Poplar Cytospora canker, caused by , is one of the most destructive and widespread poplar diseases worldwide, especially in northern China. However, our current understanding of its pathogenic mechanisms remains limited. Here, we showed that trehalose biosynthetic genes, such as trehalose-6-phosphate synthase 1 (Tps1), trehalose-6-phosphate phosphatase (Tps2), and the regulatory subunit (Tps3), play important roles in the development and virulence of . The targeted deletion mutants showed reduced trehalose synthesis and were defective in hyphal growth and conidiation. Deletion of any of the three genes attenuated virulence in poplar twigs and stronger poplar defense responses were triggered once inoculated by the mutants. Additionally, the mutants exhibited increased sensitivity to HO and cell wall stressors. Taken together, the finding suggests that trehalose biosynthetic genes contribute to fungal development, stress responses, and full virulence in .

4'-Phosphopantetheinyl transferases (PPTases) play important roles in the posttranslational modifications of bacterial carrier proteins, which are involved in various metabolic pathways. Here, we found that and encoded a functional AcpS-type and Sfp-type PPTase, respectively, in GMI1000, and both are capable of modifying AcpP1, AcpP2, AcpP3, and AcpP5 proteins. is located on the megaplasmid, which does not affect strain growth and fatty acid synthesis but significantly contributes to the virulence of and preferentially participates in secondary metabolism. We found that deletion of did not affect the abilities of cellulose degradation, biofilm formation, and resistance to NaCl, sodium dodecyl sulfate, and HO and attenuated pathogenicity only in the assay of soil-drenching infection but not stem injection of tomato. It is hypothesized that RsPcpS plays a role in cell viability in complex environments and in the process during which the strain recognizes and approaches plants. These results suggest that both RsAcpS and RsPcpS may be potential targets for controlling diseases caused by .

The development of novel improved varieties adapted to unstable environmental conditions is possible through the genetic diversity of breeding materials. Potato is among the most important food crops worldwide, however, there are still significant hindrances to breeding gains attributed to its autotetraploid and highly heterozygous genome. Bacterial wilt caused by the species complex (RSSC) is an important disease affecting potato among many economically important crops worldwide. No cultivated potato genotypes have shown a satisfactory level of resistance to bacterial wilt. Nevertheless, resistance can play a crucial role in effective integrated disease management. To understand the genetic landscape of bacterial wilt resistance in cultivated potato, we evaluated the diversity of 194 accessions from the International Potato Centre (CIP) using 9,250 single nucleotide polymorphisms (SNPs) and their associations to the response to bacterial wilt disease evaluated over two independent trials. Twenty-four accessions showed high resistance throughout both trials. Genetic diversity analysis revealed three major clusters whose subgroups were mostly represented by CIP clones derived from common parents. Genome-wide association analyses have shown six major hits: two on chromosome 8, and one on each chromosome 2, 4, 5, and 9. These results facilitate genetic dissection of bacterial wilt resistance and marker-enabled breeding in elite genotypes for potato breeding initiatives.

Clubroot disease caused by the biotrophic pathogen , is one of the most serious threats to cruciferous crops production worldwide. is known for rapid adaptive evolution to overcome resistance in varieties. It is urgent to establish alternative management to control . In this study, we identified two secretory proteins that were up-regulated during infection and effected plant defense. We established a method for transient expression in the roots of seedlings and demonstrated that could take up substances from the environment of root cells. Using a RNA interference (RNAi)-based host-induced gene silencing (HIGS) by expression of hairpin RNAi constructs with sequence homology to effector or in susceptible plants enhanced host disease resistance. After silencing these two effectors, the transcription levels of cytokinin biosynthesis gene and the regulation gene of auxin homeostasis were down-regulated. These results suggested that RNAi-based HIGS of effectors has a great practical application of improving crop resistance against and can contribute to environmentally sustainable agriculture.

Charcoal rot, caused by the soilborne fungus (Mp) poses a serious threat to soybean health and harvests at a global scale. Mp exhibits varying distribution patterns across fields, which complicates our ability to predict disease occurrences and outbreaks. Therefore, determining the spatial distribution of Mp abundance and its relation with soil physicochemical properties would help to inform precision management decisions for mitigating charcoal rot. To achieve this, Mp colony forming units (CFU) and edaphic properties were evaluated in 297 soybean fields located in the main soybean growing regions across 7 Departments of Paraguay. A pattern of decreasing CFU density was observed from the south-eastern to the western part of the country. While several edaphic factors are positively correlated with Mp CFU, pH showed a significant negative correlation with CFU. Both spatial and non-spatial model suggest that cation exchange capacity, percentage of clay, and pH could be potential predictors of Mp CFU abundance. Including spatial dependence of edaphic factors improved the prediction of Mp CFU more effectively than classical statistical models. We demonstrated that the occurrence of Mp shows a significant spatial clustering pattern as indicated by Moran's I. Our findings will help growers and policy-makers make informed decisions for managing Mp by improving our ability to predict which agricultural fields and soils are at greatest risk for charcoal rot.

In several plant species, thiamin foliar application primes plant immunity and can be effective in controlling various diseases. However, the effectiveness of thiamin against potato pathogens has seldom been investigated. Additionally, the transcriptomics and metabolomics of immune priming by thiamin have not previously been investigated. Here, we tested the effect of thiamin application against , the causal agent of early blight in potato, and identified associated changes in gene expression and metabolite content. Thiamin applied on foliage at an optimal concentration of 10 mM reduced lesion size by ~33%. However, prevention of lesion growth was temporally limited, as a reduction of lesion size occurred when leaves were inoculated 4 h, but not 24 h, following thiamin treatment. Additionally, the effect of thiamin on lesion size was restricted to the application site and was not systemic. RNA-seq analysis showed that thiamin affected the expression of 308 genes involved in the synthesis of salicylic acid, secondary metabolites, fatty acid, chitin, and primary metabolism, and photosynthesis, which were also amongst the thousands of genes differentially regulated in the response to pathogen alone. Several of these genes and pathways were more differentially expressed and enriched when thiamin and the pathogen were combined. Thiamin also delayed the downregulation of photosynthesis-associated genes in plants inoculated with . Metabolite analyses revealed that thiamin treatment in the absence of pathogen decreased the amounts of several organic compounds involved in the citric acid cycle. We hypothesize that thiamin primes plant defenses through perturbation of primary metabolism.

Bacterial blight (BB) caused by pv. is one of the epidemic diseases in rice. Rapid changes in the pathogenicity of the pv. pathogen demand the identification and characterization of novel BB resistance genes. Here, we report the transfer and mapping of a new BB resistance gene from acc. CR100098A. Inheritance studies on the BCF population, BCF progenies, and backcross-derived recombinant inbred lines derived from a cross between Pusa44/ acc. CR100098A//2PR114 showed that a single recessive gene confers resistance in acc. CR100098A. Bulked segregant analysis using 203 simple sequence repeat (SSR) markers localized the BB resistance gene on chromosome 11 bracketed between two SSR markers, RM27235 and RM2136. Using PR114 and acc. CR100098A genotyping by sequencing data, 86 KASP markers within the bracketed region were designed and tested for bulked segregant analysis. Only five KASP markers showed polymorphism between parents, and three were associated with the target gene. Seventy-seven new SSR markers were designed from the same interval. A total of 33 polymorphic markers were analyzed on the whole population and mapped the BB gene in an interval of 2.8 cM flanked by SSR markers PAU11_65 and PAU11_44 within a physical distance of 376.3 kb. The BB resistance gene mapped in this study is putatively new and designated as . Fourteen putative candidate genes were identified within the region having a role in biotic stress resistance. The linked markers to the gene were validated in other rice cultivars for its successful deployment in BB resistance breeding.

We report high-quality genomes of three strains of pv. (), the causal agent of mango bacterial canker disease, including the pathotype strain of this pathovar and two strains from Burkina Faso that emerged a decade ago. These strains hosted two to three plasmids of sizes ranging from 19 to 86 kb. Genome mining revealed the presence of several secretion systems (SS) and effectors involved in virulence of xanthomonads with (i) a T1SS of the hlyDB group, (ii) xps and xcs T2SSs, (iii) a T3SS with several type three effectors (T3E), including transcription activator-like effectors (TALE), (iv) several T4SSs associated with plasmid or integrative conjugative elements (ICE) mobility, (v) three T5SS subclasses (Va, Vb and Vc) and (vi) a single i3* T6SS. The two strains isolated in Burkina Faso from mango ( L.) and cashew ( L.) differed by only 14 SNPs and shared identical secretion systems and T3E repertoire. Several TALEs were identified in each strain, some of which may target plant genes previously found implicated in disease development in other xanthomonad-associated pathosystems. These results support the emergence in Burkina Faso a decade ago of very closely related strains that became epidemic on mango and cashew, i.e., two distinct host genera of a same plant family. These new genomic resources will contribute to better understand the biology and evolution of this agriculturally major crop pathogen.

Apple replant disease (ARD) is a serious soilborne disease in apple nurseries and orchards worldwide. ARD is the result of an unbalanced soil microbiome in which multiple soil-borne plant pathogenic fungi, oomycetes and nematodes form a disease complex. Biphenyl and dibenzofuran phytoalexins are found in greater quantities in the roots of apple plants grown in ARD soil compared to disinfected ARD soil. However, the contribution of these compounds to plant health or disease is not yet understood. Here, the antimicrobial activity of fourteen chemically synthesized biphenyl and dibenzofuran phytoalexins was tested against eight selected microorganisms isolated from either rhizosphere soils or apple roots. These included five potentially beneficial bacteria ( strain R79, strain R85, strain ES16, GS2, strain B1), two ARD fungal pathogens ( H131 and N3) and one oomycete (). Two phytoalexin mixtures reflecting the percentages of the individual compounds inside the roots (Mixture A) and the root exudate (Mixture B) were also tested. The two phytoalexin mixtures demonstrated a higher antimicrobial activity than the individual phytoalexins, suggesting a synergistic effect. The minimum inhibitory concentration (MIC) and the half maximal effective concentration (EC) values determined to be active against the eight microbes were within a range of 2.5-fold the ecologically relevant phytoalexin concentration (approximately 33 and 24 µg ml in roots and exudates, respectively). The results contribute to our understanding of the impact of apple root phytoalexins on ARD and suggest potential strategies for disease management.

Rapid, field-deployable assays such as loop-mediated isothermal amplification (LAMP) are critical for detecting nursery and forest pathogens like and to prevent pathogen spread. We developed and validated four LAMP assays for genus-level detection of spp., species-level detection of and and lineage-level detection of the NA1 lineage. Cross reactivity of the two species-specific LAMP assays was evaluated using a set of 18 spp. known to infect nursery crop hosts. The correct target species were detected by the species-level LAMP assays. The spp. LAMP assay was evaluated against 27 spp. and other bacterial and fungal pathogens and reacted with all the spp. evaluated but no other bacterial or fungal species. The limit of detection (LOD) of the LAMP was 100 fg/µl and the LOD of the LAMP assay was 1 pg/µl of DNA. The NA1 LAMP assay was tested against the NA1, NA2, EU1, and EU2 lineages of and was lineage-specific but had a higher LOD (100pg/µl) than the species-specific LAMP assays. Both and LAMP assays were highly precise (>0.94) in detecting the respective pathogens in symptomatic rhododendron leaves and co-inoculation experiments. The set of four LAMP assays were run in tandem on a microfluidic chip and smartphone platform and can be used in the field to detect and monitor spread of these regulatory spp. in forest and/or nursery settings.

Due to a lack of understanding of the disease epidemiology and comprehensive control measures, tea leaf spot caused by has a significant negative impact on tea yield and quality in the tea plantations of Southwest China. Phenazine-1-carboxamide (PCN) is a phenazine compound derived from species, which exhibits antimicrobial activity against various pathogens. However, its inhibitory mechanism is not yet clear. The current study evaluated the inhibitory activity of PCN against various phytopathogenic fungi and found that PCN has inhibitory activity against multiple pathogens, with a half-maximal effective concentration (EC) value for of 16.11 μg/mL in vitro and a maximum in-vivo curative activity of 72.28% toward tea leaf spot. Morphological changes in the hyphae after exposure to PCN were observed through microstructure and ultrastructure analysis, and indicated that PCN causes abnormalities in the hyphae, such as cytoplasmic coagulation, shortened hyphal inter-septum distances, and unclear boundaries of organelles. Transcriptomic analysis revealed that PCN upregulated the expression of genes related with energy metabolism. PCN significantly reduced the ATP concentration in the hyphae and decreased mitochondrial membrane potential. Molecular docking analysis indicated that PCN binds to one of the candidate target proteins, pyruvate dehydrogenase, with lower free energy of -10.7 kcal/mol. This study indicated that PCN can interfere with energy metabolism, reducing ATP generation, ultimately affecting hyphal growth. Overall, PCN shows potential for future application in the control of tea leaf spot due to its excellent antifungal activity and unique mode of action.

The development of xylem embolism in 1-year-old stems of Japanese black pine () seedlings was monitored by compact magnetic resonance imaging (MRI) after inoculation with the pinewood nematode (). In parallel, the nematode distribution and population structure in the stems were examined by isolating the nematodes using the Baermann funnel technique. The vertical length and volume of massive embolisms in each seedling were strongly correlated with the maximum relative embolized area (REA) in stem cross-sections. Embolism development and nematode reproduction were not restricted to the inoculation site, as any portion of the stem could be the initial point of a population burst. The nematode population in the stem xylem was strongly correlated with the REA and with the circumferential proportion of cambial death in cross-sections monitored by MRI. The proportion of second-stage juveniles was also correlated with the REA in the xylem. In contrast, the nematode population in bark tissue was not correlated with either the REA or cambial death. These results suggested that nematode reproduction in the cambial zone is the key step in pine wilt disease, and second-stage juveniles were suggested to induce massive embolisms in the advanced stage of the disease.

Tea leaf spot caused by is a newly discovered fungal disease in southwest China. Due to a lack of knowledge of its epidemiology and control strategies, the disease has a marked impact on tea yield and quality. Pyriofenone is a new fungicide belonging to the aryl phenyl ketone fungicide group, which has shown marked efficacy in controlling various fungal diseases. However, its mechanism of action is not yet understood. This study found that pyriofenone exhibits strong in vitro inhibitory activity against various phytopathogenic fungi. Specifically, it showed strong inhibitory activity against , with a half-maximal effective concentration (EC) value of 0.428 μg/ml determined by measuring mycelial growth rate. Morphological observations, using optical, scanning electron, and transmission electron microscopy, revealed that pyriofenone induces morphological abnormalities in hyphae. At lower doses, the hyphae became swollen, the distance between septa decreased, and the hyphal growth rate slowed. At higher doses and longer exposures, the hyphae collapsed. Transcriptomic and bioinformatic analyses indicated that pyriofenone can affect the expression of genes related to membrane transporters. Homology modeling suggested that pyriofenone may bind to a candidate target protein of the major facilitator superfamily (MFS) transporter, with a free binding energy of -7.1 kcal/mol. This study suggests that pyriofenone may potentially regulate the transport of metabolites in , thus affecting hyphal metabolism and interfering with hyphal growth. Pyriofenone exhibits in vitro inhibitory activity against various tea foliar pathogens and holds promise for future applications to the control of tea foliar diseases.

A major resistance gene of the melon accession PI414723 to zucchini yellow mosaic virus (ZYMV) is located at the locus on chromosome 2, but the underlying defense mechanisms are poorly understood. The physiological responses and expression of selected genes at were assessed in PI414723 and in the susceptible genotype Védrantais. Viral titers and the expression of genes related to systemic acquired resistance (SAR) were evaluated in inoculated (Inoc) and non-inoculated (Non-Inoc) portions of the cotyledons at 3, 7 and 10 days after inoculation (dai) and in apical leaves at 10 dai. ZYMV was detected in both portions of the cotyledons but not in the apical leaves of PI414723 plants. Also, ZYMV was recovered in a susceptible zucchini only from Inoc portions at 3 dai. By contrast, in Védrantais ZYMV was detected and recovered from all tissues at high concentrations. Starchy local lesions and accumulation of transcripts of the SAR marker genes PR1 and PR4 were also detected in the resistant genotype. Plus, transcripts of one candidate resistance gene analog previously located at and of two melon homologs of restricted tobacco etch virus movement 2 (RTM2) genes located close to , accumulated only in PI414723. It is proposed that resistance results from the combined action of the R gene, involved in restricting ZYMV replication after a supposed recognition event and of the RTM genes which impact viral systemic movement to distal apical tissues.

f. sp. (FOV) is a significant cotton ( spp.) pathogen causing vascular wilt, browning of the vascular tissues, and plant death in the most severe cases. This global disease is responsible for sizeable crop losses annually and is found in many cotton producing regions, including the Republic of Uzbekistan and the USA. Specifically, FOV race 4 (FOV4) has been disrupting production for years. This study aimed to genetically characterize FOV4 isolates causing disease in the main cotton producing region of Uzbekistan and compare with FOV4 isolates from the USA. A field study conducted in the Bukhara region of the Republic of Uzbekistan in the spring of 2022 identified both FOV4 and new isolates from Upland cotton exhibiting typical Fusarium wilt symptoms. Molecular markers were initially used to identify isolates of interest, and a phylogenetic analysis was performed using partial -α sequences, followed by a comparative genomic analysis. We also report for the first time the isolation of and causing Fusarium wilt in Uzbekistan. Furthermore, we show that the FOV4 population within our sampling region of Uzbekistan may be dominated by a single biotype with an effector profile similar to that of FOV race 7 (FOV7). One of these effector proteins is also present in the isolate showing virulence to cotton. Whole genome comparisons between FOV races can identify unique genetic markers for FOV4 and aid in the development of tools for breeding FOV resistant cotton varieties.

is a plant family that includes several species of interest in the food, medicinal, and ornamental industries. The most relevant species are the purple and yellow varieties of , which are among the most highly prized tropical fruits in the international markets. Unfortunately, the rapid expansion of this crop worldwide has resulted in the emergence of several viral diseases that endangered the productivity of this crop. In this work, we performed an integrated analysis of the virome using public data. We investigated Pubmed and Genbank records and analyzed all the transcriptome data available for members of this plant family. This analysis resulted in the identification of six novel virus associations and six putative new viral species. We also used RNAseq to inspect virus accumulation levels and mixed infections. Using network analysis, we also examined the global distribution of Passiflora viruses and their associations with alternative hosts, which is valuable information in implementing viral disease management strategies. Our data suggest that a large diversity of viruses remains to be discovered. Finally, we used the information gathered in this work to estimate the cross-transmission risk of viruses in Colombian Passiflora fields.

Understanding the ecology of pathogens is important for disease management. Recently a devastating canker disease was found on red alder () planted as landscape trees. Bacteria were isolated from two groups of symptomatic trees located approximately 1 kilometer apart and one strain from each group was used to complete Koch's postulates. Results showed that these bacteria can not only cause disease on red alder but also on two other alder species. Unexpectedly, analyses of genome sequences of bacterial strains identified them as , a pathogenic species previously known to cause dieback of oak species, but not alder. Additionally, a core genome phylogeny clustered bacterial strains isolated from red alder within a subclade of strains isolated from symptomatic oak trees. Consistent with the close phylogenetic relationship, there was no obvious evidence for divergence in genome composition of strains isolated from red alder and oak. Altogether, findings indicate that is a potential threat to species.

is a major postharvest pathogen of apples, causing loss in fruits through tissue damage, as well as in apple products due to contamination with the mycotoxin patulin. During infections, patulin is a cultivar-dependent virulence factor that facilitates apple lesion development. Patulin also has characterized antimicrobial activity and is important for inhibiting other competitive phytopathogens, but the role of this inhibitory activity has not been investigated in the context of the apple microbiome. In our current study, we isolated 68 apple microbiota and characterized their susceptibility to extracts. We found Gram-negative bacteria and Basidiomycete yeast to demonstrate largely patulin-specific growth inhibition compared to Gram-positive and Ascomycete isolates. From co-cultures, we identified a and pairing that reduced biomass and found that alone is sufficient to reduce apple disease progression in vivo. We investigated possible mechanisms of biocontrol activity and found modest inhibition on apple puree plates, as well as a trend toward lower patulin levels at the wound site. Active biocontrol activity required live yeast, which also were effective in controlling apple infections. Lastly, we explored the breadth of biocontrol activity with over 30 isolates and found consistent inhibition of apple disease.

f. sp. (FOLac) is a soil- and seedborne fungal pathogen that causes Fusarium wilt of lettuce, an important disease threatening global lettuce production. Based on pathogenicity on differential lettuce cultivars, four races (1-4) have been identified, with race 1 the only race detected in the United States, and the closely related, emerging race 4 known only in Europe. The development of race-specific diagnostic tools is hindered by insufficient genomic data to distinguish between the two races and FOLac from other and nonpathogenic isolates. Here, we describe a systematic approach for developing diagnostic markers for FOLac race 1 that utilized a comprehensive sequence database of to identify 15 unique genomic sequences. Marker specificity was validated through an exhaustive screening process against genomic data from 797 isolates representing 64 and various plants and non-plant substrates. One of the unique sequences was used to develop a TaqMan quantitative polymerase chain reaction assay and a recombinase polymerase amplification assay, both exhibiting 100% sensitivity and specificity when tested against purified DNA from 171 isolates and 69 lettuce samples. The relationship between qPCR C values and colony forming units (CFU)/g values was also determined. This study not only introduces a new marker for FOLac race 1 diagnostics and soil quantitation, but also underscores the value of an extensive genomic database and screening software pipeline for developing molecular diagnostics for and other fungal taxa.

Rice blast is one of the most hazardous diseases affecting rice production. Previously, we discovered that the Atp2 protein of could significantly inhibit the appressorium formation and pathogenicity of However, the molecular mechanism of this fungus has remained unknown. This study revealed that Atp2 can enter the cell and interact with the ribosomal protein MoRpl12 of , directly affecting the expression of the MoRpl12 protein. Silencing the gene can affect cell wall integrity, growth, conidiogenesis, and fungal pathogenicity. The quantitative reverse transcription PCR results showed significant changes in the expression of conidiation-related genes in the gene-silenced mutants or in the Atp2 protein-treated plants. We further found that Atp2 treatment can influence the expression of ribosomal-related genes, such as , in . Our study revealed a novel antifungal mechanism by which the Atp2 protein binds to the ribosomal protein MoRpl12 and inhibits the pathogenicity of rice blast fungus, providing a new potential target for rice blast prevention and control.

Tea leaf spot caused by is a disease that has recently been discovered in the tea plantations of Southwest China, and which has a significant negative impact on the yield and quality of tea leaves. Wuyiencin is a nucleotide antimicrobial that is effective against a range of fungal diseases. However, its mode of action is still unclear. The current study found that wuyiencin inhibited the mycelial growth of in vitro. Meanwhile, in vivo experiments confirmed that wuyiencin had a significant curative effect on tea leaf spot. Microscopic observation represented it damaged the organelles and nucleus in fungal cells. Reverse transcription quantitative PCR assays revealed that mycelium treated with wuyiencin at the half-maximal effective concentration (EC) dosage for 1 hour exhibited 3.23 times lower expression of () gene, which is responsible for producing pyruvate. The wild type (WT) strain had a 1.77-fold higher pyruvate concentration than that in the mutant ( < 0.05). The mutant was more sensitive than the WT to wuyiencin treatment, with the EC value in the mutant being 30.01 μg/ml, compared with 82.34 μg/ml in the WT. Molecular docking demonstrated that wuyiencin bound to Td, with a binding energy of -10.47 kcal/mol. Compared with the WT strain, wuyiencin significantly reduced ATP concentration of the mutant strain at dosages of 80.0 and 160.0 µg/ml. In total, wuyiencin reduced Td activity, inhibited pyruvate production, and decreased ATP content in the phytopathogenic fungus, ultimately disturbing the growth of the mycelium.