Pectate lyase affects pathogenicity in natural isolates of Colletotrichum coccodes and in pelA gene-disrupted and gene-overexpressing mutant lines

Unveiling the Arsenal of Apple Bitter Rot Fungi: Comparative Genomics Identifies Candidate Effectors, CAZymes, and Biosynthetic Gene Clusters in Colletotrichum Species

The bitter rot of apple is caused by Colletotrichum spp. and is a serious pre-harvest disease that can manifest in postharvest losses on harvested fruit. In this study, we obtained genome sequences from four different species, C. chrysophilum, C. noveboracense, C. nupharicola, and C. fioriniae, that infect apple and cause diseases on other fruits, vegetables, and flowers. Our genomic data were obtained from isolates/species that have not yet been sequenced and represent geographic-specific regions. Genome sequencing allowed for the construction of phylogenetic trees, which corroborated the overall concordance observed in prior MLST studies. Bioinformatic pipelines were used to discover CAZyme, effector, and secondary metabolic (SM) gene clusters in all nine Colletotrichum isolates. We found redundancy and a high level of similarity across species regarding CAZyme classes and predicted cytoplastic and apoplastic effectors. SM gene clusters displayed the most diversity in type and the most common cluster was one that encodes genes involved in the production of alternapyrone. Our study provides a solid platform to identify targets for functional studies that underpin pathogenicity, virulence, and/or quiescence that can be targeted for the development of new control strategies. With these new genomics resources, exploration via omics-based technologies using these isolates will help ascertain the biological underpinnings of their widespread success and observed geographic dominance in specific areas throughout the country.

Selection of stable reference genes for qPCR expression of Colletotrichum lindemuthianum, the bean anthracnose pathogen

Phaseolus vulgaris L., commonly known as the common bean, is a highly nutritious crop often called the "poor man's meat". However, it is susceptible to various diseases throughout the cropping season, with anthracnose caused by Colletotrichum lindemuthianum being a significant threat that leads to substantial losses. There is still a lack of understanding about the molecular basis of C. lindemuthianum pathogenicity. The first step in understanding this is to identify pathogenicity genes that express more during infection of common beans. A reverse transcription quantitative real-time PCR (qPCR) method can be used for virulence gene expression. However, this approach requires selecting appropriate reference genes to normalize relative gene expression data. Currently, there is no reference gene available for C. lindemuthianum. In this study, we selected eight candidate reference genes from the available genome of C. lindemuthianum to bridge the gap. These genes were ACT (Actin), β-tub (β-tubulin), EF (Elongation Factor), Cyt C (Cytochrome C), His H3 (Histone H3), CHS1 (Chitin synthetase), GAPDH (Glyceraldehyde-3-phosphate dehydrogenase) and abfA (Alpha-l-Arabinofuranosidase A). The primers for these candidate reference genes were able to amplify cDNA only from the pathogen, demonstrating their specificity. The qPCR efficiency of the primers ranged from 80% to 103%. We analyzed the stability of gene expression in C. lindemuthianum by exposing the mycelium to nine different stress conditions. We employed algorithms, such as GeNorm, NormFinder, BestKeeper, and RefFinder tools, to identify the most stable gene. The analysis using these tools revealed that EF, GAPDH, and β-tub most stable genes, while ACT and CHS1 showed relatively low expression stability. A large number of potential effector genes have been identified through bioinformatics analysis in C. lindemuthianum. The stable genes for qPCR (EF and GAPDH) discovered in this study will aid the scientific community in determining the relative expression of C. lindemuthianum effector genes.

The proteome of Penicillium expansum during infection of postharvest apple is revealed using Label-Free and Parallel Reaction Monitoring(PRM)Techniques

Penicillium expansum is the main pathogen in the postharvest storage of apples. Penicilliosis caused by P. expansum infection not only seriously affects the appearance and quality of fruits, but also the secondary metabolite Patulin (PAT) can cause harm to human health. Until now, little attention has been paid to the molecular mechanism of P. expansum infecting apples. Studying its molecular mechanism can help us better prevent and control apple postharvest blue mold. In this present investigation, we will use Label-Free technology to perform proteomic sequencing on apple samples at key time points of P. expansum infection, explore and screen key proteins and metabolic pathways during infection, and use Parallel Reaction Monitoring (PRM) technology to thoroughly validate proteomic data. The infection of P. expansum activates the MAPK signaling pathway, plant-pathogen interaction metabolic pathway and phenylpropanoid biosynthesis pathway of apple, participates in the regulation of ROS generation and oxidative stress process, promotes the synthesis of lignin and flavonoids, and the synthesis of Pathogenesis-Related Protein helps apple directly defend against P. expansum infection. This study provides the foundation for relevant postharvest control strategies, paving the way for further exploration of the proteome of pathogens infecting fruit and vegetables. SIGNIFICANCE: Proteins are macromolecules essential to the life of organisms, as they participate in the function and structure of cells. Proteomics technology is currently one of the important means to study the the response mechanism of pathogenic bacteria to plant infection, which can reveal the essence of physiological and pathological processes and help to clarify the possible relationship between protein abundance and plant stress. The present study essentially uses recent proteome analysis technology, namely label-free and PRM techniques, and lays the foundations for studying the of the infection response between P. expansum and apples. In particular, it provides a broad perspective on the molecular mechanism of P. expansum in the early stage of apple infection through detailed functional exploration and verification of associated proteins. Thus, it provides a theoretical basis for preventing and treating apple postharvest blue mold.

Comparative secretome analysis of Striga and Cuscuta species identifies candidate virulence factors for two evolutionarily independent parasitic plant lineages

BACKGROUND

Many parasitic plants of the genera Striga and Cuscuta inflict huge agricultural damage worldwide. To form and maintain a connection with a host plant, parasitic plants deploy virulence factors (VFs) that interact with host biology. They possess a secretome that represents the complement of proteins secreted from cells and like other plant parasites such as fungi, bacteria or nematodes, some secreted proteins represent VFs crucial to successful host colonisation. Understanding the genome-wide complement of putative secreted proteins from parasitic plants, and their expression during host invasion, will advance understanding of virulence mechanisms used by parasitic plants to suppress/evade host immune responses and to establish and maintain a parasite-host interaction.

RESULTS

We conducted a comparative analysis of the secretomes of root (Striga spp.) and shoot (Cuscuta spp.) parasitic plants, to enable prediction of candidate VFs. Using orthogroup clustering and protein domain analyses we identified gene families/functional annotations common to both Striga and Cuscuta species that were not present in their closest non-parasitic relatives (e.g. strictosidine synthase like enzymes), or specific to either the Striga or Cuscuta secretomes. For example, Striga secretomes were strongly associated with 'PAR1' protein domains. These were rare in the Cuscuta secretomes but an abundance of 'GMC oxidoreductase' domains were found, that were not present in the Striga secretomes. We then conducted transcriptional profiling of genes encoding putatively secreted proteins for the most agriculturally damaging root parasitic weed of cereals, S. hermonthica. A significant portion of the Striga-specific secretome set was differentially expressed during parasitism, which we probed further to identify genes following a 'wave-like' expression pattern peaking in the early penetration stage of infection. We identified 39 genes encoding putative VFs with functions such as cell wall modification, immune suppression, protease, kinase, or peroxidase activities, that are excellent candidates for future functional studies.

CONCLUSIONS

Our study represents a comprehensive secretome analysis among parasitic plants and revealed both similarities and differences in candidate VFs between Striga and Cuscuta species. This knowledge is crucial for the development of new management strategies and delaying the evolution of virulence in parasitic weeds.

Oomycete pathogen pectin acetylesterase targets host lipid transfer protein to reduce salicylic acid signaling

During initial stages of microbial invasion, the extracellular space (apoplast) of plant cells is a vital battleground between plants and pathogens. The oomycete plant pathogens secrete an array of apoplastic carbohydrate active enzymes, which are central molecules for understanding the complex plant-oomycete interactions. Among them, pectin acetylesterase (PAE) plays a critical role in the pathogenesis of plant pathogens including bacteria, fungi, and oomycetes. Here, we demonstrated that Peronophythora litchii (syn. Phytophthora litchii) PlPAE5 suppresses litchi (Litchi chinensis) plant immunity by interacting with litchi lipid transfer protein 1 (LcLTP1). The LcLTP1-binding activity and virulence function of PlPAE5 depend on its PAE domain but not on its PAE activity. The high expression of LcLTP1 enhances plant resistance to oomycete and fungal pathogens, and this disease resistance depends on BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 (BAK1) and Suppressor of BIR1 (SOBIR1) in Nicotiana benthamiana. LcLTP1 activates the plant salicylic acid (SA) signaling pathway, while PlPAE5 subverts the LcLTP1-mediated SA signaling pathway by destabilizing LcLTP1. Conclusively, this study reports a virulence mechanism of oomycete PAE suppressing plant LTP-mediated SA immune signaling and will be instrumental for boosting plant resistance breeding.

Infection of postharvest pear by Penicillium expansum is facilitated by the glycoside hydrolase (eglB) gene

The primary reason for postharvest loss is blue mold disease which is mainly caused by Penicillium expansum. Strategies for disease control greatly depend on the understanding of mechanisms of pathogen-fruit interaction. A member of the glycoside hydrolase family, β-glucosidase 1b (eglB), in P. expansum was significantly upregulated during postharvest pear infection. Glycoside hydrolases are a large group of enzymes that can degrade plant cell wall polymers. High homology was found between the glycoside hydrolase superfamily in P. expansum. Functional characterization and analysis of eglB were performed via gene knockout and complementation analysis. Although eglB deletion had no notable effect on P. expansum colony shape or microscopic morphology, it did reduce the production of fungal hyphae, thereby reducing P. expansum's sporulation and patulin (PAT) accumulation. Moreover, the deletion of eglB (ΔeglB) reduced P. expansum pathogenicity in pears. The growth, conidia production, PAT accumulation, and pathogenicity abilities of ΔeglB were restored to that of wild-type P. expansum by complementation of eglB (ΔeglB-C). These findings indicate that eglB contributes to P. expansum's development and pathogenicity. This research is a contribution to the identification of key effectors of fungal pathogenicity for use as targets in fruit safety strategies.

The glycoside hydrolase 28 member VdEPG1 is a virulence factor of Verticillium dahliae and interacts with the jasmonic acid pathway-related gene GhOPR9

Glycoside hydrolase (GH) family members act as virulence factors and regulate plant immune responses during pathogen infection. Here, we characterized the GH28 family member endopolygalacturonase VdEPG1 in Verticillium dahliae. VdEPG1 acts as a virulence factor during V. dahliae infection. The expression level of VdEPG1 was greatly increased in V. dahliae inoculated on cotton roots. VdEPG1 suppressed VdNLP1-mediated cell death by modulating pathogenesis-related genes in Nicotiana benthamiana. Knocking out VdEPG1 led to a significant decrease in the pathogenicity of V. dahliae in cotton. The deletion strains were more susceptible to osmotic stress and the ability of V. dahliae to utilize carbon sources was deficient. In addition, the deletion strains lost the ability to penetrate cellophane membrane, with mycelia showing a disordered arrangement on the membrane, and spore development was affected. A jasmonic acid (JA) pathway-related gene, GhOPR9, was identified as interacting with VdEPG1 in the yeast two-hybrid system. The interaction was further confirmed by bimolecular fluorescence complementation and luciferase complementation imaging assays in N. benthamiana leaves. GhOPR9 plays a positive role in the resistance of cotton to V. dahliae by regulating JA biosynthesis. These results indicate that VdEPG1 may be able to regulate host immune responses as a virulence factor through modulating the GhOPR9-mediated JA biosynthesis.

VmPacC-mediated pH regulation of Valsa mali confers to host acidification identified by comparative proteomics analysis

Apple valsa canker caused by the Ascomycete fungus Valsa mali is one of the most serious diseases of apple, resulting in huge economic losses in the apple-growing area of China. Previous study found that the pathogen could acidify the infected tissues to make lower ambient pH (from 6.0 to 3.5) for their successfully colonization. The pH signaling transcription factor VmPacC is required for acidification of its environment and for full virulence in V. mali. It is known that the functional cooperation of proteins secreted by V. mali plays pivotal role in its successful colonization of host plants. In this study, we used tandem mass tag (TMT) labeling coupled with LC-MS/MS-based quantitative proteomics to analyze the VmPacC-mediated pH regulation in V. mali, focusing on differentially expressed proteins (DEPs). We identified 222 DEPs specific to VmPacC deletion, and 921 DEPs specific to different pH conditions (pH 6.0 and 3.4). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that these DEPs were mainly involved in pathways associated with carbon metabolism, biosynthesis of antibiotics, citrate cycle (TCA cycle), glycolysis/gluconeogenesis, glutathione metabolism, ribosomes, and pentose phosphate pathways. Additionally, we identified 119 DEPs that were shared among the VmPacC deletion mutant and different pH conditions, which were mainly related to energy metabolism pathways, providing the energy required for the hyphal growth and responses to environmental stresses. A protein-protein interaction (PPI) network analysis indicated that most of the shared proteins were mapped to an interaction network with a medium confidence score of 0.4. Notably, one uncharacterized protein (KUI69106.1), and two known proteins (heat shock protein 60 (KUI73579.1), aspartate aminotransferase (KUI73864.1)) located in the core of the network were highly connected (with ≥ 38 directed edges) with the other shared DEPs. Our results suggest that VmPacC participates in the pathogen's regulation to ambient pH through the regulation of energy metabolism pathways such as the glycolysis/gluconeogenesis pathway and TCA cycle. Finally, we proposed a sophisticated molecular regulatory network to explain pH decrease in V. mali. Our study, by providing insights into V. mali regulating pH, helps to elucidate the mechanisms of host acidification during pathogen infection.

Pectate Lyase from Fusarium sacchari Induces Plant Immune Responses and Contributes to Virulence

Fusarium sacchari is one of the primary pathogens causing Pokkah Boeng disease (PBD) in sugarcane in China. Pectate lyases (PL), which play a critical role in pectin degradation and fungal virulence, have been extensively studied in major bacterial and fungal pathogens of a wide range of plant species. However, only a few PLs have been functionally investigated. In this study, we analyzed the function of the pectate lyase gene, FsPL, from F. sacchari. FsPL is a key virulence factor of F. sacchari and can induce plant cell death. FsPL also triggers the pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) response in Nicotiana benthamiana, as reflected by increases in reactive oxygen species (ROS) production, electrolyte leakage, and callose accumulation, as well as the upregulation of defense response genes. In addition, our study also found that the signal peptide of FsPL was necessary for induced cell death and PTI responses. Virus-induced gene silencing showed that FsPL-induced cell death in Nicotiana benthamiana was mediated by leucine-rich repeat (LRR) receptor-like kinases BAK1 and SOBIR1. Thus, FsPL may not only be a critical virulence factor for F. sacchari but may also induce plant defense responses. These findings provide new insights into the functions of pectate lyase in host-pathogen interactions. IMPORTANCE Pokkah Boeng disease (PBD) is one of the main diseases affecting sugarcane in China, seriously damaging sugarcane production and economic development. Therefore, it is important to clarify the pathogenic mechanisms of this disease and to provide a theoretical basis for the breeding of PBD-resistant sugarcane strains. The present study aimed to analyze the function of FsPL, a recently identified pectate lyase gene from F. sacchari. FsPL is a key virulence factor of F. sacchari that induces plant cell death. Our results provide new insights into the function of pectate lyase in host-pathogen interactions.

Genomic and Transcriptomic Survey Provides Insights into Molecular Basis of Pathogenicity of the Sunflower Pathogen Phoma macdonaldii

Phoma macdonaldii (teleomorph Leptosphaeria lindquistii) is the causal agent of sunflower (Helianthus annuus L.) black stem. In order to investigate the molecular basis for the pathogenicity of P. ormacdonaldii, genomic and transcriptomic analyses were performed. The genome size was 38.24 Mb and assembled into 27 contigs with 11,094 putative predicted genes. These include 1133 genes for CAZymes specific for plant polysaccharide degradation, 2356 for the interaction between the pathogen and host, 2167 for virulence factors, and 37 secondary metabolites gene clusters. RNA-seq analysis was conducted at the early and late stages of the fungal spot formation in infected sunflower tissues. A total of 2506, 3035, and 2660 differentially expressed genes (DEGs) between CT and each treatment group (LEAF-2d, LEAF-6d, and STEM) were retrieved, respectively. The most significant pathways of DEGs from these diseased sunflower tissues were the metabolic pathways and biosynthesis of secondary metabolites. Overall, 371 up-regulated DEGs were shared among LEAF-2d, LEAF-6d, and STEM, including 82 mapped to DFVF, 63 mapped to PHI-base, 69 annotated as CAZymes, 33 annotated as transporters, 91 annotated as secretory proteins, and a carbon skeleton biosynthetic gene. The most important DEGs were further confirmed by RT-qPCR. This is the first report on the genome-scale assembly and annotation for P. macdonaldii. Our data provide a framework for further revealing the underlying mechanism of the pathogenesis of P. macdonaldii, and also suggest the potential targets for the diseases caused by this fungal pathogen.

Pectate Lyase Genes Abundantly Expressed During the Infection Regulate Morphological Development of Colletotrichum camelliae and CcPEL16 Is Required for Full Virulence to Tea Plants

Colletotrichum camelliae is the dominant species causing foliar diseases of tea plants (Camellia sinensis) in China. Transcriptome data and reverse transcription-quantitative PCR (qRT-PCR) analysis have demonstrated that the pectate lyase genes in C. camelliae (CcPELs) were significantly upregulated during infectious development on tea plants (cv. Longjing43). To further evaluate the biological functions of CcPELs, we established a polyethylene glycol (PEG)-mediated protoplast transformation system of C. camelliae and generated targeted deletion mutants of seven CcPELs. Phenotypic assays showed that the genes contribute to mycelial growth, conidiation, and appressorium development. The polypeptides encoded by each CcPEL gene contained a predicted N-terminal signal peptide, and a yeast invertase secretion assay suggested that each CcPEL protein could be secreted. Cell death-suppressive activity assays confirmed that all seven CcPELs did not suppress Bax-induced cell death in tobacco leaf cells. However, deletion of CcPEL16 significantly reduced necrotic lesions on tea leaves. Taken together, these results indicated that CcPELs play essential roles in regulating morphological development, and CcPEL16 is required for full virulence in C. camelliae. IMPORTANCE In this study, we first established a PEG-mediated protoplast transformation system of C. camelliae and used it to investigate the biological functions of seven pectate lyase genes (CcPELs) which were abundantly expressed during infection. The results provided insights into the contributions of pectate lyase to mycelial growth, conidial production, appressorium formation, and the pathogenicity of C. camelliae. We also confirmed the secretory function of CcPEL proteins and their role in suppressing Bax-induced cell death. Overall, this study provides an effective method for generating gene-deletion transformants in C. camelliae and broadens our understanding of pectate lyase in regulating morphological development and pathogenicity.

Transcription Factor VdCf2 Regulates Growth, Pathogenicity, and the Expression of a Putative Secondary Metabolism Gene Cluster in Verticillium dahliae

Verticillium dahliae is an important soilborne phytopathogen which can ruinously attack numerous host plants and cause significant economic losses. Transcription factors (TFs) were reported to be involved in various biological processes, such as hyphal growth and virulence of pathogenic fungi.

Selection of potential reference genes for RT-qPCR in the plant pathogenic fungus Colletotrichum fructicola

Colletotrichum is widespread, and these pathogenic fungi can cause various plant diseases. Studies have shown that Colletotrichum fructicola cause oil-tea (Camellia oleifera) anthracnose and is widely distributed as a dominant fungus in all Ca. oleifera-producing regions. Real-time quantitative PCR(RT-qPCR) is considered the most reliable technique for simultaneously measuring relative gene expression levels in different tissues. Target genes are typically quantified using RT-qPCR to explore gene function, and reliable RT-qPCR results require data normalization using stable reference genes. No studies have reported a suitable reference gene in C. fructicola. This study has eight candidate reference genes (CfCk, CfRpp, CfUce, CfRrp, CfAdrh, CfDd, CfAct, and CfTub) which were selected from C. fructicola-Ca. oleifera transcriptome data and evaluated and sequenced using geNorm, NormFinder, and BestKeeper algorithms. The results showed that CfRrp had better stability in C. fructicola, both during the growth of pure pathogenic fungi and during the invasion of different oil-tea leaves. After normalization with CfRrp, the differentially expressed target genes were similar to the transcriptome. Our work provides suitable reference genes for future studies to quantify target gene expression levels in C. fructicola.

Pectinolytic arsenal of Colletotrichum lindemuthianum and other fungi with different lifestyles

AIM

To identify and analyze genes that encode pectinases in the genome of the fungus C. lindemuthianum, evaluate the expression of these genes, and compare putative pectinases found in C. lindemuthianum with pectinases produced by other fungi and oomycetes with different lifestyles.

METHODS AND RESULTS

Genes encoding pectinases in the genome of C. lindemuthianum were identified and analyzed. The expression of these genes was analyzed. Pectinases from C. lindemuthianum were compared with pectinases from other fungi that have different lifestyles, and the pectinase activity in some of these fungi was quantified. Fifty-eight genes encoding pectinases were identified in C. lindemuthianum. At least six types of enzymes involved in pectin degradation were identified, with pectate lyases and polygalacturonases being the most abundant. Twenty-seven genes encoding pectinases were differentially expressed at some point in C. lindemuthianum during their interactions with their host. For each type of pectinase, there were at least three isoenzyme groups. The number of pectinases present in fungi with different lifestyles seemed to be related more to the lifestyle than to the taxonomic relationship between them. Only phytopathogenic fungi showed pectate lyase activity.

CONCLUSIONS

The collective results demonstrate the pectinolytic arsenal of C. lindemuthianum, with many and diverse genes encoding pectinases more than that found in other phytopathogens, which suggests that at least part of these pectinases must be important for the pathogenicity of the fungus C. lindemuthianum.

SIGNIFICANCE AND IMPACT OF THE STUDY

Knowledge of these pectinases could further the understanding of the importance of this broad pectinolytic arsenal in the common bean infection, and could be exploited for biotechnological purposes.

Genome Analysis of the Broad Host Range Necrotroph Nalanthamala psidii Highlights Genes Associated With Virulence

Guava wilt disease is caused by the fungus Nalanthamala psidii. The wilt disease results in large-scale destruction of orchards in South Africa, Taiwan, and several Southeast Asian countries. De novo assembly, annotation, and in-depth analysis of the N. psidii genome were carried out to facilitate the identification of characteristics associated with pathogenicity and pathogen evolution. The predicted secretome revealed a range of CAZymes, proteases, lipases and peroxidases associated with plant cell wall degradation, nutrient acquisition, and disease development. Further analysis of the N. psidii carbohydrate-active enzyme profile exposed the broad-spectrum necrotrophic lifestyle of the pathogen, which was corroborated by the identification of putative effectors and secondary metabolites with the potential to induce tissue necrosis and cell surface-dependent immune responses. Putative regulatory proteins including transcription factors and kinases were identified in addition to transporters potentially involved in the secretion of secondary metabolites. Transporters identified included important ABC and MFS transporters involved in the efflux of fungicides. Analysis of the repetitive landscape and the detection of mechanisms linked to reproduction such as het and mating genes rendered insights into the biological complexity and evolutionary potential of N. psidii as guava pathogen. Hence, the assembly and annotation of the N. psidii genome provided a valuable platform to explore the pathogenic potential and necrotrophic lifestyle of the guava wilt pathogen.

The Role of Glycoside Hydrolases in Phytopathogenic Fungi and Oomycetes Virulence

Phytopathogenic fungi need to secrete different hydrolytic enzymes to break down complex polysaccharides in the plant cell wall in order to enter the host and develop the disease. Fungi produce various types of cell wall degrading enzymes (CWDEs) during infection. Most of the characterized CWDEs belong to glycoside hydrolases (GHs). These enzymes hydrolyze glycosidic bonds and have been identified in many fungal species sequenced to date. Many studies have shown that CWDEs belong to several GH families and play significant roles in the invasion and pathogenicity of fungi and oomycetes during infection on the plant host, but their mode of function in virulence is not yet fully understood. Moreover, some of the CWDEs that belong to different GH families act as pathogen-associated molecular patterns (PAMPs), which trigger plant immune responses. In this review, we summarize the most important GHs that have been described in eukaryotic phytopathogens and are involved in the establishment of a successful infection.

Comparative Transcriptomics and RNA-Seq-Based Bulked Segregant Analysis Reveals Genomic Basis Underlying Cronartium ribicola vcr2 Virulence

Breeding programs of five-needle pines have documented both major gene resistance (MGR) and quantitative disease resistance (QDR) to Cronartium ribicola (Cri), a non-native, invasive fungal pathogen causing white pine blister rust (WPBR). WPBR is one of the most deadly forest diseases in North America. However, Cri virulent pathotypes have evolved and can successfully infect and kill trees carrying resistance (R) genes, including vcr2 that overcomes MGR conferred by the western white pine (WWP, Pinus monticola) R gene (Cr2). In the absence of a reference genome, the present study generated a vcr2 reference transcriptome, consisting of about 20,000 transcripts with 1,014 being predicted to encode secreted proteins (SPs). Comparative profiling of transcriptomes and secretomes revealed vcr2 was significantly enriched for several gene ontology (GO) terms relating to oxidation-reduction processes and detoxification, suggesting that multiple molecular mechanisms contribute to pathogenicity of the vcr2 pathotype for its overcoming Cr2. RNA-seq-based bulked segregant analysis (BSR-Seq) revealed genome-wide DNA variations, including about 65,617 single nucleotide polymorphism (SNP) loci in 7,749 polymorphic genes shared by vcr2 and avirulent (Avcr2) pathotypes. An examination of the distribution of minor allele frequency (MAF) uncovered a high level of genomic divergence between vcr2 and Avcr2 pathotypes. By integration of extreme-phenotypic genome-wide association (XP-GWAS) analysis and allele frequency directional difference (AFDD) mapping, we identified a set of vcr2-associated SNPs within functional genes, involved in fungal virulence and other molecular functions. These included six SPs that were top candidate effectors with putative activities of reticuline oxidase, proteins with common in several fungal extracellular membrane (CFEM) domain or ferritin-like domain, polysaccharide lyase, rds1p-like stress responsive protein, and two Cri-specific proteins without annotation. Candidate effectors and vcr2-associated genes provide valuable resources for further deciphering molecular mechanisms of virulence and pathogenicity by functional analysis and the subsequent development of diagnostic tools for monitoring the virulence landscape in the WPBR pathosystems.

Pectin lyase enhances cotton resistance to Verticillium wilt by inducing cell apoptosis of Verticillium dahliae

Verticillium wilt caused by Verticillium dahliae Kleb. is a major disease in cotton. We found that pectin lyase can enhance cotton resistance to Verticillium wilt and induce cell apoptosis of V. dahliae strain Vd080. The biocontrol effect of pectin lyase on Vd080 reached 61.9%. Pectin lyase increased ERG4 (Delta (24 (24 (1)))-sterol reductase) expression, the ergosterol content of the cell membrane, the collapse of mitochondrial membrane potential, hydrogen peroxide content, metacaspase activity, and Ca²⁺ content in the cytoplasm in the Vd080 strain and induced endoplasmic reticulum (ER) stress. Pectin lyase also increased the expression levels of the ER molecular chaperone glucose regulating protein Grp78 (BiP), protein disulfide isomerase (PDI) and calnexin (CNX), reduced the expression levels of the protein Hsp40. When the PDI and BiP genes of Vd080 were knocked out, the mutants △BiP and △PDI had reduced sensitivity to pectin lyase. In the absence of external stress, ER stress appeared in mutant △BiP cells. Pectin lyase affects the ergosterol content of the Vd080 cell membrane, which causes ER stress and increases the level of BiP to induce Vd080 cell apoptosis. These results demonstrate that pectin lyase can be used to control Verticillium wilt in cotton.

A Conserved Glycoside Hydrolase Family 7 Cellobiohydrolase PsGH7a of Phytophthora sojae Is Required for Full Virulence on Soybean

Phytopathogens deploy glycoside hydrolases (GHs) to disintegrate plant cell walls for nutrition and invasion. However, the pathogenic mechanisms of the majority of GHs in virulence remain unknown, especially in oomycetes. In this study, a Phytophthora sojae gene encodes a GH7 family cellobiohydrolase, named PsGH7a, was identified. PsGH7a was highly induced during the cyst germination and infection stages. PsGH7a is conserved in oomycetes, and shares a high amino acid sequence identity (>85%) within Phytophthora genus. The recombinant PsGH7a catalyzes the hydrolysis of β-1,4-glucan and avicel, which represent the major components of cellulose in plant cell wall. The mutation of catalytic residue Glu236 to alanine resulted in a lower catalytic activity. In addition, the PsGH7a promotes Phytophthora invasion, while the mutant can not. Notably, PsGH7a protein triggers hypersensitive cell death in diverse plants. PsGH7a knockout mutants were generated via CRISPR/Cas9 system, to investigate its biological function. Compared to wild-type strain P6497, the mutants showed reduced virulence on susceptible soybean, indicates PsGH7a is indispensable to P. sojae virulence.

Pectate lyases: Their role in plants and importance in fruit ripening

Plant cell walls are complex structures that are modified throughout development. They are a major contributor to the properties of plant structure and act as barriers against pathogens. The primary cell walls of plants are composed of polysaccharides and proteins. The polysaccharide fraction is divided into components cellulose, hemicelluloses and pectin, are all modified during fruit ripening. Pectin plays an important role in intercellular adhesion and controlling the porosity of the wall. A large number of pectin degrading enzymes have been characterised from plants and they are involved in numerous aspects of plant development. The role of pectate lyases in plant development has received little attention, probably because they are normally associated with the action of plant pathogenic organisms. However their importance in plant development and ripening is now becoming well established and new information about the role of pectate lyases in plant development forms the focus of this review.

Validation of Reliable Reference Genes for RT-qPCR Studies of Target Gene Expression in Colletotrichum camelliae During Spore Germination and Mycelial Growth and Interaction With Host Plants

The tea plant [Camellia sinensis (L.) O. Kuntze] is one of the most important leaf crops, and it is widely used for the production of non-alcoholic beverages worldwide. Tea also has a long history of medicinal use. Colletotrichum camelliae Massee is one of the dominant fungal pathogens that infects tea leaves and causes severe tea anthracnose disease. To analyze the molecular biology of C. camelliae, the quantification of pathogen gene expression by the RT-qPCR method is necessary. Reliable RT-qPCR results require the use of stable reference genes for data normalization. However, suitable reference genes have not been reported in C. camelliae thus far. In this study, 12 candidate genes (i.e., CcSPAC6B12.04c, CcWDR83, Cchp11, Ccnew1, CcHplo, CcRNF5, CcHpcob, CcfaeB-2, CcYER010C, CcRNM1, CcUP18, and CcACT) were isolated from C. camelliae and assessed as potential reference genes. The expression stability of these genes in C. camelliae during spore germination and mycelial growth and interaction with host plants was first evaluated using several statistical algorithms, such as geNorm, NormFinder, and Bestkeeper. A web-based analysis program, Refinder, was then used to find the most suitable reference genes. Our results indicated that Cenew1, CcHplo, and CcSPAC6B12.04c were the most stable reference genes in C. camelliae under all conditions. Our work provided the most suitable reference genes for future studies performed to quantify the target gene expression levels of C. camelliae.

Blast Fungal Genomes Show Frequent Chromosomal Changes, Gene Gains and Losses, and Effector Gene Turnover

Pyricularia is a fungal genus comprising several pathogenic species causing the blast disease in monocots. Pyricularia oryzae, the best-known species, infects rice, wheat, finger millet, and other crops. As past comparative and population genomics studies mainly focused on isolates of P. oryzae, the genomes of the other Pyricularia species have not been well explored. In this study, we obtained a chromosomal-level genome assembly of the finger millet isolate P. oryzae MZ5-1-6 and also highly contiguous assemblies of Pyricularia sp. LS, P. grisea, and P. pennisetigena. The differences in the genomic content of repetitive DNA sequences could largely explain the variation in genome size among these new genomes. Moreover, we found extensive gene gains and losses and structural changes among Pyricularia genomes, including a large interchromosomal translocation. We searched for homologs of known blast effectors across fungal taxa and found that most avirulence effectors are specific to Pyricularia, whereas many other effectors share homologs with distant fungal taxa. In particular, we discovered a novel effector family with metalloprotease activity, distinct from the well-known AVR-Pita family. We predicted 751 gene families containing putative effectors in 7 Pyricularia genomes and found that 60 of them showed differential expression in the P. oryzae MZ5-1-6 transcriptomes obtained under experimental conditions mimicking the pathogen infection process. In summary, this study increased our understanding of the structural, functional, and evolutionary genomics of the blast pathogen and identified new potential effector genes, providing useful data for developing crops with durable resistance.

The Botrytis cinerea Xylanase BcXyl1 Modulates Plant Immunity

Botrytis cinerea is one of the most notorious pathogenic species that causes serious plant diseases and substantial losses in agriculture throughout the world. We identified BcXyl1 from B. cinerea that exhibited xylanase activity. Expression of the BcXyl1 gene was strongly induced in B. cinerea infecting Nicotiana benthamiana and tomato plants, and BcXyl1 deletion strains severely compromised the virulence of B. cinerea. BcXyl1 induced strong cell death in several plants, and cell death activity of BcXyl1 was independent of its xylanase activity. Purified BcXyl1 triggered typically PAMP-triggered immunity (PTI) responses and conferred resistance to B. cinerea and TMV in tobacco and tomato plants. A 26-amino acid peptide of BcXyl1 was sufficient for elicitor function. Furthermore, the BcXyl1 death-inducing signal was mediated by the plant LRR receptor-like kinases (RLKs) BAK1 and SOBIR1. Our data suggested that BcXyl1 contributed to B. cinerea virulence and induced plant defense responses.

A Verticillium dahliae Pectate Lyase Induces Plant Immune Responses and Contributes to Virulence

Verticillium dahliae is a wide-host-range fungal pathogen that causes soil-borne disease in hundreds of dicotyledonous hosts. In search of V. dahliae Vd991 cell death-inducing proteins, we identified a pectate lyase (VdPEL1) that exhibited pectin hydrolytic activity, which could induce strong cell death in several plants. Purified VdPEL1 triggered defense responses and conferred resistance to Botrytis cinerea and V. dahliae in tobacco and cotton plants. Our results demonstrated that the mutant VdPEL1^rec lacking the enzymatic activity lacked functions to induce both cell death and plant resistance, implying that the enzymatic activity was necessary. In addition, VdPEL1 was strongly induced in V. dahliae infected Nicotiana benthamiana and cotton roots, and VdPEL1 deletion strains severely compromised the virulence of V. dahliae. Our data suggested that VdPEL1 contributed to V. dahliae virulence and induced plant defense responses. These findings provide a new insight for the function of pectate lyase in the host-pathogen interaction.

Plant Pathogenic Fungi

Fungi are among the dominant causal agents of plant diseases. To colonize plants and cause disease, pathogenic fungi use diverse strategies. Some fungi kill their hosts and feed on dead material (necrotrophs), while others colonize the living tissue (biotrophs). For successful invasion of plant organs, pathogenic development is tightly regulated and specialized infection structures are formed. To further colonize hosts and establish disease, fungal pathogens deploy a plethora of virulence factors. Depending on the infection strategy, virulence factors perform different functions. While basically all pathogens interfere with primary plant defense, necrotrophs secrete toxins to kill plant tissue. In contrast, biotrophs utilize effector molecules to suppress plant cell death and manipulate plant metabolism in favor of the pathogen. This article provides an overview of plant pathogenic fungal species and the strategies they use to cause disease.

Investigation of the Fusarium virguliforme Transcriptomes Induced during Infection of Soybean Roots Suggests that Enzymes with Hydrolytic Activities Could Play a Major Role in Root Necrosis

Sudden death syndrome (SDS) is caused by the fungal pathogen, Fusarium virguliforme, and is a major threat to soybean production in North America. There are two major components of this disease: (i) root necrosis and (ii) foliar SDS. Root symptoms consist of root necrosis with vascular discoloration. Foliar SDS is characterized by interveinal chlorosis and leaf necrosis, and in severe cases by flower and pod abscission. A major toxin involved in initiating foliar SDS has been identified. Nothing is known about how root necrosis develops. In order to unravel the mechanisms used by the pathogen to cause root necrosis, the transcriptome of the pathogen in infected soybean root tissues of a susceptible cultivar, 'Essex', was investigated. The transcriptomes of the germinating conidia and mycelia were also examined. Of the 14,845 predicted F. virguliforme genes, we observed that 12,017 (81%) were expressed in germinating conidia and 12,208 (82%) in mycelia and 10,626 (72%) in infected soybean roots. Of the 10,626 genes induced in infected roots, 224 were transcribed only following infection. Expression of several infection-induced genes encoding enzymes with oxidation-reduction properties suggests that degradation of antimicrobial compounds such as the phytoalexin, glyceollin, could be important in early stages of the root tissue infection. Enzymes with hydrolytic and catalytic activities could play an important role in establishing the necrotrophic phase. The expression of a large number of genes encoding enzymes with catalytic and hydrolytic activities during the late infection stages suggests that cell wall degradation could be involved in root necrosis and the establishment of the necrotrophic phase in this pathogen.

A Colletotrichum graminicola mutant deficient in the establishment of biotrophy reveals early transcriptional events in the maize anthracnose disease interaction

BACKGROUND

Colletotrichum graminicola is a hemibiotrophic fungal pathogen that causes maize anthracnose disease. It progresses through three recognizable phases of pathogenic development in planta: melanized appressoria on the host surface prior to penetration; biotrophy, characterized by intracellular colonization of living host cells; and necrotrophy, characterized by host cell death and symptom development. A "Mixed Effects" Generalized Linear Model (GLM) was developed and applied to an existing Illumina transcriptome dataset, substantially increasing the statistical power of the analysis of C. graminicola gene expression during infection and colonization. Additionally, the in planta transcriptome of the wild-type was compared with that of a mutant strain impaired in the establishment of biotrophy, allowing detailed dissection of events occurring specifically during penetration, and during early versus late biotrophy.

RESULTS

More than 2000 fungal genes were differentially transcribed during appressorial maturation, penetration, and colonization. Secreted proteins, secondary metabolism genes, and membrane receptors were over-represented among the differentially expressed genes, suggesting that the fungus engages in an intimate and dynamic conversation with the host, beginning prior to penetration. This communication process probably involves reception of plant signals triggering subsequent developmental progress in the fungus, as well as production of signals that induce responses in the host. Later phases of biotrophy were more similar to necrotrophy, with increased production of secreted proteases, inducers of plant cell death, hydrolases, and membrane bound transporters for the uptake and egress of potential toxins, signals, and nutrients.

CONCLUSIONS

This approach revealed, in unprecedented detail, fungal genes specifically expressed during critical phases of host penetration and biotrophic establishment. Many encoded secreted proteins, secondary metabolism enzymes, and receptors that may play roles in host-pathogen communication necessary to promote susceptibility, and thus may provide targets for chemical or biological controls to manage this important disease. The differentially expressed genes could be used as 'landmarks' to more accurately identify developmental progress in compatible versus incompatible interactions involving genetic variants of both host and pathogen.

A Phytophthora sojae Glycoside Hydrolase 12 Protein Is a Major Virulence Factor during Soybean Infection and Is Recognized as a PAMP

We identified a glycoside hydrolase family 12 (GH12) protein, XEG1, produced by the soybean pathogen Phytophthora sojae that exhibits xyloglucanase and β-glucanase activity. It acts as an important virulence factor during P. sojae infection but also acts as a pathogen-associated molecular pattern (PAMP) in soybean (Glycine max) and solanaceous species, where it can trigger defense responses including cell death. GH12 proteins occur widely across microbial taxa, and many of these GH12 proteins induce cell death in Nicotiana benthamiana. The PAMP activity of XEG1 is independent of its xyloglucanase activity. XEG1 can induce plant defense responses in a BAK1-dependent manner. The perception of XEG1 occurs independently of the perception of ethylene-inducing xylanase. XEG1 is strongly induced in P. sojae within 30 min of infection of soybean and then slowly declines. Both silencing and overexpression of XEG1 in P. sojae severely reduced virulence. Many P. sojae RXLR effectors could suppress defense responses induced by XEG1, including several that are expressed within 30 min of infection. Therefore, our data suggest that PsXEG1 contributes to P. sojae virulence, but soybean recognizes PsXEG1 to induce immune responses, which in turn can be suppressed by RXLR effectors. XEG1 thus represents an apoplastic effector that is recognized via the plant's PAMP recognition machinery.

Characterization of Cell-Death-Inducing Members of the Pectate Lyase Gene Family in Phytophthora capsici and Their Contributions to Infection of Pepper

Pectate lyases (PL) play a critical role in pectin degradation. PL have been extensively studied in major bacterial and fungal pathogens of a wide range of plant species. However, the contribution of PL to infection by oomycete pathogens remains largely unknown. Here, we cloned 22 full-length pectate lyase (PcPL) genes from a highly aggressive strain of Phytophthora capsici SD33. Of these, PVX agroinfiltration revealed that 12 PcPL genes were found to be highly induced during infection of pepper by SD33 but the induction level was twofold less in a mildly aggressive strain, YN07. The four genes with the highest transcript levels as measured by by quantitative reverse-transcription polymerase chain reaction (PcPL1, PcPL15, PcPL16, and PcPL20) also produced a severe cell death response following transient expression in pepper leaves but the other eight PcPL genes did not. Overexpression of these four genes increased the virulence of SD33 on pepper slightly, and increased it more substantially during infection of tobacco. Overexpression of the genes in YN07 restored its aggressiveness to near that of SD33. Gene silencing experiments with the 12 PcPL genes produced diverse patterns of silencing of PcPL genes, from which it could be inferred from regression analysis that PcPL1, PcPL16, and PcPL20 could account for nearly all of the contributions of the PcPL genes to virulence.

Utilizing FTIR-ATR spectroscopy for classification and relative spectral similarity evaluation of different Colletotrichum coccodes isolates

Colletotrichum coccodes (C. coccodes) is a pathogenic fungus which causes anthracnose on tomatoes and black dot disease in potatoes. It is important to differentiate among these isolates and to detect the origin of newly discovered isolates, in order to treat the disease in its early stages. However, distinguishing between isolates using common biological methods is time-consuming, and not always available. We used Fourier Transform Infra-Red (FTIR)-Attenuated Total Reflectance (ATR) spectroscopy and advanced mathematical and statistical methods to distinguish between different isolates of C. coccodes. To our knowledge, this is the first time that FTIR-ATR spectroscopy was used, combined with multivariate analysis, to classify such a large number of 15 isolates belonging to the same species. We obtained a success rate of approximately 90% which was achieved using the region 800-1775 cm(-1). In addition we succeeded in determining the relative spectral similarity between different fungal isolates by developing a new algorithm. This method could be an important potential diagnostic tool in agricultural research, since it may outline the extent of the biological similarity between fungal isolates. Based on the PCA calculations, we grouped the fifteen isolates included in this study into four different degrees of similarity.