions based on SNP-derived trees, and also contained isolates similar to both the Pieria and Larissa regions. In contrast, isolates of the Pieria and Larissa were less diverse and distinct from one another. Asexual reproduction appeared to be typical, with no MAT1-2 locus detected in any isolate. Genome-based prediction of infection mode indicated hemibiotrophic and saprotrophic adaptations, consistent with its long latent phase. Gene prediction and orthology clustering generated a pan-genome-wide gene set of 21,174 loci. A total of 59 ortholog groups were predicted to contain candidate effector proteins, with 36 (61%) of these either having homologs to known effectors from other species or could be assigned predicted functions from matches to conserved domains. Overall, effector prediction suggests that S. pistaciarum employs a combination of defensive effectors with roles in suppression of host defenses, and offensive effectors with a range of cytotoxic activities. Some effector-like ortholog groups presented as divergent versions of the same protein, suggesting region-specific adaptations may have occurred. These findings provide insights and future research directions in uncovering the pathogenesis and population dynamics of S. pistaciarum toward the efficient management of Septoria leaf spot of pistachio.

This study describes the first genome sequence and analysis of Coniella granati, a fungal pathogen with a broad host range, which is responsible for postharvest crown rot, shoot blight, and canker diseases in pomegranates. C. granati is a geographically widespread pathogen which has been reported across Europe, Asia, the Americas, and Africa. Our analysis revealed a 46.8 Mb genome with features characteristic of hemibiotrophic fungi. Approximately one third of its genome was compartmentalised within ‘AT-rich’ regions exhibiting a low GC content (30 to 45%). These regions primarily comprised transposable elements that are repeated at a high frequency and interspersed throughout the genome. Transcriptome-supported gene annotation of the C. granati genome revealed a streamlined proteome, mirroring similar observations in other pathogens with a latent phase. The genome encoded a relatively compact set of 9568 protein-coding genes with a remarkable 95% having assigned functional annotations. Despite this streamlined nature, a set of 40 cysteine-rich candidate secreted effector-like proteins (CSEPs) was predicted as well as a gene cluster involved in the synthesis of a pomegranate-associated toxin. These potential virulence factors were predominantly located near repeat-rich and AT-rich regions, suggesting that the pathogen evades host defences through Repeat-Induced Point mutation (RIP)-mediated pseudogenisation. Furthermore, 23 of these CSEPs exhibited homology to known effector and pathogenicity genes found in other hemibiotrophic pathogens. The study establishes a foundational resource for the study of the genetic makeup of C. granati, paving the way for future research on its pathogenicity mechanisms and the development of targeted control strategies to safeguard pomegranate production.

Pear brown rot and blossom blight caused by Monilinia laxa seriously affect pear production worldwide. Here, we compared the transcriptomic profiles of petals after inoculation with M. laxa using two pear cultivars with different levels of sensitivity to disease (Sissy, a relatively tolerant cultivar, and Kristalli, a highly susceptible cultivar). Physiological indexes were also monitored in the petals of both cultivars at 2 h and 48 h after infection (2 HAI and 48 HAI). RNA-seq data and weighted gene co-expression network analysis (WGCNA) allowed the identification of key genes and pathways involved in immune- and defense-related responses that were specific for each cultivar in a time-dependent manner. In particular, in the Kristalli cultivar, a significant transcriptome reprogramming occurred early at 2 HAI and was accompanied either by suppression of key differentially expressed genes (DEGs) involved in the modulation of any defense responses or by activation of DEGs acting as sensitivity factors promoting susceptibility. In contrast to the considerably high number of DEGs induced early in the Kristalli cultivar, upregulation of specific DEGs involved in pathogen perception and signal transduction, biosynthesis of secondary and primary metabolism, and other defense-related responses was delayed in the Sissy cultivar, occurring at 48 HAI. The WGCNA highlighted one module that was significantly and highly correlated to the relatively tolerant cultivar. Six hub genes were identified within this module, including three WRKY transcription factor-encoding genes: WRKY 65 (pycom05g27470), WRKY 71 (pycom10g22220), and WRKY28 (pycom17g13130), which may play a crucial role in enhancing the tolerance of pear petals to M. laxa. Our results will provide insights into the interplay of the molecular mechanisms underlying immune responses of petals at the pear–M. laxa pathosystem.

Olive anthracnose outbreaks caused by the Colletotrichum species complex in the Mediterranean region decrease both fruit yield and olive oil production while also drastically degrading olive oil quality. The presence of various Colletotrichum species able to produce disease symptoms in olive fruits significantly deteriorates the efforts for an efficient crop protection strategy. In this report, the major olive productive area of Peloponnese was screened for Colletotrichum species capable of generating anthracnose symptoms. Olive fruits of 12 different olive cultivars were collected from 60 groves distributed analogously in the Peloponnese. Thirty-two fungal strains isolated from asymptomatic olive drupes were identified morphologically as Colletotrichum spp. and were multilocus genetically analyzed. The 32 isolates were grouped into two primary lineages resembling the previously characterized Colletotrichum acutatum and Colletotrichum nymphaeae based on the conducted genetic analysis for five genetic loci. The virulence of 16 Colletotrichum spp. strains were evaluated in a detached fruit assay of 10 Greek olive cultivars. The results clearly suggested that fungal isolates belonging to both C. acutatum and C. nymphaeae exhibited different levels of pathogenicity in a cultivar-dependent manner. Thus, cultivars examined in terms of the % Disease Index (%DI) were divided into highly tolerant, tolerant, and susceptible, and those analyzed regarding the % Disease Severity Index (%DSI) were divided into tolerant and susceptible. Our results suggest that the Greek cultivars of Athinolia and Megaritiki are highly tolerant to the vast majority of Colletotrichum strains isolated from Peloponnesian groves and consist of a significant genetic material for the future design of crop protection programs against anthracnose breakouts.

Aspergillus carbonarius causes severe decays on berries in vineyards and is among the main fungal species responsible for grape contamination by ochratoxin A (OTA), which is the foremost mycotoxin produced by this fungus. The main goal of this study was to investigate at the transcriptome level the comparative profiles between two table grape varieties (Victoria and Fraoula, the white and red variety, respectively) after their inoculation with a virulent OTA-producing A. carbonarius strain. The two varieties revealed quite different transcriptomic signatures and the expression profiles of the differential expressed genes (DEGs) highlighted distinct and variety-specific responses during the infection period. The significant enrichment of pathways related to the modulation of transcriptional dynamics towards the activation of defence responses, the triggering of the metabolic shunt for the biosynthesis of secondary metabolites, mainly phenylpropanoids, and the upregulation of DEGs encoding phytoalexins, transcription factors, and genes involved in plant–pathogen interaction and immune signaling transduction was revealed in an early time point in Fraoula, whereas, in Victoria, any transcriptional reprogramming was observed after a delay. However, both varieties, to some extent, also showed common expression dynamics for specific DEG families, such as those encoding for laccases and stilbene synthases. Jasmonate (JA) may play a critical modulator role in the defence machinery as various JA-biosynthetic DEGs were upregulated. Along with the broader modulation of the transcriptome that was observed in white grape, expression profiles of specific A. carbonarius genes related to pathogenesis, fungal sporulation, and conidiation highlight the higher susceptibility of Victoria. Furthermore, the A. carbonarius transcriptional patterns directly associated with the regulation of the pathogen OTA-biosynthesis gene cluster were more highly induced in Victoria than in Fraoula. The latter was less contaminated by OTA and showed substantially lower sporulation. These findings contribute to uncovering the interplay beyond this plant–microbe interaction.

Fusarium oxysporum f. sp. lentis (Fol) is considered the most destructive disease for lentil (Lens culinaris Medik.) worldwide. Despite the extensive studies elucidating plants’ metabolic response to fungal agents, there is a knowledge gap in the biochemical mechanisms governing Fol-resistance in lentil. Τhis study aimed at comparatively evaluating the metabolic response of two lentil genotypes, with contrasting phenotypes for Fol-resistance, to Fol-inoculation. Apart from gaining insights into the metabolic reprogramming in response to Fol-inoculation, the study focused on discovering novel biomarkers to improve early selection for Fol-resistance. GC-MS-mediated metabolic profiling of leaves and roots was employed to monitor changes across genotypes and treatments as well as their interaction. In total, the analysis yielded 178 quantifiable compounds, of which the vast majority belonged to the groups of carbohydrates, amino acids, polyols and organic acids. Despite the magnitude of metabolic fluctuations in response to Fol-inoculation in both genotypes under study, significant alterations were noted in the content of 18 compounds, of which 10 and 8 compounds referred to roots and shoots, respectively. Overall data underline the crucial contribution of palatinitol and L-proline in the metabolic response of roots and shoots, respectively, thus offering possibilities for their exploitation as metabolic biomarkers for Fol-resistance in lentil. To the best of our knowledge, this is the first metabolomics-based approach to unraveling the effects of Fol-inoculation on lentil’s metabolome, thus providing crucial information related to key aspects of lentil–Fol interaction. Future investigations in metabolic aspects of lentil–Fol interactions will undoubtedly revolutionize the search for metabolites underlying Fol-resistance, thus paving the way towards upgrading breeding efforts to combat fusarium wilt in lentil.

Pomegranate fruit dry rot is caused by Coniella granati, also referred as Pilidiella granati. In order to decipher the induced responses of mature pomegranates inoculated with the pathogen, an RNA-seq analysis was employed. A high number of differentially expressed genes (DEGs) were observed through a three-time series inoculation period. The transcriptional reprogramming was time-dependent, whereas the majority of DEGs were suppressed and the expression patterns of specific genes may facilitate the pathogen colonization at 1 day after inoculation (dai). In contrast, at 2 dai and mainly thereafter at 3 dai, defense responses were partially triggered in delay. Particularly, DEGs were mainly upregulated at the latest time point. Among them, specific DEGs involved in cell wall modification and degradation processes, pathogen recognition and signaling transduction cascades, activation of specific defense and metabolite biosynthesis-related genes, as well in induction of particular families of transcriptional factors, may constitute crucial components of a defense recruiting strategy employed by pomegranate fruit upon C. granati challenge. Overall, our findings provide novel insights to the compatible interaction of pomegranates—C. granati and lay the foundations for establishing integrated pest management (IPM) strategies involving advanced approaches, such as gene editing or molecular breeding programs for disease resistance, according to European Union (EU) goals.

Taphrina deformans is the causal agent of leaf curl, a serious peach disease which causes significant losses in peach production worldwide. Nowadays, in order to control plant diseases, it is necessary to adopt novel and low-cost alternatives to conventional chemical fungicides. These promising strategies are targeted at eliciting host defense mechanisms via priming the host through the consecutive application of plant immunity inducers prior to pathogen challenge. In this study, we investigated whether chitosan or yeast cell wall extracts could provide enhanced tolerance against leaf curl in two-season field trials. Furthermore, we addressed the possible molecular mechanisms involved beyond the priming of immune responses by monitoring the induction of key defense-related genes. The efficacy of spraying treatments against peach leaf curl with both inducers was significantly higher compared to the untreated control, showing efficacy in reducing disease severity of up to 62.6% and 73.9% for chitosan and yeast cell wall extracts, respectively. The application of chitosan in combination with copper hydroxide was more efficient in reducing disease incidence and severity, showing efficacy values in the range of 79.5–93.18%. Peach plantlets were also spray-treated with immunity inducers three times prior to leaf inoculation with T. deformans blastospores in their yeast phase. The relative expression levels of nine key defense and priming genes, including those encoding members of pathogenesis-related (PR) proteins and hub genes associated with hormone biosynthesis, were monitored by RT-qPCR across three days after inoculation (dai). The results indicate that pre-treatments with these plant immunity inducers activated the induction of genes involved in salicylic acid (SA) and jasmonate (JA) defense signaling pathways that may offer systemic resistance, coupled with the upregulation of genes conferring direct antimicrobial effects. Our experiments suggest that these two plant immunity inducers could constitute useful components towards the effective control of T. deformans in peach crops.

Brown rot disease caused by Monilinia fructicola is one of the most important peach fruit threats in the world. The use of biological control agents (BCAs), instead of synthetic fungicides, to successfully inhibit postharvest disease development is a challenge in sustainable and efficient crop management. The commercially available BCA Bacillus amyloliquefaciens QST 713 (formerly Bacillus subtilis QST713) is able to inhibit a variety of fungal pathogens and suppress several plant diseases. Our results showed that this BCA inhibited mycelial growth in vitro, and was able to suppress the disease’s severity in peach fruits via delaying and reducing brown rot symptoms. A transcriptomic analysis of fruits during their pre-treatment with this biocontrol agent following M. fructicola challenge revealed a significant upregulation of specific differentially expressed genes (DEGs) at 48 h after inoculation (HAI). These genes are related to the activation of several transcriptional factors, such as members of the WRKY and NAC families, and receptors that are involved in pathogen recognition and signaling transduction (e.g., LRR-RLKs). Furthermore, the inhibition of M. fructicola by this biocontrol agent was confirmed by analyzing the expression profiles of specific fungal genes, which highlighted the direct antimicrobial impact of this bacterial strain against the fungus. Hence, these findings clearly suggest that B. amyloliquefaciens QST 713 is an efficient BCA against brown rot disease, which can directly inhibit M. fructicola and improve peach fruit tolerance.

The dimorphic fungus Taphrina deformans is the causal agent of peach leaf curl disease, which affects leaves, flowers, and fruits. An RNA-seq approach was employed to gain insights into the transcriptional reprogramming of a peach cultivar during leaf inoculation with the yeast phase of the fungus across a compatible interaction. The results uncovered modulations of specific peach differentially expressed genes (DEGs) in peaches and pathways related to either the induction of host defense responses or pathogen colonization and disease spread. Expression profiles of DEGs were shown to be highly time-dependent and related to the presence of the two forms of the fungal growth, the inoculated yeast form and the later biotrophic phase during mycelial development. In parallel, this differential reprogramming was consistent with a diphasic detection of fungal load in the challenged leaves over the 120 h after inoculation (HAI) period. Leaf defense responses either occurred during the early yeast phase inoculation at 24 HAI, mediated primarily by cell wall modification processes, or more pronouncedly during the biotrophic phase at 72 HAI, as revealed by the activation of DEGs related to pathogen perception, signaling transduction, and secondary metabolism towards restraining further hypha proliferation. On the contrary, the expression patterns of specific DEGs at 120 HAI might further contribute to host susceptibility. These findings will further allow us to elucidate the molecular responses beyond the peach—T. deformans interaction.

The peach (Prunus persica L.) is one of the most important stone-fruit crops worldwide. Nevertheless, successful peach fruit production is seriously reduced by losses due to Monilinia fructicola the causal agent of brown rot. Chitosan has a broad spectrum of antimicrobial properties and may also act as an elicitor that activate defense responses in plants. As little is known about the elicitation potential of chitosan in peach fruits and its impact at their transcriptional-level profiles, the aim of this study was to uncover using RNA-seq the induced responses regulated by the action of chitosan in fruit–chitosan–M. fructicola interaction. Samples were obtained from fruits treated with chitosan or inoculated with M. fructicola, as well from fruits pre-treated with chitosan and thereafter inoculated with the fungus. Chitosan was found to delay the postharvest decay of fruits, and expression profiles showed that its defense-priming effects were mainly evident after the pathogen challenge, driven particularly by modulations of differentially expressed genes (DEGs) related to cell-wall modifications, pathogen perception, and signal transduction, preventing the spread of fungus. In contrast, as the compatible interaction of fruits with M. fructicola was challenged, a shift towards defense responses was triggered with a delay, which was insufficient to limit fungal expansion, whereas DEGs involved in particular processes have facilitated early pathogen colonization. Physiological indicators of peach fruits were also measured. Additionally, expression profiles of particular M. fructicola genes highlight the direct antimicrobial activity of chitosan against the fungus. Overall, the results clarify the possible mechanisms of chitosan-mediated tolerance to M. fructicola and set new foundations for the potential employment of chitosan in the control of brown rot in peaches.

Monilinia laxa, Monilinia fructicola and Monilinia fructigena are the three main causal agents of brown rot, which is one of the most important diseases of stone fruits in pre- and postharvest conditions. Nowadays, the need for the precise genotyping of these Monilinia species in terms of the genetic diversity of their populations or differences in their pathogenicity and host range is a prerequisite for any efficient disease management. In our study, the genetic structure of Monilinia populations in Serbia from three geographically distinct regions was investigated employing a high-resolution melting (HRM) analysis which is a sensitive and rapid molecular approach in fungal ge­notyping and diagnostics. Using species-specific primer pairs genotype-specific HRM melting curve profiles were generated allowing to efficiently decipher the genetic diversity of the Monilinia populations. The Monilinia genotypes could be easily distinguished according to their melting curves. The isolates from the northern region were assigned to distinct genotypes and grouped rather independently compared to the isolates of the other two regions among all three tested Monilinia spp. M. fructicola and M. fructigena showed a higher genetic diversity among their populations (44%) compared with the genetic diversity among the M. laxa populations (7%). In contrast, the genetic variance within the pathogen populations was higher in the case of M. laxa (93%). Our data revealed an absence of host specificity in the Monilinia spp. populations.

Evaluating microbial-based alternatives to conventional fungicides and biofertilizers enables us to gain a deeper understanding of the biocontrol and plant growth-promoting activities. Two genetically distinct Bacillus halotolerans strains (Cal.l.30, Cal.f.4) were evaluated for the levels of their compatibility. They were applied individually or in combination under in vitro and greenhouse conditions, using seed bio-priming and soil drenching as inoculum delivery systems, for their plant growth-promoting effect. Our data indicate that application of Cal.l.30 and Cal.f.4 as single strains and as a mixture significantly enhanced growth parameters of Arabidopsis and tomato plants. We investigated whether seed and an additional soil treatment with these strains could induce the expression of defense-related genes in leaves of young tomato seedling plants. These treatments mediated a long lasting, bacterial-mediated, systemic-induced resistance as evidenced by the high levels of expression of RP3, ACO1 and ERF1 genes in the leaves of young tomato seedlings. Furthermore, we presented data showing that seed and soil treatment with B. halotolerans strains resulted in an effective inhibition of Botrytis cinerea attack and development on tomato leaves. Our findings highlighted the potential of B. halotolerans strains as they combine both direct antifungal activity against plant pathogens and the ability to prime plant innate immunity and enhance plant growth.

Apple scab caused by Venturia inaequalis has the most destructive effects among other phytopathogens in apple crops all over the world. The integration of resistance genes from local and domestic cultivars is a prerequisite for the efficient control of this disease and is a main target in efficient breeding approaches. Across Greece, many domestic apple cultivars are reported without deep knowledge about the presence and diversity of scab resistance genes. In this study, the presence of five resistance genes (Rvi2, Rvi4, Rvi6, Rvi8 and Rvi11) was evaluated across twenty local and domestic apple genotypes, employing twelve molecular markers closely linked to known apple scab resistance loci. Significant differences and polymorphisms among the tested cultivars were detected suggesting that some of them carry a sufficient number of resistance genes. This observed genetic diversity could be exploited in ongoing breeding approaches as a natural source of polygenic resistance against apple scab.

The phytopathogenic oomycetes of the genus Phytophthora cause devastating economic losses worldwide. Naphthodianthrone compounds, present in plant extracts of buckwheat and Saint John's wort act as photosensitiser agents and exhibit antimicrobial activity against a number of pathogens. In this study, we investigated the potential inhibitory effects of fagopyrin and hypericin on Phytophthora citrophthora (R.E. Sm. & E.H. Sm.) Leonian 1906, the main causal agent of rot diseases in deciduous trees. Fagopyrin had the highest inhibitory effect in the colony growth at a concentration of 2% of a stock solution (3 mg/mL), inducing clubbed hyphae with round tips. Notably, hypericin also inhibited the radial colony growth and increased the hyphal branching at the subapical region, while also promo­ting the formation of enlarged cells with irregular shapes growing collectively as biofilm-like structures. In terms of the mycelial dry weight, although both photosensitisers had considerable inhibitory effects, the fagopyrin treatment was most effective. Leaf bioassays showed that under dark conditions the photosensitiser pre-treated zoospores formed a dense, but aberrant, mycelial growth with penetration defects. In contrast, when the zoospore production was perfor­med under light conditions, the zoospores failed to cause necrotic lesions and penetration events implying that their virulence was impaired. These findings shed light on the biological effects of fagopyrin and hypericin in the regulation of the mycelial growth, morphology and pathogenicity of P. citrophthora.

The excessive use of fungicides against Venturia inaequalis, the causal agent of apple scab, has led to the emergence of resistant populations to multiple fungicides over the years. In Greece, there is no available information on fungicide resistance, despite the fact that control failures have been reported on certain areas. An amount of 418 single-spore isolates were collected from three major apple production areas and tested for their sensitivity to eight commonly used fungicides from unrelated chemical groups. The isolates were tested on malt extract agar media enriched with the discriminatory dose of each fungicide using the point inoculation method. To define the discriminatory dose for assessing the levels of resistance, EC50 values on both spore germination and mycelial growth assays were previously determined. Isolates exhibiting high resistance to trifloxystrobin (92% in total) and difenoconazole (3%); and moderate resistance to cyprodinil (75%), dodine (28%), difenoconazole (36%), boscalid (5%), and fludioxonil (7%) were found for the first time in Greece. A small percentage of the isolates were also found less sensitive to captan (8%) and dithianon (6%). Two isolates showed various levels of resistance to all eight fungicides. Despite the occurrence of strains with multiple resistances to many fungicides, we concluded that this practical resistance in the field arose mainly due to the poor control of apple scab with trifloxystrobin and difenoconazole.

The number of invasive alien pest and pathogen species affecting ecosystem functioning, human health and economies has increased dramatically over the last decades. Discoveries of invasive pests and pathogens previously unknown to science or with unknown host associations yet damaging on novel hosts highlights the necessity of developing novel tools to predict their appearance in hitherto naïve environments. The use of sentinel plant systems is a promising tool to improve the detection of pests and pathogens before introduction and to provide valuable information for the development of preventative measures to minimize economic or environmental impacts. Though sentinel plantings have been established and studied during the last decade, there still remains a great need for guidance on which tools and protocols to put into practice in order to make assessments accurate and reliable. The sampling and diagnostic protocols chosen should enable as much information as possible about potential damaging agents and species identification. Consistency and comparison of results are based on the adoption of common procedures for sampling design and sample processing. In this paper, we suggest harmonized procedures that should be used in sentinel planting surveys for effective sampling and identification of potential pests and pathogens. We also review the benefits and limitations of various diagnostic methods for early detection in sentinel systems, and the feasibility of the results obtained supporting National Plant Protection Organizations in pest and commodity risk analysis.

Plants develop a plethora of defense strategies during their acclimation and interactions with various environmental stresses. Secondary metabolites play a pivotal role in the processes during stress acclimation, therefore deciphering their relevant responses exchange the interpretation of the underlying molecular mechanisms that may contribute to improved adaptability and efficacy. In the current study, tomato plants were exposed to short-term cold stress (5 °C for 16 h) or inoculated (20 d) with either Cucumber Mosaic Virus (CMV) or Potato Virus Y (PVY). Responses were recorded via the assessments of leaf total phenolic (TP) content, total flavonoid (TF) levels, and phenylalanine ammonia-lyase (PAL) enzyme activity. The transcription of the gene families regulating the core phenylpropanoid biosynthetic pathway (PBP) at an early (PAL, cinnamic acid 4-hydroxylase, 4-coumarate-CoA ligase) or late (chalcone synthase and flavonol synthase) stage was also evaluated. The results showed that cold stress stimulated an increase in TP and TF contents, while PAL enzyme activity was also elevated compared to viral infection. Besides genes transcription of the enzymes involved in the core PBP was mostly induced by cold stress, whereas transcription of the genes regulating flavonoid biosynthesis was mainly triggered by viral infection. In conclusion, abiotic and biotic stressors induced differential regulation of the core PBP and flavonoid biosynthetic metabolism. Taking the above into consideration, our results highlight the complexity of tomato responses to diverse stimuli allowing for better elucidation of stress tolerance mechanisms at this crop.

The bacterial diversity in rhizosphere soil of pear trees (Pyrus communis L. cv. Krystalli) from an orchard at Thessaly region of Greece was characterized employing amplicon-based metagenomics analysis. Pathogenic filamentous oomycetes of the genus Phytophthora comprises more than 150 recognized species and cause highly destructive soil-borne diseases in deciduous trees crops worldwide. Moreover, the treatment of soil microbiota with amino acids is an alternative strategy to achieve desirable effects even against phytopathogenic oomycetes. In our study, samples from rhizosphere soil were collected either from naturally Phytophthora-infected trees, from completely asymptomatic ones, or from trees as above subjected also to treatments with amino acids (Amino16®) under different fertilization regimes. The interactions of bacterial communities with plant pathogenic oomycetes are crucial to determine the course of infection and the pathogenicity encompassing various functional contexts like biofilm formation. Thus, for deciphering the structure and diversity of these soil bacterial communities, we applied a 16S rRNA Illumina sequencing approach targeting the V3-V4 gene region. After quality check 478,479 sequences were obtained in the dataset comprising a total read length of 192,291,625 base pairs. Proteobacteria were the dominant phylum (46.1%) followed by Acidobacteria (13.2%) and Actinobacteria (12.4%). Different distributions of phyla were observed among our samples which is indicative of various alterations of soil bacterial communities in rhizosphere. The metagenome data from this survey are available at NCBI Sequence Read Archive (SRA) database and Biosample under accession number PRJNA542725. Keywords: Deep amplicon sequencing, Metagenomics, 16S bacteriome communities, Phytophthora, Oomycetes

A new molecular method via the high resolution melting (HRM) analysis of the Ypt1 gene non-coding regions was validated for ten Phytophthora species with a broad host range from forest trees to crop species. The melting curve analysis of the amplicons specifically grouped all species into 10 respective unique and distinct HRM curve profiles. The analysis of the normalised HRM melting curves, assigning P. nicotianae as a normalised reference genotype, revealed that the genotype similarities among all the species were adequately low, indicating that Ypt1 marker was sufficient to identify and differentiate the tested species. This HRM method is rapid and reproducible allowing the identification of Phytophthora species and the screening of eventual variants eliminating the separate steps and reducing the risk of contamination.

ABSTRACT: The phenotypic and genetic analysis of apple (Malus × domestica Borkh) genotypes is essential for breeding species. Information on the morphology and genetic structure of apple offers significant help for germplasm maintenance and selection of suitable material to breed superior cultivars. This study shows the results of an investigation on the morphology and the genetic diversity for 19 apple cultivars, which are preserved in an ex situ collection in Naoussa, Central Macedonia, Greece. Information was recorded over a 5-year period for 47 traits describing plant morphology and phenotype, as well as leaf and fruit quality. Data were analyzed using the principal component analysis (PCA) method. The Euclidean distance metric and the Ward’s agglomeration method were used in an unsupervised hierarchical cluster analysis of all cultivars. The cultivars were grouped into four main clusters, suggesting that the characterized apple collection has a high potential for specific breeding goals. Furthermore, the cultivars were genotyped using seven microsatellite primers. Moderate levels of polymorphism were detected, and 38 distinctive alleles (5.4 alleles per primer pair) were identified. Both multivariate clustering approach (phenotypic data) and the genetic distance clustering approach (genetic data) grouped the apple cultivars according to their type. Hence, these data could be used for protection or patenting processes of existing or new apple cultivars carried out by the EU-Community Plant Variety Office.