Redefining Plant-Necrotroph Interactions: The Thin Line Between Hemibiotrophs and Necrotrophs

Omic characterisation of multi-component defences against the necrotrophic pathogen Pyrenophora tritici-repentis in wheat

Tan Spot disease is caused by the necrotrophic pathogen Pyrenophora tritici-repentis (Ptr) and poses a significant threat to global wheat production. Therefore, novel sources of resistance need to be identified, coupled with a fuller mechanistic understanding of host responses to Ptr. Herein, we characterise the interaction between a ToxA-positive Ptr strain and parental wheat lines from a multiparent advanced generation intercross (MAGIC) population. Genotypes displaying moderate resistance ('Robigus') or susceptibility ('Hereward') to Ptr challenge were identified and characterised through histological, metabolomic, and transcriptomic approaches. Histological investigations indicated the prominence of papilla-based defences in Robigus. Transcriptomic analyses could link this to the expression of barrier-related genes i.e. actin polymerisation, callose deposition, vesicle trafficking, and cellulose synthesis. Inhibiting actin polymerisation with cytochalasin E increased lesion numbers but did not augment lesion growth, suggesting the deployment of other defence mechanisms. These may be influenced by auxin, as its exogenous application exacerbated symptom development. Transcriptomic and metabolomic analyses in Hereward following challenge with Ptr suggested shifts in primary metabolism, affecting glycolysis, the TCA cycle, and the γ-aminobutyric acid (GABA) shunt. Activation of salicylic acid (SA)-associated genes, including NPR1 and WRKY33, was specific to Hereward, and exogenous SA increased susceptibility to Ptr in both genotypes. This study suggests barrier defences could be effective against Ptr as well as a lack of susceptibility factors like SA or the appropriate processing of IAA. These findings offer potential avenues for enhancing wheat resistance to Ptr.

Chitins and chitosans-A tale of discovery and disguise, of attachment and attainment

Chitin polymers are an essential structural component of fungal cell walls, but host chitinases can weaken them, contributing to disease resistance in fungal pathogens. Chitin oligomers thus produced are immunogenic signal molecules eliciting additional disease resistance mechanisms. Fungi may counteract these, e.g. by partial deacetylation of chitin, converting it into chitosans, protecting the cell walls against chitinase attack, and inactivating elicitor active oligomers. This molecular stealth hypothesis for fungal pathogenicity has repeatedly been tested by mutating single or multiple chitin deacetylase genes, supporting the hypothesis but simultaneously suggesting additional roles for chitin deacetylation in virulence, such as surface attachment and sensing, host tissue penetration and colonization, as well as spore formation, stabilization, and germination. Interestingly, recent evidence suggests that host plants have evolved counter strategies by inhibiting fungal chitin deacetylases, lending further credibility to the suggested action of these enzymes as pathogenicity/virulence factors, and possibly offering leads toward novel functional fungicides.

Whole genome regulatory effect of MoISW2 and consequences for the evolution of the rice plant pathogenic fungus Magnaporthe oryzae

Isw2 proteins, ubiquitous across eukaryotes, exhibit a propensity for DNA binding and exert dynamic influences on local chromosome condensation in an ATP-dependent fashion, thereby modulating the accessibility of neighboring genes to transcriptional machinery. Here, we report the deletion of a putative MoISW2 gene, yielding substantial ramifications on plant pathogenicity. Subsequent gene complementation and chromatin immunoprecipitation sequencing (ChIP-seq) analyses were conducted to delineate binding sites. RNA sequencing (RNA-seq) assays revealed discernible impacts on global gene regulation along chromosomes in both mutant and wild-type strains, with comparative analyses against 55 external RNA-seq data sets corroborating these findings. Notably, MoIsw2-mediated binding and activities delineate genomic loci characterized by pronounced gene expression variability proximal to MoIsw2 binding sites, juxtaposed with comparatively stable expression in surrounding regions. The contingent genes influenced by MoIsw2 activity predominantly encompass niche-determinant genes, including those encoding secreted proteins, secondary metabolites, and stress-responsive elements, alongside avirulence genes. Furthermore, our investigations unveil a spatial correlation between MoIsw2 binding motifs and known transposable elements (TEs), suggesting a potential interplay wherein TE transposition at these loci could modulate the transcriptional landscape of Magnaporthe oryzae in a strain-specific manner. Collectively, these findings position MoIsw2 as a plausible master regulator orchestrating the delicate equilibrium between genes vital for biomass proliferation, akin to housekeeping genes, and niche-specific determinants crucial for ecological adaptability. Stress-induced TE transposition, in conjunction with MoIsw2 activity, emerges as a putative mechanism fostering enhanced mutagenesis and accelerated evolution of niche-determinant genes relative to housekeeping counterparts.IMPORTANCEIsw2 proteins are conserved in plants, fungi, animals, and other eukaryotes. We show that a fungal Isw2 protein in the rice pathogen Magnaporthe oryzae binds to retrotransposon (RT) DNA motifs and affects the epigenetic gene expression landscape of the fungal genome. Mainly ecological niche determinant genes close to the binding motifs are affected. RT elements occur frequently in DNA between genes in most organisms. They move place and multiply in the genome, especially under physiological stress. We further discuss the Isw2 and RT combined activities as a possible sought-after mechanism that can cause biased mutation rates and faster evolution of genes necessary for reacting to abiotic and biotic challenges. The most important biotic challenges for plant pathogens are the ones from the host plants' innate immunity. The overall result of these combined activities will be an adaptation-directed evolution of niche-determinant genes.

Volatile Organic Compounds Produced by Trichoderma asperellum with Antifungal Properties against Colletotrichum acutatum

Managing plant diseases caused by phytopathogenic fungi, such as anthracnose caused by Colletotrichum species, is challenging. Different methods have been used to identify compounds with antibiotic properties. Trichoderma strains are a source of novel molecules with antifungal properties, including volatile organic compounds (VOCs), whose production is influenced by the nutrient content of the medium. In this study, we assessed the VOCs produced in dual confrontation systems performed in two culture media by Trichoderma strains (T. atroviride IMI206040, T. asperellum T1 and T3, and Trichoderma sp. T2) on Colletotrichum acutatum. We analysed the VOC profiles using gas chromatography coupled with mass spectrometry. The Luria Bertani (LB) medium stimulated the production of VOCs with antifungal properties in most systems. We identified 2-pentyl furan, dimethyl disulfide, and α-phellandrene and determined their antifungal activity in vitro. The equimolar mixture of those VOCs (250 µM ea.) resulted in 14% C. acutatum diametral growth inhibition. The infective ability and disease severity caused by the mycelia exposed to the VOCs mixture were notably diminished in strawberry leaves. Application of these VOCs as biofumigants may contribute to the management of anthracnose. LB represents a feasible strategy for identifying novel VOCs produced by Trichoderma strains with antifungal properties.

Exogenous salicylic acid treatment enhances the disease resistance of Panax vietnamensis by regulating secondary metabolite production

Introduction

Salicylic acid (SA) is a phenolic compound widely found in plants. It plays a key role in exerting plant disease resistance. Panax vietnamensis Ha & Grushv., a valuable medicinal plant, contains high levels of phenolic compounds, which contribute significantly to the resilience of the plant against stress. However, the precise role of SA in regulating the synthesis of secondary metabolites in P.vietnamensis remains elusive.

Methods

Two-year-old P. vietnamensis seedlings were treated with exogenous SA. We systematically assessed the changes in the physiological parameters of SA-treated P. vietnamensis leaves, employing transcriptome and metabolome analyses to elucidate the underlying mechanisms.

Results

Our results revealed a significant improvement of the plant's antioxidant capacity at 6 h post-treatment. Furthermore, exogenous SA treatment promoted the biosynthesis of lignin and flavonoids such as rutin, coumarin, and cyanidin. In addition, it increased the levels of endogenous SA and jasmonic acid (JA), promoting the disease resistance of the plants. Thus, SA pretreatment enhanced the defense of P. vietnamensis against pathogens.

Conclusions

Our study provided novel insights into the potential molecular mechanisms underlying SA-mediated biosynthesis of secondary metabolites. Furthermore, our results provided a theoretical foundation for optimizing the cultivation practices of P.vietnamensis and the application of SA as a plant immunomodulator.

Genomic and Transcriptomic Comparisons of the Twig Blight Pathogen, Passalora sequoiae, with Mycosphaerellaceae Foliar and Conifer Pathogens

Passalora sequoiae is a foliar pathogen to conifer tree species. In this study, we conducted whole-genome and transcriptome analyses on isolates of P. sequoiae collected from symptomatic Leyland cypress leaves from a Christmas tree farm in Mississippi. The objectives for this research were to elucidate the pathogenicity mechanisms of P. sequoiae by characterizing the genome and transcriptome and possibly identify unique and shared predicted genes in comparison with non-conifer/canker and foliar pathogens in the family Mycosphaerellaceae. P. sequoiae was found to be similar to other foliar Mycosphaerellaceae pathogens and likely represents a hemibiotrophic lifestyle based on comparisons across pathogens. The genome and in planta transcriptome highlighted some unique features of P. sequoiae: the significant presence of chitin synthases and fructose-degrading carbohydrate-degrading enzymes, trans-AT PKS genes, and antibiotic gene clusters that were unique to P. sequoiae compared with the other Mycosphaerellaceae species genomes. Several transcripts that were highly expressed in planta were identified as effectors, yet the functions were not characterized. These targets provide ample resources to continue to characterize pathogen-conifer host interactions in conifer foliar pathogens. Furthermore, this research helps build genomic resources for an important plant pathogen on Leyland cypress that will further our ability to develop novel management practices that could begin with breeding for resistance.

Grass lignin: biosynthesis, biological roles, and industrial applications

Lignin is a phenolic heteropolymer found in most terrestrial plants that contributes an essential role in plant growth, abiotic stress tolerance, and biotic stress resistance. Recent research in grass lignin biosynthesis has found differences compared to dicots such as Arabidopsis thaliana. For example, the prolific incorporation of hydroxycinnamic acids into grass secondary cell walls improve the structural integrity of vascular and structural elements via covalent crosslinking. Conversely, fundamental monolignol chemistry conserves the mechanisms of monolignol translocation and polymerization across the plant phylum. Emerging evidence suggests grass lignin compositions contribute to abiotic stress tolerance, and periods of biotic stress often alter cereal lignin compositions to hinder pathogenesis. This same recalcitrance also inhibits industrial valorization of plant biomass, making lignin alterations and reductions a prolific field of research. This review presents an update of grass lignin biosynthesis, translocation, and polymerization, highlights how lignified grass cell walls contribute to plant development and stress responses, and briefly addresses genetic engineering strategies that may benefit industrial applications.

CRISPR/Cas StNRL1 gene knockout increases resistance to late blight and susceptibility to early blight in potato

With the development of genome editing technologies, editing susceptible genes is a promising method to modify plants for resistance to stress. NPH3/RPT2-LIKE1 protein (NRL1) interacts with effector Pi02860 of Phytophthora infestans and creates a protein complex, promoting the proteasome-mediated degradation of the guanine nucleotide exchange factor SWAP70. SWAP70, as a positive regulator, enhances cell death triggered by the perception of the P. infestans pathogen-associated molecular pattern (PAMP) INF1. Using a clustered regularly interspaced short palindrome repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, a construct was made to introduce four guide RNAs into the potato cultivar Agria. A total of 60 putative transgenic lines were regenerated, in which 10 transgenic lines with deletions were selected and analyzed. A mutant line with a four-allelic knockdown of StNRL1 gene was obtained, showing an ~90% reduction in StNRL1 expression level, resulting in enhanced resistance to P. infestans. Surprisingly, mutant lines were susceptible to Alternaria alternata, suggesting that StNRL1 may play a role as a resistance gene; hence, silencing StNRL1 enhances resistance to P. infestans.

Californian thistle (Cirsium arvense): endophytes and Puccinia punctiformis

Californian thistle (Cirisum arvense) is a troublesome weed in pastures and cropping systems. The fungal biocontrol agent Puccinia punctiformis, commonly referred to as thistle rust, performs inconsistently on C. arvense. Problems with P. punctiformis establishment and control of C. arvense may be attributable to differing plant endophytic populations in various environments. This article provides an overview of the relationships between endophytes and their host, but also between endophytes and pathogens with a focus on rust pathogens. This review provides insights into reasons why P. punctiformis performs inconsistently and identifies gaps in our knowledge. Filling these gaps may help to improve performance of this classical fungal biocontrol agent. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Till death do us pair: Co-evolution of plant-necrotroph interactions

Plants use programmed cell death as a potent defense response against biotrophic pathogens that require living host cells to thrive. However, cell death can promote infection by necrotrophic pathogens. This discrepancy creates specific co-evolutionary dynamics in the interaction between plants and necrotrophs. Necrotrophic pathogens produce diverse cell death-inducing effectors that act redundantly on several plant targets and sometimes suppress plant immune responses as an additional function. Plants use surface receptors that recognize necrotrophic effectors to increase quantitative disease resistance, some of which evolved independently in several plant lineages. Co-evolution has shaped molecular mechanisms involved in plant-necrotroph interactions into robust systems, relying on degenerate and multifunctional modules, general-purpose components, and compartmentalized functioning.

Plant immune receptors interact with hemibiotrophic pathogens to activate plant immunity

Phytopathogens pose a devastating threat to the productivity and yield of crops by causing destructive plant diseases in natural and agricultural environments. Hemibiotrophic pathogens have a variable-length biotrophic phase before turning to necrosis and are among the most invasive plant pathogens. Plant resistance to hemibiotrophic pathogens relies mainly on the activation of innate immune responses. These responses are typically initiated after the plant plasma membrane and various plant immune receptors detect immunogenic signals associated with pathogen infection. Hemibiotrophic pathogens evade pathogen-triggered immunity by masking themselves in an arms race while also enhancing or manipulating other receptors to promote virulence. However, our understanding of plant immune defenses against hemibiotrophic pathogens is highly limited due to the intricate infection mechanisms. In this review, we summarize the strategies that different hemibiotrophic pathogens interact with host immune receptors to activate plant immunity. We also discuss the significant role of the plasma membrane in plant immune responses, as well as the current obstacles and potential future research directions in this field. This will enable a more comprehensive understanding of the pathogenicity of hemibiotrophic pathogens and how distinct plant immune receptors oppose them, delivering valuable data for the prevention and management of plant diseases.

Microgravity and evasion of plant innate immunity by human bacterial pathogens

Spaceflight microgravity and modeled-microgravity analogs (MMA) broadly alter gene expression and physiology in both pathogens and plants. Research elucidating plant and bacterial responses to normal gravity or microgravity has shown the involvement of both physiological and molecular mechanisms. Under true and simulated microgravity, plants display differential expression of pathogen-defense genes while human bacterial pathogens exhibit increased virulence, antibiotic resistance, stress tolerance, and reduced LD50 in animal hosts. Human bacterial pathogens including Salmonella enterica and E. coli act as cross-kingdom foodborne pathogens by evading and suppressing the innate immunity of plants for colonization of intracellular spaces. It is unknown if evasion and colonization of plants by human pathogens occurs under microgravity and if there is increased infection capability as demonstrated using animal hosts. Understanding the relationship between microgravity, plant immunity, and human pathogens could prevent potentially deadly outbreaks of foodborne disease during spaceflight. This review will summarize (1) alterations to the virulency of human pathogens under microgravity and MMA, (2) alterations to plant physiology and gene expression under microgravity and MMA, (3) suppression and evasion of plant immunity by human pathogens under normal gravity, (4) studies of plant-microbe interactions under microgravity and MMA. A conclusion suggests future study of interactions between plants and human pathogens under microgravity is beneficial to human safety, and an investment in humanity's long and short-term space travel goals.

Unraveling the role of effector proteins in Bipolaris oryzae infecting North East Indian rice cultivars through time-course transcriptomics analysis

Bipolaris oryzae, causing brown spot disease in rice, is one of the neglected diseases reducing rice productivity. Limited knowledge is available on the genetics of host-pathogen interaction. Here, we used time-course transcriptome sequencing to elucidate the differential transcriptional responses of the pathogen genes in two contradictory infection-responsive rice hosts. Evaluation of transcriptome data showed similar regulation of fungal genes within susceptible (1733) and resistant (1846) hosts at an early stage however, in the later stage, the number was significantly higher in susceptible (2877) compared to resistant (1955) hosts. GO enrichment terms for upregulated genes showed a similar pattern in both the hosts at an early stage, but in the later stage terms related to degradation of carbohydrates, carbohydrate transport, and pathogenesis are enriched extensively within the susceptible host. Likewise, similar expression responses were observed with the secretory and effector proteins. Plant pathogenic homologs genes such as those involved in appressorium and conidia formation, host cell wall degradative enzymes, etc. were reported to be highly upregulated within the susceptible host. This study predicts the successful establishment of B. oryzae BO1 in both the host surfaces at an early stage, while disease progression only occurs in the susceptible host in later stage.

Control of white mold (Sclerotinia sclerotiorum) through plant-mediated RNA interference

The causative agent of white mold, Sclerotinia sclerotiorum, is capable of infecting over 600 plant species and is responsible for significant crop losses across the globe. Control is currently dependent on broad-spectrum chemical agents that can negatively impact the agroecological environment, presenting a need to develop alternative control measures. In this study, we developed transgenic Arabidopsis thaliana (AT1703) expressing hairpin (hp)RNA to silence S. sclerotiorum ABHYDROLASE-3 and slow infection through host induced gene silencing (HIGS). Leaf infection assays show reduced S. sclerotiorum lesion size, fungal load, and ABHYDROLASE-3 transcript abundance in AT1703 compared to wild-type Col-0. To better understand how HIGS influences host-pathogen interactions, we performed global RNA sequencing on AT1703 and wild-type Col-0 directly at the site of S. sclerotiorum infection. RNA sequencing data reveals enrichment of the salicylic acid (SA)-mediated systemic acquired resistance (SAR) pathway, as well as transcription factors predicted to regulate plant immunity. Using RT-qPCR, we identified predicted interacting partners of ABHYDROLASE-3 in the polyamine synthesis pathway of S. sclerotiorum that demonstrate co-reduction with ABHYDROLASE-3 transcript levels during infection. Together, these results demonstrate the utility of HIGS technology in slowing S. sclerotiorum infection and provide insight into the role of ABHYDROLASE-3 in the A. thaliana-S. sclerotiorum pathosystem.

A small cysteine-rich fungal effector, BsCE66 is essential for the virulence of Bipolaris sorokiniana on wheat plants

The Spot Blotch (SB) caused by hemibiotrophic fungal pathogen Bipolaris sorokiniana is one of the most devastating wheat diseases leading to 15-100% crop loss. However, the biology of Triticum-Bipolaris interactions and host immunity modulation by secreted effector proteins remain underexplored. Here, we identified a total of 692 secretory proteins including 186 predicted effectors encoded by B. sorokiniana genome. Gene Ontology categorization showed that these proteins belong to cellular, metabolic and signaling processes, and exhibit catalytic and binding activities. Further, we functionally characterized a cysteine-rich, B. sorokiniana Candidate Effector 66 (BsCE66) that was induced at 24-96 hpi during host colonization. The Δbsce66 mutant did not show vegetative growth defects or stress sensitivity compared to wild-type, but developed drastically reduced necrotic lesions upon infection in wheat plants. The loss-of-virulence phenotype was rescued upon complementing the Δbsce66 mutant with BsCE66 gene. Moreover, BsCE66 does not form homodimer and conserved cysteine residues form intra-molecular disulphide bonds. BsCE66 localizes to the host nucleus and cytosol, and triggers a strong oxidative burst and cell death in Nicotiana benthamiana. Overall, our findings demonstrate that BsCE66 is a key virulence factor that is necessary for host immunity modulation and SB disease progression. These findings would significantly improve our understanding of Triticum-Bipolaris interactions and assist in the development of SB resistant wheat varieties.

Genetics and breeding for resistance against four leaf spot diseases in wheat (Triticum aestivum L.)

In wheat, major yield losses are caused by a variety of diseases including rusts, spike diseases, leaf spot and root diseases. The genetics of resistance against all these diseases have been studied in great detail and utilized for breeding resistant cultivars. The resistance against leaf spot diseases caused by each individual necrotroph/hemi-biotroph involves a complex system involving resistance (R) genes, sensitivity (S) genes, small secreted protein (SSP) genes and quantitative resistance loci (QRLs). This review deals with resistance for the following four-leaf spot diseases: (i) Septoria nodorum blotch (SNB) caused by Parastagonospora nodorum; (ii) Tan spot (TS) caused by Pyrenophora tritici-repentis; (iii) Spot blotch (SB) caused by Bipolaris sorokiniana and (iv) Septoria tritici blotch (STB) caused by Zymoseptoria tritici.

The nuclear effector ArPEC25 from the necrotrophic fungus Ascochyta rabiei targets the chickpea transcription factor CaβLIM1a and negatively modulates lignin biosynthesis, increasing host susceptibility

Fungal pathogens deploy a barrage of secreted effectors to subvert host immunity, often by evading, disrupting, or altering key components of transcription, defense signaling, and metabolic pathways. However, the underlying mechanisms of effectors and their host targets are largely unexplored in necrotrophic fungal pathogens. Here, we describe the effector protein Ascochyta rabiei PEXEL-like Effector Candidate 25 (ArPEC25), which is secreted by the necrotroph A. rabiei, the causal agent of Ascochyta blight disease in chickpea (Cicer arietinum), and is indispensable for virulence. After entering host cells, ArPEC25 localizes to the nucleus and targets the host LIM transcription factor CaβLIM1a. CaβLIM1a is a transcriptional regulator of CaPAL1, which encodes phenylalanine ammonia lyase (PAL), the regulatory, gatekeeping enzyme of the phenylpropanoid pathway. ArPEC25 inhibits the transactivation of CaβLIM1a by interfering with its DNA-binding ability, resulting in negative regulation of the phenylpropanoid pathway and decreased levels of intermediates of lignin biosynthesis, thereby suppressing lignin production. Our findings illustrate the role of fungal effectors in enhancing virulence by targeting a key defense pathway that leads to the biosynthesis of various secondary metabolites and antifungal compounds. This study provides a template for the study of less explored necrotrophic effectors and their host target functions.

Transcriptome Analysis of the Necrotrophic Pathogen Alternaria brassicae Reveals Insights into Its Pathogenesis in Brassica juncea

Alternaria blight or leaf spot caused by Alternaria brassicae has an enormous economic impact on the Brassica crops grown worldwide. Although the genome of A. brassicae has been sequenced, little is known about the genes that play a role during the infection of the host species. In this study, the transcriptome expression profile of A. brassicae during growth and infection was determined. Differential expression analysis revealed that 4,430 genes were differentially expressed during infection. Weighted gene coexpression network analysis helped identify 10 modules, which were highly correlated with growth and infection. Subsequent gene ontology (GO) enrichment analysis of the modules highlighted the involvement of biological processes such as toxin metabolism, ribosome biogenesis, polysaccharide catabolism, copper ion transport, and vesicular trafficking during infection. Additionally, 200 carbohydrate-active enzymes (CAZymes) and 80 potential effectors were significantly upregulated during infection. Furthermore, 18 secondary metabolite gene clusters were also differentially expressed during infection. The clusters responsible for the production of destruxin B, brassicicene C, and HC-toxin were significantly upregulated during infection. Collectively, these results provide an overview of the critical pathways underlying the pathogenesis of A. brassicae and highlight the distinct gene networks that are temporally regulated. The study thus provides novel insights into the transcriptional plasticity of a necrotrophic pathogen during infection of its host. Additionally, the in planta expression evidence for many potential effectors provides a theoretical basis for further investigations into the effector biology of necrotrophic pathogens such as A. brassicae. IMPORTANCE Alternaria brassicae is a necrotrophic pathogen that can infect almost all members of the Brassicaceae family. A. brassicae causes extensive yield losses in oilseed mustard and has practically restricted the cultivation of oilseed brassicas in regions with cool and foggy climatic conditions (foothills and mountainous terrains) where the severity of the pathogen is the highest. In this study, I identified the differentially expressed genes associated with the pathogenicity of A. brassicae through transcriptome sequencing. Also, I have been able to delineate pathways that are active during the early and late stages of infection. Consequently, this study has provided crucial insights into the molecular mechanisms underlying the pathogenesis of A. brassicae, an important necrotrophic pathogen.

Identification and analysis of the secretome of plant pathogenic fungi reveals lifestyle adaptation

The secretory proteome plays an important role in the pathogenesis of phytopathogenic fungi. However, the relationship between the large-scale secretome of phytopathogenic fungi and their lifestyle is not fully understood. In the present study, the secretomes of 150 plant pathogenic fungi were predicted and the characteristics associated with different lifestyles were investigated. In total, 94,974 secreted proteins (SPs) were predicted from these fungi. The number of the SPs ranged from 64 to 1,662. Among these fungi, hemibiotrophic fungi had the highest number (average of 970) and proportion (7.1%) of SPs. Functional annotation showed that hemibiotrophic and necrotroph fungi, differ from biotrophic and symbiotic fungi, contained much more carbohydrate enzymes, especially polysaccharide lyases and carbohydrate esterases. Furthermore, the core and lifestyle-specific SPs orthogroups were identified. Twenty-seven core orthogroups contained 16% of the total SPs and their motif function annotation was represented by serine carboxypeptidase, carboxylesterase and asparaginase. In contrast, 97 lifestyle-specific orthogroups contained only 1% of the total SPs, with diverse functions such as PAN_AP in hemibiotroph-specific and flavin monooxygenases in necrotroph-specific. Moreover, obligate biotrophic fungi had the largest number of effectors (average of 150), followed by hemibiotrophic fungi (average of 120). Among these effectors, 4,155 had known functional annotation and pectin lyase had the highest proportion in the functionally annotated effectors. In addition, 32 sets of RNA-Seq data on pathogen-host interactions were collected and the expression levels of SPs were higher than that of non-SPs, and the expression level of effector genes was higher in biotrophic and hemibiotrophic fungi than in necrotrophic fungi, while secretase genes were highly expressed in necrotrophic fungi. Finally, the secretory activity of five predicted SPs from Setosphearia turcica was experimentally verified. In conclusion, our results provide a foundation for the study of pathogen-host interaction and help us to understand the fungal lifestyle adaptation.

A detailed landscape of CRISPR-Cas-mediated plant disease and pest management

Genome editing technology has rapidly evolved to knock-out genes, create targeted genetic variation, install precise insertion/deletion and single nucleotide changes, and perform large-scale alteration. The flexible and multipurpose editing technologies have started playing a substantial role in the field of plant disease management. CRISPR-Cas has reduced many limitations of earlier technologies and emerged as a versatile toolbox for genome manipulation. This review summarizes the phenomenal progress of the use of the CRISPR toolkit in the field of plant pathology. CRISPR-Cas toolbox aids in the basic studies on host-pathogen interaction, in identifying virulence genes in pathogens, deciphering resistance and susceptibility factors in host plants, and engineering host genome for developing resistance. We extensively reviewed the successful genome editing applications for host plant resistance against a wide range of biotic factors, including viruses, fungi, oomycetes, bacteria, nematodes, insect pests, and parasitic plants. Recent use of CRISPR-Cas gene drive to suppress the population of pathogens and pests has also been discussed. Furthermore, we highlight exciting new uses of the CRISPR-Cas system as diagnostic tools, which rapidly detect pathogenic microorganism. This comprehensive yet concise review discusses innumerable strategies to reduce the burden of crop protection.

Cytokinin Regulates Energy Utilization in Botrytis cinerea

The plant hormone cytokinin (CK) is an important developmental regulator. Previous work has demonstrated that CKs mediate plant immunity and disease resistance. Some phytopathogens have been reported to secrete CKs and may manipulate CK signaling to improve pathogenesis. In recent work, we demonstrated that CK directly inhibits the development and virulence of fungal phytopathogens by attenuating the cell cycle and reducing cytoskeleton organization. Here, focusing on Botrytis cinerea, we report that CK possesses a dual role in fungal biology, with role prioritization being based on sugar availability. In a sugar-rich environment, CK strongly inhibited B. cinerea growth and deregulated cytoskeleton organization. This effect diminished as sugar availability decreased. In its second role, we show using biochemical assays and transgenic redox-sensitive fungal lines that CK can promote glycolysis and energy consumption in B. cinerea, both in vitro and in planta. Glycolysis and increased oxidation mediated by CK were stronger in low sugar availability, indicating that sugar availability could indeed be one possible element determining the role of CK in the fungus. Transcriptomic data further support our findings, demonstrating significant upregulation to glycolysis, oxidative phosphorylation, and sucrose metabolism upon CK treatment. Thus, the effect of CK in fungal biology likely depends on energy status. In addition to the plant producing CK during its interaction with the pathogen for defense priming and pathogen inhibition, the pathogen may take advantage of this increased CK to boost its metabolism and energy production, in preparation for the necrotrophic phase of the infection.

IMPORTANCE The hormone cytokinin (CK) is a plant developmental regulator. Previous research has highlighted the involvement of CK in plant defense. Here, we report that CK has a dual role in plant-fungus interactions, inhibiting fungal growth while positively regulating B. cinerea energy utilization, causing an increase in glucose utilization and energy consumption. The effect of CK on B. cinerea was dependent on sugar availability, with CK primarily causing increases in glycolysis when sugar availability was low, and growth inhibition in a high-sugar environment. We propose that CK acts as a signal to the fungus that plant tissue is present, causing it to activate energy metabolism pathways to take advantage of the available food source, while at the same time, CK is employed by the plant to inhibit the attacking pathogen.

Plant-microbe interactions in the apoplast: Communication at the plant cell wall

The apoplast is a continuous plant compartment that connects cells between tissues and organs and is one of the first sites of interaction between plants and microbes. The plant cell wall occupies most of the apoplast and is composed of polysaccharides and associated proteins and ions. This dynamic part of the cell constitutes an essential physical barrier and a source of nutrients for the microbe. At the same time, the plant cell wall serves important functions in the interkingdom detection, recognition, and response to other organisms. Thus, both plant and microbe modify the plant cell wall and its environment in versatile ways to benefit from the interaction. We discuss here crucial processes occurring at the plant cell wall during the contact and communication between microbe and plant. Finally, we argue that these local and dynamic changes need to be considered to fully understand plant-microbe interactions.

Tracking of Diversity and Evolution in the Brown Rot Fungi Monilinia fructicola, Monilinia fructigena, and Monilinia laxa

Monilinia species are among the most devastating fungi worldwide as they cause brown rot and blossom blight on fruit trees. To understand the molecular bases of their pathogenic lifestyles, we compared the newly assembled genomes of single strains of Monilinia fructicola, M. fructigena and M. laxa, with those of Botrytis cinerea and Sclerotinia sclerotiorum, as the closest species within Sclerotiniaceae. Phylogenomic analysis of orthologous proteins and syntenic investigation suggest that M. laxa is closer to M. fructigena than M. fructicola, and is closest to the other investigated Sclerotiniaceae species. This indicates that M. laxa was the earliest result of the speciation process. Distinct evolutionary profiles were observed for transposable elements (TEs). M. fructicola and M. laxa showed older bursts of TE insertions, which were affected (mainly in M. fructicola) by repeat-induced point (RIP) mutation gene silencing mechanisms. These suggested frequent occurrence of the sexual process in M. fructicola. More recent TE expansion linked with low RIP action was observed in M. fructigena, with very little in S. sclerotiorum and B. cinerea. The detection of active non-syntenic TEs is indicative of horizontal gene transfer and has resulted in alterations in specific gene functions. Analysis of candidate effectors, biosynthetic gene clusters for secondary metabolites and carbohydrate-active enzymes, indicated that Monilinia genus has multiple virulence mechanisms to infect host plants, including toxins, cell-death elicitor, putative virulence factors and cell-wall-degrading enzymes. Some species-specific pathogenic factors might explain differences in terms of host plant and organ preferences between M. fructigena and the other two Monilinia species.

The Multifaceted Roles of Fungal Cutinases during Infection

Cuticles cover the aerial epidermis cells of terrestrial plants and thus represent the first line of defence against invading pathogens, which must overcome this hydrophobic barrier to colonise the inner cells of the host plant. The cuticle is largely built from the cutin polymer, which consists of C16 and C18 fatty acids attached to a glycerol backbone that are further modified with terminal and mid-chain hydroxyl, epoxy, and carboxy groups, all cross-linked by ester bonds. To breach the cuticle barrier, pathogenic fungal species employ cutinases-extracellular secreted enzymes with the capacity to hydrolyse the ester linkages between cutin monomers. Herein, we explore the multifaceted roles that fungal cutinases play during the major four stages of infection: (i) spore landing and adhesion to the host plant cuticle; (ii) spore germination on the host plant cuticle; (iii) spore germ tube elongation and the formation of penetrating structures; and (iv) penetration of the host plant cuticle and inner tissue colonisation. Using previous evidence from the literature and a comprehensive molecular phylogenetic tree of cutinases, we discuss the notion whether the lifestyle of a given fungal species can predict the activity nature of its cutinases.

Cytokinin Inhibits Fungal Development and Virulence by Targeting the Cytoskeleton and Cellular Trafficking

Cytokinin (CK) is an important plant developmental regulator, having activities in many aspects of plant life and response to the environment. CKs are involved in diverse processes in the plant, including stem cell maintenance, vascular differentiation, growth and branching of roots and shoots, leaf senescence, nutrient balance, and stress tolerance. In some cases, phytopathogens secrete CKs. It has been suggested that to achieve pathogenesis in the host, CK-secreting biotrophs manipulate CK signaling to regulate the host cell cycle and nutrient allocation. CK is known to induce host plant resistance to several classes of phytopathogens from a few works, with induced host immunity via salicylic acid signaling suggested to be the prevalent mechanism for this host resistance. Here, we show that CK directly inhibits the growth, development, and virulence of fungal phytopathogens. Focusing on Botrytis cinerea (Bc), we demonstrate that various aspects of fungal development can be reversibly inhibited by CK. We also found that CK affects both budding and fission yeast in a similar manner. Investigating the mechanism by which CK influences fungal development, we conducted RNA next-generation sequencing (RNA-NGS) on mock- and CK-treated B. cinerea samples, finding that CK alters the cell cycle, cytoskeleton, and endocytosis. Cell biology experiments demonstrated that CK affects cytoskeleton components and cellular trafficking in Bc, lowering endocytic rates and endomembrane compartment sizes, likely leading to reduced growth rates and arrested developmental programs. Mutant analyses in yeast confirmed that the endocytic pathway is altered by CK. Our work uncovers a remarkably conserved role for a plant growth hormone in fungal biology, suggesting that pathogen-host interactions resulted in fascinating molecular adaptations on fundamental processes in eukaryotic biology.