Insights into the Transcriptional Reprogramming of Peach Leaves Inoculated with Taphrina deformans.

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.

Comparative transcriptome profiling and co-expression network analysis uncover the key genes associated with pear petal defense responses against Monilinia laxa infection.

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.

Global Transcriptome Analysis of the Peach (Prunus persica) in the Interaction System of Fruit-Chitosan-Monilinia fructicola.

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.

Combined Transcriptomic and Metabolomic Analysis Reveals Insights into Resistance of Arabidopsis bam3 Mutant against the Phytopathogenic Fungus Fusarium oxysporum.

The wilt-inducing strains of Fusarium oxysporum are responsible for severe damage to many economically important plant species. The most cost-effective and environmentally safe method for the management of Fusarium wilt is the use of resistant cultivars when they are available. In the present study, the Arabidopsis genotype with disruptions in the ß-amylase 3 (BAM3) gene, which encodes the major hydrolytic enzyme that degrades starch to maltose, had significantly lower susceptibility to Fusarium oxysporum f. sp. raphani (For) compared to wild-type (wt) plants. It showed the lowest disease severity and contained reduced quantities of fungal DNA in the plant vascular tissues when analyzed with real-time PCR. Through metabolomic analysis using gas chromatography (GC)-mass spectrometry (MS) and gene-expression analysis by reverse-transcription quantitative PCR (RT-qPCR), we observed that defense responses of Arabidopsis bam3 mutants are associated with starch-degradation enzymes, the corresponding modification of the carbohydrate balance, and alterations in sugar (glucose, sucrose, trehalose, and myo-inositol) and auxin metabolism.

Grapevine wood microbiome analysis identifies key fungal pathogens and potential interactions with the bacterial community implicated in grapevine trunk disease appearance.

BACKGROUND: Grapevine trunk diseases (GTDs) is a disease complex caused by wood pathogenic fungi belonging to genera like Phaeomoniella, Phaeoacremonium, Fomitiporia, Eutypa and members of the family Botryosphaeriaceae. However, the co-occurrence of these fungi in symptomatic and asymptomatic vines at equivalent abundances has questioned their role in GTDs. Hence, we still lack a good understanding of the fungi involved in GTDs, their interactions and the factors controlling their assemblage in vines. We determined the fungal and bacterial microbiome in wood tissues of asymptomatic and symptomatic vines of three main Greek cultivars (Agiorgitiko, Xinomavro, Vidiano), each cultivated in geographically distinct viticultural zones, using amplicon sequencing. RESULTS: We noted that cultivar/biogeography (lumped factor) was the strongest determinant of the wood fungal microbiome (p < 0.001, 22.7%), while GTD symptoms condition had a weaker but still significant effect (p < 0.001, 3.5%), being prominent only in the cultivar Xinomavro. Several fungal Amplicon Sequence Variants (ASVs), reported as GTD-associated pathogens like Kalmusia variispora, Fomitiporia spp., and Phaemoniella chlamydosporα (most dominant in our study), were positively correlated with symptomatic vines in a cultivar/viticultural zone dependent manner. Random Forest analysis pointed to P. chlamydosporα, K. variispora, A. alternata and Cladosporium sp., as highly accurate predictors of symptomatic vines (0% error rate). The wood bacterial microbiome showed similar patterns, with biogeography/cultivar being the main determinant (p < 0.001, 25.5%) of its composition, followed by the GTD status of vines (p < 0.001, 5.2%). Differential abundance analysis revealed a universal positive correlation (p < 0.001) of Bacillus and Streptomyces ASVs with asymptomatic vines. Network analysis identified a significant negative co-occurrence network between these bacterial genera and Phaemoniella, Phaeoacrominum and Seimatosporium. These results point to a plant beneficial interaction between Bacillus/Streptomyces and GTD pathogens. CONCLUSIONS: Our study (a) provides evidence that GTD symptomatic plants support a wood fungal microbiome, showing cultivar and biogeography-dependent patterns, that could be used as a proxy to distinguish between healthy and diseased vines, (b) points to strong interactions between the bacterial and fungal wood microbiome in asymptomatic vines that should be further pursued in the quest for discovery of novel biocontrol agents.

Disruption and Overexpression of the Gene Encoding ACC (1-Aminocyclopropane-1-Carboxylic Acid) Deaminase in Soil-Borne Fungal Pathogen Verticillium dahliae Revealed the Role of ACC as a Potential Regulator of Virulence and Plant Defense.

It has been suggested that some microorganisms, including plant growth-promoting rhizobacteria, manipulate the level of ethylene in plants by degrading 1-aminocyclopropane-1-carboxylic acid (ACC), an ethylene precursor, into α-ketobutyrate and ammonia, using ACC deaminase (ACCd). Here, we investigated whether ACCd of Verticillium dahliae, a soil-borne fungal pathogen of many important crops, is involved in causing vascular wilt disease. Overexpression of the V. dahliae gene encoding this enzyme, labeled as ACCd, significantly increased virulence in both tomato and eggplant, while disruption of ACCd reduced virulence. Both types of mutant produced more ethylene than a wild-type (70V-WT) strain, although they significantly differed in ACC content. Overexpression strains lowered ACC levels in the roots of infected plants, while the amount of ACC in the roots of plants infected with deletion mutants increased. To test the hypothesis that ACC acts as a signal for controlling defense, roots of WT and Never-ripe (Nr) tomato plants were treated with ACC before V. dahliae inoculation. Plants pretreated with ACC displayed less severe symptoms than untreated controls. Collectively, our results suggest a novel role of ACC as a regulator of both plant defense and pathogen virulence.

The Innate Immune Signaling System as a Regulator of Disease Resistance and Induced Systemic Resistance Activity Against Verticillium dahliae.

In the last decades, the plant innate immune responses against pathogens have been extensively studied, while biocontrol interactions between soilborne fungal pathogens and their hosts have received much less attention. Treatment of Arabidopsis thaliana with the nonpathogenic bacterium Paenibacillus alvei K165 was shown previously to protect against Verticillium dahliae by triggering induced systemic resistance (ISR). In the present study, we evaluated the involvement of the innate immune response in the K165-mediated protection of Arabidopsis against V. dahliae. Tests with Arabidopsis mutants impaired in several regulators of the early steps of the innate immune responses, including fls2, efr-1, bak1-4, mpk3, mpk6, wrky22, and wrky29 showed that FLS2 and WRKY22 have a central role in the K165-triggered ISR, while EFR1, MPK3, and MPK6 are possible susceptibility factors for V. dahliae and bak1 shows a tolerance phenomenon. The resistance induced by strain K165 is dependent on both salicylate and jasmonate-dependent defense pathways, as evidenced by an increased transient accumulation of PR1 and PDF1.2 transcripts in the aerial parts of infected plants treated with strain K165.

Successful Agrobacterium mediated transformation of Thielaviopsis basicola by optimizing multiple conditions.

Thielaviopsis basicola is a hemibiotrophic root pathogen causing black root rot in a wide range of economically important crops. Our initial attempts to transform T. basicola using standard Agrobacterium tumefaciens-mediated transformation (ATMT) protocols were unsuccessful. Successful transformation required the addition of V8 juice (to induce germination of T. basicola chlamydospores) and higher concentrations of acetosyringone in the co-cultivation medium, and of chlamydospores/endoconidia, A. tumefaciens cells during co-cultivation. With these modifications, two T. basicola strains were successfully transformed with the green (egfp) or red (AsRed) fluorescent protein genes. Chlamydospores/endoconidia transformed with the egfp gene exhibited strong green fluorescence, but their fluorescence became weaker as the germ tubes emerged. Transformants harbouring the AsRed gene displayed strong red fluorescence in both chlamydospores/endoconidia and germ tubes. Fluorescent microscopic observations of an AsRed-labelled strain colonizing roots of transgenic Nicotiana benthamiana plants, which express the actin filaments labelled with EGFP, at 24 hours post inoculation showed varying levels of fungal germination and penetration. At this stage, the infection appeared to be biotrophic with the EGFP-labelled host actin filaments not being visibly degraded, even in host root cells in close contact with the hyphae. This is the first report of ATMT of T. basicola, and the use of an AsRed-labelled strain to directly observe the root infection process.

The G protein ß subunit controls virulence and multiple growth- and development-related traits in Verticillium dahliae.

To gain insight into the role of G protein-mediated signaling in virulence and development of the soilborne, wilt causing fungus Verticillium dahliae, the G protein ß subunit gene (named as VGB) was disrupted in tomato race 1 strain of V. dahliae. A resulting mutant strain, 70ΔGb15, displayed drastic reduction in virulence, increased microsclerotia formation and conidiation, and decreased ethylene production compared to the corresponding wild type (wt) strain 70wt-r1. Moreover, 70ΔGb15 exhibited an elongated rather than radial growth pattern on agar media. A transformant of 70ΔGb15 (named as 70ΔGbPKAC1) that carries an extra copy of VdPKAC1, a V. dahliae gene encoding the catalytic subunit of the cAMP-dependent protein kinase A, exhibited wt growth pattern and conidiation, was unable to form microsclerotia, produced high amounts of ethylene, and exhibited virulence between that of 70ΔGb15 and 70wt-r1 on tomato plants. Phenotypical changes observed in 70ΔGb15 and 70ΔGbPKAC1 correlated with transcriptional changes in several genes involved in signaling (MAP kinase VMK1) and development (hydrophobin VDH1 and ACC synthase ACS1) of V. dahliae. Results from the present work suggest a linkage between VGB and VdPKAC1 signaling pathways in regulating virulence, hormone production and development in V. dahliae.

VdSNF1, the sucrose nonfermenting protein kinase gene of Verticillium dahliae, is required for virulence and expression of genes involved in cell-wall degradation.

Verticillium dahliae is a soilborne fungus causing vascular wilt in a diverse array of plant species. Its virulence has been attributed, among other factors, to the activity of hydrolytic cell wall-degrading enzymes (CWDE). The sucrose nonfermenting 1 gene (VdSNF1), which regulates catabolic repression, was disrupted in V. dahliae tomato race 1. Expression of CWDE in the resulting mutants was not induced in inductive medium and in simulated xylem fluid medium. Growth of the mutants was significantly reduced when grown with pectin or galactose as a carbon source whereas, with glucose, sucrose, and xylose, they grew similarly to wild-type and ectopic transformants. The mutants were severely impaired in virulence on tomato and eggplant (final disease severity reduced by an average of 87%). Microscopic observation of the infection behavior of a green fluorescent protein (gfp)-labeled VdSNF1 mutant (70ΔSF-gfp1) showed that it was defective in initial colonization of roots. Cross sections of tomato stem at the cotyledonary level showed that 70ΔSF-gfp1 colonized xylem vessels considerably less than the wild-type strain. The wild-type strain heavily colonized xylem vessels and adjacent parenchyma cells. Quantification of fungal biomass in plant tissues further confirmed reduced colonization of roots, stems, and cotyledons by 70ΔSF-gfp1 relative to that by the wild-type strain.

Ethylene perception via ETR1 is required in Arabidopsis infection by Verticillium dahliae.

Vascular wilts caused by Verticillium spp. are very difficult to control and, as a result, are the cause of severe yield losses in a wide range of economically important crops. The responses of Arabidopsis thaliana mutant plants impaired in known pathogen response pathways were used to explore the components in defence against Verticillium dahliae. Analysis of the mutant responses revealed enhanced resistance in etr1-1[ethylene (ET) receptor mutant] plants, but not in salicylic acid-, jasmonic acid- or other ET-deficient mutants, indicating a crucial role of ETR1 in defence against this pathogen. Quantitative polymerase chain reaction analysis revealed that the decrease in symptom severity shown in etr1-1 plants was associated with significant reductions in the growth of the pathogen in the vascular tissues of the plants, suggesting that impaired perception of ET via ETR1 results in increased disease resistance. Furthermore, the activation and increased accumulation of the PR-1, PR-2, PR-5, GSTF12, GSTU16, CHI-1, CHI-2 and Myb75 genes, observed in etr1-1 plants after V. dahliae inoculation, indicate that the outcome of the induced defence response of etr1-1 plants seems to be dependent on a set of defence genes activated on pathogen attack.

Roles of the catalytic subunit of cAMP-dependent protein kinase A in virulence and development of the soilborne plant pathogen Verticillium dahliae.

Verticillium dahliae is a soilborne fungus that causes vascular wilt disease in a broad range of hosts and survives for many years in the soil in the form of microsclerotia. Although the role of cAMP-dependent protein kinase A (PKA) has been extensively studied in foliar pathogens, there is limited information about its role in soilborne fungal pathogens that infect through the root system. Genome database search revealed the presence of two PKA catalytic subunit genes in V. dahliae, named VdPKAC1 and VdPKAC2. A phylogenetic analysis showed that VdPKAC2 groups with fungal PKA catalytic subunits that appear to play a minor role in PKA activity. This gene was expressed considerably lower than that of VdPKAC1. Although disruption of VdPKAC1 did not affect the ability of V. dahliae to infect through the roots of tomato and eggplant, disease severity was significantly reduced. Since pathogen-derived ethylene is presumed to play a major role in symptom induction in vascular wilt diseases, ethylene generation was measured in fungal culture. The mutants defective in VdPKAC1 produced less ethylene than the corresponding wild type strains, suggesting a regulatory role of PKA in ethylene biosynthesis. Growth rates of these mutants were similar to those of wild type strains, while the rate of spore germination was slightly elevated and conidia production was significantly reduced. When grown on minimal media, the mutants showed greater microsclerotia production compared with the wild type strains. These results suggest multiple roles of VdPKAC1, including virulence, conidiation, microsclerotia formation, and ethylene biosynthesis, in the soilborne fungus V. dahliae.

Phenolic Responses of Resistant and Susceptible Olive Cultivars Induced by Defoliating and Nondefoliating Verticillium dahliae Pathotypes.

Verticillium wilt is the most serious olive disease worldwide. The olive-infecting Verticillium dahliae pathotypes have been classified as defoliating (D) and nondefoliating (ND), and the disease is mainly controlled in olive orchards by using resistant or tolerant cultivars. Limited information is available about the nature of resistance in most of the olive cultivars. In the present study, the phenolic responses of the susceptible to V. dahliae olive cv. Amfissis and the resistant cv. Koroneiki upon D and ND V. dahliae infection were monitored in relation to the fungal DNA levels in the vascular tissues with the purpose to explore the defense mechanisms of olive trees against V. dahliae. Quantitative polymerase chain reaction revealed that the decrease in symptom severity shown in Koroneiki trees was associated with significant reduction in the growth of both V. dahliae pathotypes in the vascular tissues compared with Amfissis. In Koroneiki trees, the levels of o-diphenols and verbascoside were positively associated with the DNA levels of the D and ND pathotypes. In addition, a positive association was observed between the levels of verbascoside and the fungal DNA level in Amfissis trees, whereas a negative association was revealed between the fungal DNA level and the total phenols and oleuropein content in both cultivars. The levels of verbascoside were clearly higher in Koroneiki trees compared with Amfissis trees, indicating for the first time in the literature the involvement of verbascoside in the defense mechanism of olive trees against V. dahliae.

Induction of resistance to Verticillium dahliae in Arabidopsis thaliana by the biocontrol agent K-165 and pathogenesis-related proteins gene expression.

The biocontrol bacterium Paenibacillus alvei K165 has the ability to protect Arabidopsis thaliana against Verticillium dahliae. A direct antagonistic action of strain K165 against V. dahliae was ruled out, making it likely that K165-mediated protection results from induced systemic resistance (ISR) in the host. K165-mediated protection was tested in various Arabidopsis mutants and transgenic plants impaired in defense signaling pathways, including NahG (transgenic line degrading salicylic acid [SA]), etr1-1 (insensitive to ethylene), jar1-1 (insensitive to jasmonate), npr1-1 (nonexpressing NPR1 protein), pad3-1 (phytoalexin deficient), pad4-1 (phytoalexin deficient), eds5/sid1 (enhanced disease susceptibility), and sid2 (SA-induction deficient). ISR was blocked in Arabidopsis mutants npr1-1, eds5/sid1, and sid2, indicating that components of the pathway from isochorismate and a functional NPR1 play a crucial role in the K165-mediated ISR. Furthermore, the concomitant activation and increased transient accumulation of the PR-1, PR-2, and PR-5 genes were observed in the treatment in which both the inducing bacterial strain and the challenging pathogen were present in the rhizosphere of the A. thaliana plants.

Molecular characterization and biological response to respiration inhibitors of Pyricularia isolates from ctenanthe and rice plants.

The molecular profile and the biological response of isolates of Pyricularia oryzae Cavara obtained from ctenanthe to two strobilurins (azoxystrobin, kresoxim-methyl) and the phenylpyridinamine fungicide fluazinam were characterized, and compared with isolates from rice plants. Five different isozymes (alpha-esterase, lactate, malate, isocitrate and sorbitol dehydrogenases) and five random decamer primers for RAPD-PCR were used to generate molecular markers. Using unweighted pair-group with arithmetic average analysis, ctenanthe isolates were found to form a separate group distinct from that of the rice isolates for both sets of markers. Amplified polymorphic sequences of mitochondrial cytochrome b that were digested with Fnu4HI or StyI revealed no differences among Pyricularia isolates at amino acid positions 143 or 129 which confer resistance to strobilurins in several fungi. In absence of the alternative respiration inhibitor salicylhydroxamic acid (SHAM) the three fungicides showed inferior and variable efficacy, with a trend toward the rice isolate being less sensitive. The addition of SHAM enhanced the effectiveness of all fungicides against isolates regardless of their origin. Appressorium formation was the most vulnerable target of action of the respiration inhibitors and azoxystrobin the most effective. This is the first report of a comparison between the molecular profiles and sensitivities to respiration inhibitors for Pyricularia oryzae isolates from a non-gramineous host and from rice.

Pyricularia Leaf Spot: A New Disease of Ornamental Plants of the Family Marantaceae.

A severe leaf spot disease incited by the fungus Pyricularia oryzae was identified on Ctenanthe oppenheimiana and C. setosa "Greystar." Primary symptoms on young leaves consisted of individual circular to slightly irregular pinpoint spots with white necrotic centers zonated by narrow brown-yellow halos. On mature leaves, extended necrotic areas resembling those caused by phytotoxicity were formed. Artificially inoculated leaves with a spore suspension of the isolated fungus from the above case showed symptoms after 3 to 4 days' incubation at 25°C and high humidity. Fungal isolates obtained from Ctenanthe plants of Brazilian origin were found to be highly pathogenic on various plants within the family Marantaceae when they were tested by an excised leaf assay method. By contrast, P. oryzae isolates obtained from rice plants grown in Greece caused either hypersensitivity or immune response symptoms in various Marantaceae. Analysis of esterase and lactate dehydrogenase isozymes showed different banding patterns for rice and Ctenanthe isolates of P. oryzae. Conditions of prolonged leaf wetness combined with prevailing high temperature and humidity favored the epidemic appearance of the Pyricularia leaf spot disease on glasshouse-grown plants during the summer months of 1995 in Greece.