We present draft genome sequences of the peanut leaf spot pathogens Passalora arachidicola isolate Ca1604 and Nothopassalora personata isolate Cp1602 that were generated using PacBio sequencing. The assemblies comprise 194 and 571 contigs with total lengths of approximately 37.75 and 49.04 Mb, respectively.

Phytopathogenic fungi can weaken the effectiveness of antifungal chemicals from plants and artificial synthesis through a xenobiotic detoxification system. Nevertheless, the transcription factors responsible for transcriptional activation of xenobiotic detoxification genes in phytopathogenic fungi are rarely reported. Here, we show that a GATA transcription factor, SsGATA1, regulates the transcription of drug efflux pump genes, thus contributing to tolerance to various types of chemical fungicides, including propiconazole, caspofungin, and azoxystrobin in Sclerotinia sclerotiorum. Similarly, SsGATA1 also confers tolerance to isothiocyanate and flavonols, two compounds reported as broad-spectrum antifungal chemicals, by mediating the transcription of the isothiocyanate hydrolase SsSaxA. Importantly, SsGATA1 positively regulates pathogenicity, which is attributed to the upregulation of hydrolases and SsSaxA during infection. Furthermore, SsGATA1 is responsible for tolerance to several stresses. Our findings demonstrate that SsGATA1 plays roles in multidrug resistance and pathogenicity by activating the transcription of hydrolases and xenobiotic detoxification genes.

Invasive, lethal tree diseases continue to have devastating effects on forest ecology, commercial timber production, the horticultural trade, and agriculture production. Laurel wilt, caused by the recently introduced fungus Harringtonia lauricola, is one such lethal disease threatening both native ecosystems and avocado production. Previous transcriptomic analyses determined that a massive upregulation of pathogen genes involved in the uptake and metabolism of sulfur compounds occurs during host colonization. The creation of a loss-of-function mutant for pathogen-encoded HlCys3, a bZIP transcriptional regulator of alternative sulfur utilization, abolished colonization and disease. This phenotype was complemented genetically and chemically by reintroduction of the wild-type Hlcys3 gene in the mutant and by exogenously supplying methionine during mutant infection, respectively. These findings establish pathogen sulfur metabolism as a basic compatibility factor for this disease. The role of basic compatibility was further explored by establishing the temporal-spatial and morphological dynamics of tree host colonization by H. lauricola in comparison with the nonpathogenic species H. aguacate. The nonpathogen was able to colonize Lauraceae hosts at and adjacent to the inoculation zone, similarly to the pathogen, but was unable to systemically colonize trees. Differences in these colonization patterns were not associated with the timing or magnitude of tylosis development at the infection point. These findings indicate that basic compatibility for niche occupation must be coupled with specific compatibility factors for systemic colonization and symptom development. Determining the universality of these findings in other vascular tree wilting diseases may suggest strategies for mitigating tree mortality in ecosystems and agriculture. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Sclerotinia stem rot is a devastating disease affecting vegetables and oil crops worldwide. It is caused by the necrotrophic ascomycete Sclerotinia (S.) sclerotiorum. Host-induced gene silencing (HIGS) has shown promise in disease control against insects and fungal pathogens, but effective HIGS target genes against S. sclerotiorum remain limited. In this study, we identified a GDP-mannose pyrophosphorylase (GMPP) SsMPG2 through forward genetic analysis. Ssmpg2 mutants exhibit abnormal sclerotia and compound appressoria, along with defective cell wall integrity and attenuated virulence. Meanwhile, knocking out SsMPG2 reduced the GMPP activity and glycosylation of proteins. In addition, SsMPG2 interacts with SsMPG1, which is essential in S. sclerotiorum. Downstream of the SsMPG1-SsMPG2 complex, SsPMT4, which encodes an O-mannosyltransferase, is also critical for compound appressoria formation and virulence. Notably, MPG2 is essential for the virulence of several other fungal pathogens such as Botrytis cinerea, Magnaporthe oryzae, and Fusarium graminearum. Furthermore, expressing hairpin RNAs against SsMPG1 and SsMPG2 in Nicotiana benthamiana and Arabidopsis thaliana significantly reduced disease symptoms caused by S. sclerotiorum. Collectively, our findings demonstrate the critical roles of GMPP in the virulence of phytopathogenic fungi and suggest that MPGs are promising HlGS targets for controlling S. sclerotiorum.

Bipolaris gigantea is a pathogen of the invasive grass Microstegium vimineum and is an emerging pathogen of other hosts such as hemp and barley, causing characteristic eyespot foliar lesions. The fungus is characterized by long pale hyaline conidia measuring approximately 300 to 350 mu m. Previously, this pathogen was classified in the Drechslera genus; it was recently reassigned as Bipolaris based on molecular identification. Here, we generated a high-quality draft genome sequence of B. gigantea isolate BGF using long- and short-read DNA sequencing. The assembled genome, 30.23 Mb in size with a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score of 98.4%, exhibited synteny with the common grass pathogen B. sorokiniana isolate 10943. Average nucleotide identity (ANI) and single nucleotide polymorphism (SNP) analyses revealed high sequence identity with B. gigantea isolates from Cannabis sativa fields in Kentucky. This research provides a genomic resource that will contribute to future studies to understand the host range evolution and pathogenicity of this novel pathogen.Copyright (c) 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Chloroplasts are crucial players in immunity and photosynthesis. However, how chloroplasts arrange the transition between photosynthesis and immunity and how pathogens manipulate this transition remains elusive. Here we report an effector SsCm1 from Sclerotinia sclerotiorum, one of devastating phytopathogenic fungi, inhibits chloroplast immunity and resistance to pathogens, and alleviates photoinhibition in immune state. This is accomplished through stabilizing the conserved chloroplast protein MORF2, which is degraded during immunization and is a suppressor of photoinhibition, cell death, and chloroplast immunity. Overexpression of SsCm1 or MORF2 in plants represses basic immunity and resistance to pathogens, whereas deletion of SsCm1 reduces S. sclerotiorum virulence. Notably, SsCm1 possesses no chorismate mutase activity, which is different from the previously reported Cm effectors. This work reveals a strategy to fine-tune growth-defense balance in chloroplasts by manipulating MORF2, and a pathogenic strategy to subvert the process and promote infection via enzymatically nonfunctional effector stabilizing MORF2.

Autophagy is a recycling process by which eukaryotic cells degrade their own components, and the fruiting body (sexual structure) is a necessary structure for some plant pathogenic fungi to start the infection cycle. However, the transcriptional regulation of plant pathogenic fungal autophagy and autophagy regulating sexual reproduction remains elusive. Here, we provide the report linking autophagy transcription and fruiting body development in phytopathogenic fungi. The forkhead box transcription factor (FOX TF) SsFoxE2 in Sclerotinia sclerotiorum (Ss) binds to the promoters of ATG genes, thus promoting their transcription. SsFoxE2 is phosphorylated by AMP-activated protein kinase (AMPK) SsSnf1, and the phosphorylated SsFoxE2 interacts with (translationally controlled tumor protein) SsTctp1, leading to enhanced stability and ATG transcription activity of SsFoxE2. Importantly, the regulation of autophagy by SsFoxE2 affects the balance of the ubiquitination system and the early development of the fruiting body, which directly determines the occurrence and prevalence of plant disease. Furthermore, transcriptional binding of FOX TF to ATG gene promoters is conserved in phytopathogenic fungi. Taken together, our results bring new insights into pathogen initiation in phytopathogenic fungi and connect it to other autophagy-regulated processes in plant pathogens.

Thielaviopsis paradoxa sensu lato is a soilborne fungal pathogen that causes Thielaviopsis trunk rot and heart rot in palms. The loss of structural integrity resulting from trunk rot can cause the palm trunk to collapse suddenly and poses a serious threat to life and property. Even though rudimentary knowledge about the Thielaviopsis infection process in palms is available, nothing is known about the T. paradoxa species complex in the US. The aim of this study was to characterize T. paradoxa s. lat. isolates collected from diseased palms grown in Florida. Multi-locus phylogeny using three genes, ITS, β-tubulin, and tef1-α, revealed that the isolates separate into two distinct clades with high bootstrap support. The majority of the isolates clustered with the species T. ethacetica, while two isolates formed a separate clade, distinct from T. musarum, and might represent an undescribed Thielaviopsis species. One representative isolate from each clade, when grown on three distinct media and at four different temperatures, showed differences in gross colony morphology, as well as growth rates. The T. ethacetica isolate TP5448 and the Thielaviopsis sp. isolate PLM300 grew better at opposite ends of the temperature spectrum tested in this study, i.e., 35 °C and 10 °C, respectively. In pathogenicity assays on whole plants, the T. ethacetica isolate proved to be more aggressive than Thielaviopsis sp. isolate PLM300, as it produced larger lesions when inoculated on wounded leaflets. An unequal distribution was observed for the mating-type locus of T. ethacetica, as 12 isolates carried the MAT1-1-1 allele, while the status for four isolates remained undefined. Variation in mycelial growth in response to different fungicides was also observed between the two clades. These results demonstrate the existence of two Thielaviopsis clades that can infect palms in Florida and underscore the need for targeted sampling to help uncover the diversity of Thielaviopsis species across palm-growing regions in the US.

In warm and humid regions, the productivity of sorghum is significantly limited by the fungal hemibiotrophic pathogen Colletotrichum sublineola, the causal agent of anthracnose, a problematic disease of sorghum (Sorghum bicolor (L.) Moench) that can result in grain and biomass yield losses of up to 50%. Despite available genomic resources of both the host and fungal pathogen, the molecular basis of sorghum-C. sublineola interactions are poorly understood. By employing a dual-RNA sequencing approach, the molecular crosstalk between sorghum and C. sublineola can be elucidated. In this study, we examined the transcriptomes of four resistant sorghum accessions from the sorghum association panel (SAP) at varying time points post-infection with C. sublineola. Approximately 0.3% and 93% of the reads mapped to the genomes of C. sublineola and Sorghum bicolor, respectively. Expression profiling of in vitro versus in planta C. sublineola at 1-, 3-, and 5-days post-infection (dpi) indicated that genes encoding secreted candidate effectors, carbohydrate-active enzymes (CAZymes), and membrane transporters increased in expression during the transition from the biotrophic to the necrotrophic phase (3 dpi). The hallmark of the pathogen-associated molecular pattern (PAMP)-triggered immunity in sorghum includes the production of reactive oxygen species (ROS) and phytoalexins. The majority of effector candidates secreted by C. sublineola were predicted to be localized in the host apoplast, where they could interfere with the PAMP-triggered immunity response, specifically in the host ROS signaling pathway. The genes encoding critical molecular factors influencing pathogenicity identified in this study are a useful resource for subsequent genetic experiments aimed at validating their contributions to pathogen virulence. This comprehensive study not only provides a better understanding of the biology of C. sublineola but also supports the long-term goal of developing resistant sorghum cultivars.

Apple Glomerella leaf spot (GLS) is an emerging fungal disease caused by Colletotrichum fructicola and other Colletotrichum species. These species are polyphyletic and it is currently unknown how these pathogens convergently evolved to infect apple. We generated chromosome-level genome assemblies of a GLS-adapted isolate and a non-adapted isolate in C. fructicola using long-read sequencing. Additionally, we resequenced 17 C. fructicola and C. aenigma isolates varying in GLS pathogenicity using short-read sequencing. Genome comparisons revealed a conserved bipartite genome architecture involving minichromosomes (accessory chromosomes) shared by C. fructicola and other closely related species within the C. gloeosporioides species complex. Moreover, two repeat-rich genomic regions (1.61 Mb in total) were specifically conserved among GLS-pathogenic isolates in C. fructicola and C. aenigma. Single-gene deletion of 10 accessory genes within the GLS-specific regions of C. fructicola identified three that were essential for GLS pathogenicity. These genes encoded a putative non-ribosomal peptide synthetase, a flavin-binding monooxygenase and a small protein with unknown function. These results highlight the crucial role accessory genes play in the evolution of Colletotrichum pathogenicity and imply the significance of an unidentified secondary metabolite in GLS pathogenesis.

Plant secondary metabolism represents an important and ancient form of defense against pathogens. Phytopathogens secrete effectors to suppress plant defenses and promote infection. However, it is largely unknown, how fungal effectors directly manipulate plant secondary metabolism. Here, we characterized a fungal defense-suppressing effector CfEC28 from Colletotrichum fructicola. Gene deletion assays showed that ∆CfEC28-mutants differentiated appressoria normally on plant surface but were almost nonpathogenic due to increased number of plant papilla accumulation at attempted penetration sites. CfEC28 interacted with a family of chloroplast-localized 3-deoxy-d-arabinose-heptulonic acid-7-phosphate synthases (DAHPSs) in apple. CfEC28 inhibited the enzymatic activity of an apple DAHPS (MdDAHPS1) and suppressed DAHPS-mediated secondary metabolite accumulation through blocking the manganese ion binding region of DAHPS. Dramatically, transgene analysis revealed that overexpression of MdDAHPS1 provided apple with a complete resistance to C. fructicola. We showed that a novel effector CfEC28 can be delivered into plant chloroplasts and contributes to the full virulence of C. fructicola by targeting the DAHPS to disrupt the pathway linking the metabolism of primary carbohydrates with the biosynthesis of aromatic defense compounds. Our study provides important insights for understanding plant-microbe interactions and a valuable gene for improving plant disease resistance.

Colletotrichum fungi are a group of damaging phytopathogens with atypical mating type loci (harboring only MAT1-2-1 but not MAT1-1-1) and complex sexual behaviors. Sex pheromones and their cognate G-protein-coupled receptors are conserved regulators of fungal mating. These genes, however, lose function frequently among Colletotrichum species, indicating a possibility that pheromone signaling is dispensable for Colletotrichum sexual reproduction. We have identified two putative pheromone-receptor pairs (PPG1:PRE2, PPG2:PRE1) in C. fructicola, a species that exhibits plus-to-minus mating type switching and plus-minus-mediated mating line development. Here, we report the generation and characterization of gene-deletion mutants for all four genes in both plus and minus strain backgrounds. Single-gene deletion of pre1 or pre2 had no effect on sexual development, whereas their double deletion caused self-sterility in both the plus and minus strains. Moreover, double deletion of pre1 and pre2 caused female sterility in plus-minus outcrossing. Double deletion of pre1 and pre2, however, did not inhibit perithecial differentiation or plus-minus-mediated enhancement of perithecial differentiation. Contrary to the results with pre1 and pre2, double deletion of ppg1 and ppg2 had no effect on sexual compatibility, development, or fecundity. We concluded that pre1 and pre2 coordinately regulate C. fructicola mating by recognizing novel signal molecule(s) distinct from canonical Ascomycota pheromones. The contrasting importance between pheromone receptors and their cognate pheromones highlights the complicated nature of sex regulation in Colletotrichum fungi.

The SWI/SNF complex is guided to the promoters of designated genes by its co-operator to activate transcription in a timely and appropriate manner to govern development, pathogenesis, and stress responses in fungi. Nevertheless, knowledge of the complexes and their co-operator in phytopathogenic fungi is still fragmented. We demonstrate that the heat shock transcription factor SsHsf1 guides the SWI/SNF complex to promoters of heat shock protein (hsp) genes and antioxidant enzyme genes using biochemistry and pharmacology. This is accomplished through direct interaction with the complex subunit SsSnf5 under heat shock and oxidative stress. This results in the activation of their transcription and mediates histone displacement to maintain reactive oxygen species (ROS) homeostasis. Genetic results demonstrate that the transcription module formed by SsSnf5 and SsHsf1 is responsible for regulating morphogenesis, stress tolerance, and pathogenicity in Sclerotinia sclerotiorum, especially by directly activating the transcription of hsp genes and antioxidant enzyme genes counteracting plant-derived ROS. Furthermore, we show that stress-induced phosphorylation of SsSnf5 is necessary for the formation of the transcription module. This study establishes that the SWI/SNF complex and its co-operator cooperatively regulate the transcription of hsp genes and antioxidant enzyme genes to respond to host and environmental stress in the devastating phytopathogenic fungi.

Sclerotinia sclerotiorum is a necrotrophic phytopathogenic fungus that cross-talks with its hosts for control of cell-death pathways for colonization. Target of rapamycin (TOR) is a central regulator that controls cell growth, intracellular metabolism, and stress responses in a variety of eukaryotes, but little is known about TOR signaling in S. sclerotiorum. In this study, we identified a conserved TOR signaling pathway and characterized SsTOR as a critical component of this pathway. Hyphal growth of S. sclerotiorum was retarded by silencing SsTOR, moreover, sclerotia and compound appressoria formation were severely disrupted. Notably, pathogenicity assays of strains shows that the virulence of the SsTOR-silenced strains were dramatically decreased. SsTOR was determined to participate in cell wall integrity (CWI) by regulating the phosphorylation level of SsSmk3, a core MAP kinase in the CWI pathway. Importantly, the inactivation of SsTOR induced autophagy in S. sclerotiorum potentially through SsAtg1 and SsAtg13. Taken together, our results suggest that SsTOR is a global regulator controlling cell growth, stress responses, cell wall integrity, autophagy, and virulence of S. sclerotiorum. IMPORTANCE TOR is a conserved protein kinase that regulates cell growth and metabolism in response to growth factors and nutrient abundance. Here, we used gene silencing to characterize SsTOR, which is a critical component of TOR signaling pathway. SsTOR-silenced strains have limited mycelium growth, and the virulence of the SsTOR-silenced strains was decreased. Phosphorylation analysis indicated that SsTOR influenced CWI by regulating the phosphorylation level of SsSmk3. Autophagy is essential to preserve cellular homeostasis in response to cellular and environmental stresses. Inactivation of SsTOR induced autophagy in S. sclerotiorum potentially through SsAtg1 and SsAtg13. These findings further indicated that SsTOR is a global regulator of the growth, development, and pathogenicity of S. sclerotiorum in multiple ways.

Phyllosticta citricarpa is a fungal pathogen causing citrus black spot (CBS). As a regulated pest in some countries, the presence of the pathogen limits the export of fruit and is therefore of agricultural and economic importance. In this study, we used high throughput sequencing data to infer the global phylogeographic distribution of this pathogen, including 71 isolates from eight countries, Argentina, Australia, Brazil, China, Cuba, Eswatini, South Africa and the United States of America. We assembled draft genomes and used a pairwise read mapping approach for the detection and enumeration of variants between isolates. We performed SSR marker discovery based on the assembled genome with the best assembly statistics, and generated genotype profiles for all isolates with 1987 SSR markers in silico. Furthermore, we identified 32,560 SNPs relative to a reference sequence followed by population genetic analyses based on the three datasets; pairwise variant counts, SSR genotypes and SNP genotypes. All three analysis approaches gave similar overall results. Possible pathways of dissemination among the populations from China, Australia, southern Africa and the Americas are postulated. The Chinese population is the most diverse, and is genetically the furthest removed from all other populations, and is therefore considered the closest to the origin of the pathogen. Isolates from Australia, Eswatini and the South African province Mpumalanga are closely associated and clustered together with those from Argentina and Brazil. The Eastern Cape, North West, and KwaZulu-Natal populations in South Africa grouped in another cluster, while isolates from Limpopo are distributed between the two aforementioned clusters. Southern African populations showed a close relationship to populations in North America, and could be a possible source of P. citricarpa populations that are now found in North America. This study represents the largest whole genome sequencing survey of P. citricarpa to date and provides a more comprehensive assessment of the population genetic diversity and connectivity of P. citricarpa from different geographic origins. This information could further assist in a better understanding of the epidemiology of the CBS pathogen, its long-distance dispersal and dissemination pathways, and can be used to refine phytosanitary regulations and management programmes for the disease.

Citrus black spot (CBS), caused by Phyllosticta citricarpa (McAlpine) van der Aa, is a disease that affects Citrus spp. causing production losses, high costs associated with management, and constraints on the fresh market trade. The present investigation aimed to confirm the identity of the CBS pathogen as P. citricarpa and determine its mating-type distribution in Cuba. Phyllosticta isolates were collected from major Cuban citrus-producing provinces (Matanzas, Cienfuegos, Camagüey, and Santiago de Cuba). P. citricarpa and the endophyte P. capitalensis (Henn.) were identified by polyphasic taxonomy, integrating morpho-physiological characteristics with the phylogenetic analysis of ITS, actA, LSU and tef1 loci. Mating-type (MAT) analysis revealed that only the MAT1-2 idiomorph of P. citricarpa is present in Cuba, providing evidence of an atypical CBS disease cycle. These results contribute to a better understanding of the epidemiology of CBS in Cuba and the improvement of CBS management.

Sclerotinia sclerotiorum is a notorious phytopathogenic Ascomycota fungus with a host range of >600 plant species worldwide. This homothallic Leotiomycetes species reproduces sexually through a multicellular apothecium that produces and releases ascospores. These ascospores serve as the primary inoculum source for disease initiation in the majority of S. sclerotiorum disease cycles. The regulation of apothecium development for this pathogen and other apothecium-producing fungi remains largely unknown. Here, we report that a C2H2 transcription factor, SsZFH1 (zinc finger homologous protein), is necessary for the proper development and maturation of sclerotia and apothecia in S. sclerotiorum and is required for the normal growth rate of hyphae. Furthermore, ΔSszfh1 strains exhibit decreased H2O2 accumulation in hyphae, increased melanin deposition, and enhanced tolerance to H2O2 in the process of vegetative growth and sclerotia formation. Infection assays on common bean leaves, with thin cuticles, and soybean and tomato leaves, with thick cuticles, suggest that the deletion of Sszfh1 slows the mycelial growth rate, which in turn affects the expansion of leaf lesions. Collectively, our results provide novel insights into a major fungal factor mediating maturation of apothecia with additional effects on hyphae and sclerotia development.

Previous research has demonstrated that sclerotia production is suppressed by exogenous cyclic AMP (cAMP) in Sclerotinia sclerotiorum and enhanced upon deletion of the adenylate cyclase gene. This study focuses on further functionally characterizing the cAMP-dependent protein kinase A (PKA) signaling pathway in S. sclerotiorum. Here, we demonstrate functions for two components of cAMP signaling: the catalytic, SsPKA, and the regulatory, SsPKAR, subunits of cAMP-dependent PKA. Growth and virulence were greatly reduced by disruption of either Sspka2 or SspkaR in addition to deficiencies in appressorium development. Surprisingly, disruption of both Sspka2 (dSspka2) and SspkaR (dSspkaR) display an up regulation of autophagy without nutrient starvation suggesting that properly regulated PKA activity is required for control of autophagy. SsPKAR is demonstrated to be required for carbohydrate metabolism and mobilization, which are required for appressorium development and sclerotium initiation. A closer examination of dSspkaR during Nicotiana benthamiana infection revealed that an oxalic acid (OA) -independent necrosis protein(s) or metabolite(s) may be involved in the lesion development in dSspkaR- N. benthamiana interaction. In summary, these data demonstrate that the cAMP-dependent PKA signaling is essential for multiple forms of S. sclerotiorum development as well as virulence which rely on optimal regulation of autophagy.

Plus-minus regulation of Colletotrichum sexual differentiation was reported in the early 1900s. Both plus and minus strains produce fertile perithecia in a homothallic but inefficient manner.