EffectorP: predicting fungal effector proteins from secretomes using machine learning

A putative elicitor CcHE1 from Cytospora chrysosperma enhances plant resistance to phytopathogenic fungi

BACKGROUND

Plant pathogens secrete a large number of effectors to host cells during the infection processes, which will manipulate plant immunity and promote fungal infection. Contrarily, some of the effectors can be recognized by the host plants, and then activate the immunity reactions. Therefore, unveiling the critical roles of effectors during the pathogen-plant interactions will benefit disease control.

RESULTS

In this study, we screened and identified a candidate effector, CcHE1, from Cytospora chrysosperma, the main agent of wood canker disease and causes serious loss annually in China. Transient expression of CcHE1 in N. benthamiana leaves showed that it triggered plant cell death in a dose-dependent manner. Subsequently, we found that infiltration injection of 5 μM CcHE1 into N. benthamiana and poplar leaves could not cause cell necrosis but triggered strong defense responses, including reactive oxygen species accumulation, callose deposition, and up-regulated expression of defense-related genes, and NbBAK1 and NbSOBIR1 are needed for plant defense response induced by CcHE1. Importantly, the CcHE1 could enhance the plant resistance to several tested pathogenic fungal species such as Botrytis cinerea, Colletotrichum gloeosporioides, C. chrysosperma, Botryosphaeria dothidea and Cryphonectria parasitica, but had no antifungal activity. Remarkably, deletion of CcHE1 did not affect the growth and pathogenicity of C. chrysosperma.

CONCLUSION

Our results found a putative elicitor CcHE1 which can induce plant immunity, and therefore improve plant broad-spectrum disease resistance. These results provide a new insight into disease control. © 2025 Society of Chemical Industry.

Transposon-Associated Small RNAs Involved in Plant Defense in Poplar

Utilizing high-throughput Illumina sequencing, we examined how small RNA (sRNA) profiles vary in Chinese white poplar (Populus tomentosa) across two pivotal infection stages by the rust fungus Melampsora larici-populina: the biotrophic growth phase (T02; 48 h post infection) and the urediniospore development and dispersal phase (T03; 168 h), both essential for plant colonization and prolonged biotrophic engagement. Far exceeding random expectations, siRNA clusters predominantly arose from transposon regions, with pseudogenes also contributing significantly, and infection-stage-specific variations were notably tied to these transposon-derived siRNAs. As the infection advanced, clusters of 24 nt siRNAs in transposon and intergenic regions exhibited pronounced abundance shifts. An analysis of targets indicated that Populus sRNAs potentially regulate 95% of Melampsora larici-populina genes, with pathogen effector genes showing heightened targeting by sRNAs during the biotrophic and urediniospore phases compared to controls, pointing to selective sRNA-target interactions. In contrast to conserved miRNAs across plant species, Populus-specific miRNAs displayed a markedly greater tendency to target NB-LRR genes. These observations collectively highlight the innovative roles of sRNAs in plant defense, their evolutionary roots, and their dynamic interplay with pathogen coevolution.

Phylogenomics and adaptive evolution of the Colletotrichum gloeosporioides species complex

The Colletotrichum gloeosporioides species complex (CGSC) is one of the most devastating fungal phytopathogens, and is composed of three main clades: Kahawae, Musae, and Theobromicola. Despite the diversity of CGSC, there is limited understanding on their evolutionary mechanisms. By analysing 49 newly assembled genomes, we found that the expansion of transposable elements, especially long terminal repeat retrotransposons, facilitates the expansion of genome size and genetic variation. In-depth analyses suggested that an intra-chromosomal inversion may have been the driving force behind the divergence of Kahawae clade from its ancestor. Within the Kahawae clade, the narrow-hosted quarantine species C. kahawae has undergone extensive chromosomal rearrangements mediated by repetitive sequences, generating highly dynamic lineage-specific genomic regions compared to the closely related broad-hosted species C. cigarro. The findings of this study highlight the role of chromosomal rearrangements in promoting genetic diversification and host adaptation, and provide new perspectives for understanding the evolution of phytopathogenic fungi.

Genomics Research on the Road of Studying Biology and Virulence of Cereal Rust Fungi

Rust fungi are highly destructive pathogens that pose a significant threat to crop production worldwide, especially cereals. Obligate biotrophy and, in many cases, complex life cycles make rust fungi particularly challenging to study. However, recent rapid advances in sequencing technologies and genomic analysis tools have revolutionised rust fungal research. It is anticipated that the increasing availability and ongoing substantial improvements in genome assemblies will propel the field of rust biology into the post-genomic era, instigating a cascade of research endeavours encompassing multi-omics and gene discoveries. This is especially the case for many cereal rust pathogens, for which continental-scale studies of virulence have been conducted over many years and historical collections of viable isolates have been sequenced and assembled. Genomic analysis plays a crucial role in uncovering the underlying causes of the high variability of virulence and the complexity of population dynamics in rust fungi. Here, we provide an overview of progress in rust genomics, discuss the strategies employed in genomic analysis, and elucidate the strides that will drive cereal rust biology into the post-genomic era.

Evolutionary genomics reveals variation in structure and genetic content implicated in virulence and lifestyle in the genus Gaeumannomyces

Gaeumannomyces tritici is responsible for take-all disease, one of the most important wheat root threats worldwide. High-quality annotated genome resources are sorely lacking for this pathogen, as well as for the closely related antagonist and potential wheat take-all biocontrol agent, G. hyphopodioides. As such, we know very little about the genetic basis of the interactions in this host-pathogen-antagonist system. Using PacBio HiFi sequencing technology we have generated nine near-complete assemblies, including two different virulence lineages for G. tritici and the first assemblies for G. hyphopodioides and G. avenae (oat take-all). Genomic signatures support the presence of two distinct virulence lineages in G. tritici (types A and B), with A strains potentially employing a mechanism to prevent gene copy-number expansions. The CAZyme repertoire was highly conserved across Gaeumannomyces, while candidate secreted effector proteins and biosynthetic gene clusters showed more variability and may distinguish pathogenic and non-pathogenic lineages. A transition from self-sterility (heterothallism) to self-fertility (homothallism) may also be a key innovation implicated in lifestyle. We did not find evidence for transposable element and effector gene compartmentalisation in the genus, however the presence of Starship giant transposable elements may contribute to genomic plasticity in the genus. Our results depict Gaeumannomyces as an ideal system to explore interactions within the rhizosphere, the nuances of intraspecific virulence, interspecific antagonism, and fungal lifestyle evolution. The foundational genomic resources provided here will enable the development of diagnostics and surveillance of understudied but agriculturally important fungal pathogens.

Genome-wide characterization of effector proteins in Fusarium zanthoxyli and their effects on plant's innate immunity responses

BACKGROUND

Stem canker of Zanthoxylum bungeanum is a destructive forest disease, caused by Fusarium zanthoxyli, poses a serious threat to the cultivation of Z. bungeanum. The lack of research on effector proteins in F. zanthoxyli has severely limited our understanding of the molecular interactions between F. zanthoxyli and Z. bungeanum, resulting in insufficient effective control technologies for this disease.

RESULTS

In this study, a total of 137 effector proteins (FzEPs) were predicted and characterized based on whole genome of F. zanthoxyli, with an average length of 215 amino acids, 8 cysteine residues, and a molecular weight of 23.06 kD. Besides, the phylogenetic evolution, conserved motifs, domains and annotation information of all the 137 effectors were comprehensively demonstrated. Moreover, transcriptomic analysis indicated that 24 effector genes were significantly upregulated in the early infection stages of F. zanthoxyli, which was confirmed by RT-qPCR. Following, the 24 effector DEGs were cloned and transiently over-expressed in the leaves of tobacco to evaluate their effects on the plant's innate immunity. It was found that effector proteins FzEP94 and FzEP123 induced pronounced programmed cell death (PCD), callose deposition, and reactive oxygen species (ROS) burst in tobacco leaves, whereas FzEP83 and FzEP93 significantly suppressed PCD induced by INF1, accompanied by a less pronounced callose accumulation and ROS burst.

CONCLUSIONS

In this study, we systematically characterized and functionally analyzed the effector proteins of F. zanthoxyli, successfully identifying four effector proteins that can impact the innate immune response of plants. These findings enhance our understanding of effector protein functions in F. zanthoxyli and offer valuable insights for future research on molecular interactions between F. zanthoxyli and Z. bungeanum.

Decoding Pecan's Fungal Foe: A Genomic Insight into Colletotrichum plurivorum Isolate W-6

Pecan (Carya illinoinensis) is a world-renowned nut crop that is highly favored by consumers for its high content of healthy nutrients. For a long time, anthracnose has severely threatened the yield and quality of pecan, causing significant economic losses to the global pecan industry. Here, we report the 54.57-Mb gapless chromosome-level assembly of the pathogenic ascomycetes Colletotrichum plurivorum isolate W-6 from pecan plantations in Southeast China. Six of 12 chromosomes contain, at least, telomeric repeats (CCCTAA)n or (TTAGGG)n at one end. A total of 14,343 protein-coding genes were predicted. Pathogenicity- and virulence-related annotations revealed 137 to 4558 genes associated with the TCDB, PHI, Cyt_P450, DFVF, effector, and secretome databases, respectively. A comparative analysis of isolate W-6, together with 51 other Colletotrichum strains, reveled 13 genes unique to the Orchidearum complex to which isolate W-6 belongs, highlighting the major facilitator superfamily transporters. The detailed analyses of MFS transporters associated with secondary metabolite gene clusters in isolate W-6 led to the identification and protein structure analyses of two key virulence factor candidates in DHA1 subclass, prlG and azaK, which were reported as efflux transporters of antibiotics in other pathogenic fungi. The assembly and further functional investigation of two pathogenic genes identified here potentially provide important resources for better understanding the biology and lifestyle of Colletotrichum and pave the way for designing more efficient strategies to control anthracnose in pecan plantations.

Characterization and Genome Analysis of Fusarium oxysporum Provides Insights into the Pathogenic Mechanisms of the Pokkah Boeng Disease in China

Pokkah Boeng Disease (PBD) is a severe and devastating disease that causes significant damage and yield losses in China. The pathogenic fungus Fusarium oxysporum is responsible for the rapid onset of top rot symptoms in sugarcane. In this study, we selected a representative strain, BS2-6, to perform morphological observations of colonies and determine pathogenicity. We examined the effects of BS2-6 infestation on the ultrastructure of sugarcane leaves. Moreover, we sequenced the whole genome of BS2-6 and examined the effects of various nitrogen sources and chemical reagents on its growth and pathogenicity. Our results indicate that sugarcane leaves inoculated with BS2-6 quickly succumb to heart leaf and growing rot. Ultrastructural analysis revealed that the surface tissues of the diseased leaves were destroyed with mycelium, and conidia blocked leaf stomata, which ultimately led to the degradation of leaf tissues. Ammoniacal nitrogen significantly promoted mycelial growth, pigment secretion, and the expression of genes related to secondary metabolite synthesis, thereby accelerating the development of PBD. In addition, we found that carbendazim effectively inhibited the growth of BS2-6 at various concentrations. These findings provide important insights for the effective prevention and control of PBD during sugarcane production.

CRISPR-Cas9 genome editing reveals that the Pgs gene of Fusarium circinatum is involved in pathogenicity, growth and sporulation

Fusarium circinatum, the causal agent of pine pitch canker, is one of the most destructive pathogens of Pinus species worldwide. Infections by this pathogen result in serious mortality of seedlings due to root and root collar disease, and growth reduction in trees due to canker formation and dieback. Although much is known about the population biology, genetics, and genomics of F. circinatum, relatively little is known regarding the molecular basis of pathogenicity in F. circinatum. In this study, a protoplast-based transformation using CRISPR-Cas9-mediated genome editing was utilized to functionally characterize a putative pathogenicity gene in three different strains of the fungus. In silico analyses suggested the gene likely encodes a small secreted protein, and all isolates in which it was deleted displayed significantly reduced vegetative growth and asexual spore production compared to the wild-type isolates. In pathogenicity tests, lesions induced by the deletion mutants on detached Pinus patula branches were significantly shorter than those produced by the wild-types. The putative pathogenicity gene was named Pgs reflecting its role in pathogenicity, growth, and sporulation. Future research will seek to explore the molecular mechanisms underlying the mutant phenotypes observed. Overall, this study represents a significant advance in F. circinatum research as the development and application of a Cas9-mediated gene deletion process opens new avenues for functional gene characterization underlying many of the pathogen's biological traits.

Comprehensive Genomic Analysis of Meyerozyma guilliermondii CECT13190: An Outstanding Biocontrol Agent

BACKGROUND/OBJECTIVES

Biocontrol agents (BCAs) are gaining attention as sustainable alternatives to chemical pesticides. Understanding their molecular mechanisms is crucial for improving plant protection. This study investigates the genomic features of Meyerozyma guilliermondii CECT13190, a promising BCA, to identify key genes involved in its biocontrol abilities.

METHODS

Whole-genome sequencing of M. guilliermondii was performed, followed by bioinformatics analysis to identify genes and pathways related to biocontrol, including gene copy number variation (CNV) analysis. Gene ontology (GO) analysis was conducted to examine gene functions, and a comparative proteomics approach assessed the presence and role of proteins in the secretome of M. guilliermondii.

RESULTS

Genomic analysis revealed key biocontrol-related pathways. CNV analysis indicated a direct correlation between gene amplification and competitive fitness, with seven genes showing gains and five genes showing losses. GO analysis identified categories such as enzymes, transcription factors, ribosomal and proteasomal complexes, transporters, membrane proteins, RNA processing, and stress-response-related proteins. Secretome analysis identified HSP70 and HSP90 as potential effectors involved in biocontrol activity.

CONCLUSIONS

This study provides insights into the genomic features of M. guilliermondii and its biocontrol potential. The identification of genes involved in the stress response and the secretome highlights the multifaceted mechanisms through which M. guilliermondii antagonizes plant pathogens. Practical outcomes include the identification of candidate genes and proteins, such as HSP70 and HSP90, which can be targeted to enhance biocontrol efficiency in agricultural applications. Additionally, the observed CNVs offer a potential avenue for strain improvement programs to optimize competitiveness and efficacy in field conditions.

Multiomic Analysis Provided Insights into the Responses of Carbon Sources by Wood-Rotting Fungi Daldinia carpinicola

Daldinia carpinicola is a newly identified species of wood-rotting fungi, with substantial aspects of its biology and ecological function yet to be clarified. A Nanopore third-generation sequencer was employed for de novo genome assembly to examine the genetic characteristics. The genome consisted of 35.93 Mb in 46 contigs with a scaffold N50 of 4.384 Mb. Glycoside hydrolases and activities enzymes accounted for a large proportion of the 522 identified carbohydrate-active enzymes (CAZymes), suggesting a strong wood degradation ability. Phylogenetic and comparative analysis revealed a close evolutionary relationship between D. carpinicola and D. bambusicola. D. carpinicola and Hypoxylon fragiforme exhibited significant collinear inter-species genome alignment. Based on transcriptome and metabolomic analyses, D. carpinicola showed a greater ability to utilize sucrose over sawdust as a carbon source, enhancing its growth by activating glycolysis/gluconeogenesis and the citrate cycle. However, compared with sucrose, sawdust as a carbon source activated D. carpinicola amino acid biosynthesis and the production of various secondary metabolites, including diterpenoid, indole alkaloid, folate, porphyrin, and biotin metabolism. The study establishes a theoretical basis for research and applications in biological processes, demonstrating a strategy to modulate the production of secondary metabolites by altering its carbon sources in D. carpinicola.

A barley MLA immune receptor is activated by a fungal nonribosomal peptide effector for disease susceptibility

The barley Mla locus contains functionally diversified genes that encode intracellular nucleotide-binding leucine-rich repeat receptors (NLRs) and confer strain-specific immunity to biotrophic and hemibiotrophic fungal pathogens. In this study, we isolated a barley gene Scs6, which is an allelic variant of Mla genes but confers susceptibility to the isolate ND90Pr (BsND90Pr) of the necrotrophic fungus Bipolaris sorokiniana. We generated Scs6 transgenic barley lines and showed that Scs6 is sufficient to confer susceptibility to BsND90Pr in barley genotypes naturally lacking the receptor. The Scs6-encoded NLR (SCS6) is activated by a nonribosomal peptide (NRP) effector produced by BsND90Pr to induce cell death in barley and Nicotiana benthamiana. Domain swaps between MLAs and SCS6 reveal that the SCS6 leucine-rich repeat domain is a specificity determinant for receptor activation by the NRP effector. Scs6 is maintained in both wild and domesticated barley populations. Our phylogenetic analysis suggests that Scs6 is a Hordeum-specific innovation. We infer that SCS6 is a bona fide immune receptor that is likely directly activated by the nonribosomal peptide effector of BsND90Pr for disease susceptibility in barley. Our study provides a stepping stone for the future development of synthetic NLR receptors in crops that are less vulnerable to modification by necrotrophic pathogens.

Repeat-induced point mutations driving Parastagonospora nodorum genomic diversity are balanced by selection against non-synonymous mutations

Parastagonospora nodorum is necrotrophic fungal pathogen of wheat with significant genomic resources. Population-level pangenome data for 173 isolates, of which 156 were from Western Australia (WA) and 17 were international, were examined for overall genomic diversity and effector gene content. A heterothallic core population occurred across all regions of WA, with asexually-reproducing clonal clusters in dryer northern regions. High potential for SNP diversity in the form of repeat-induced point mutation (RIP)-like transitions, was observed across the genome, suggesting widespread 'RIP-leakage' from transposon-rich repetitive sequences into non-repetitive regions. The strong potential for RIP-like mutations was balanced by negative selection against non-synonymous SNPs, that was observed within protein-coding regions. Protein isoform profiles of known effector loci (SnToxA, SnTox1, SnTox3, SnTox267, and SnTox5) indicated low-levels of non-synonymous and high-levels of silent RIP-like mutations. Effector predictions identified 186 candidate secreted predicted effector proteins (CSEPs), 69 of which had functional annotations and included confirmed effectors. Pangenome-based effector isoform profiles across WA were distinct from global isolates and were conserved relative to population structure, and may enable new approaches for monitoring crop disease pathotypes.

An effector protein of Fusarium graminearum targets chloroplasts and suppresses cyclic photosynthetic electron flow

Chloroplasts are important photosynthetic organelles that regulate plant immunity, growth, and development. However, the role of fungal secretory proteins in linking the photosystem to the plant immune system remains largely unknown. Our systematic characterization of 17 chloroplast-targeting secreted proteins of Fusarium graminearum indicated that Fg03600 is an important virulence factor. Fg03600 translocation into plant cells and accumulation in chloroplasts depended on its chloroplast transit peptide. Fg03600 interacted with the wheat (Triticum aestivum L.) proton gradient regulation 5-like protein 1 (TaPGRL1), a part of the cyclic photosynthetic electron transport chain, and promoted TaPGRL1 homo-dimerization. Interestingly, TaPGRL1 also interacted with ferredoxin (TaFd), a chloroplast ferredoxin protein that transfers cyclic electrons to TaPGRL1. TaFd competed with Fg03600 for binding to the same region of TaPGRL1. Fg03600 expression in plants decreased cyclic electron flow (CEF) but increased the production of chloroplast-derived reactive oxygen species (ROS). Stably silenced TaPGRL1 impaired resistance to Fusarium head blight (FHB) and disrupted CEF. Overall, Fg03600 acts as a chloroplast-targeting effector to suppress plant CEF and increase photosynthesis-derived ROS for FHB development at the necrotrophic stage by promoting homo-dimeric TaPGRL1 or competing with TaFd for TaPGRL1 binding.

Sporocadaceae revisited

Sporocadaceae is a species-rich and cosmopolitan fungal family including species of plant pathogens, endophytes or saprobes, and parasites of humans and animals. The taxonomy of Sporocadaceae has recently been revised using a polyphasic approach. However, much remains unknown about the diversity of species and their host associations. A collection of 488 strains, mostly from China and associated with 129 host plant species, was studied based on morphological comparisons and multi-locus (LSU, ITS, tef-1α, tub2, and rpb2) phylogenies. Our results revealed that they belonged to 86 species, one new genus (Cavernicola gen. nov.) and seven known genera, including Discosia, Monochaetia, Neopestalotiopsis, Pestalotiopsis, Seimatosporium, Seiridium and Sporocadus. Of these, 43 new species and three new combinations (Dis. kaki, Mon. bulbophylli, and Neo. keteleeriae) are proposed in this paper. In addition, Neo. vaccinii, Pes. kaki and Pes. nanjingensis are synonymised under Neo. hispanica, Pes. menhaiensis and Pes. sichuanensis, respectively. We also corrected seven problematic sequences of type materials of previously published species, namely Neo. iranensis (tef-1α, ITS, tub2), Pes. jesteri (tef-1α), Pes. photinicola (ITS, tub2) and Pes. yunnanensis (ITS). Based on this study, Pestalotiopsis and Neopestalotiopsis are the most commonly detected genera within the Sporocadaceae family, associated with 84 and 70 plant species, respectively. Furthermore, considering the importance of Sporocadaceae and the fact that commonly used loci provide little valid information for species delimitation in this family, especially for Neopestalotiopsis and Pestalotiopsis, we initiated a phylogenomic project in this study. It will not only contribute to the knowledge of species boundaries but will also provide an important basis for evolutionary studies and research on secondary metabolites in Sporocadaceae. Taxonomic novelties: New genus: Cavernicola P. Razaghi, F. Liu & L. Cai. New species: Cavernicola guangxiensis P. Razaghi, F. Liu & L. Cai, Discosia ascidiata P. Razaghi, F. Liu & L. Cai, Discosia jiangxiensis P. Razaghi, F. Liu & L. Cai, Discosia navicularis P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis ageratinae P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis castanopsidis P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis celtidis P. Razaghi, F. Liu, M. Raza & L. Cai, Neopestalotiopsis collariata P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis dimorphospora P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis dolichoconidiophora P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis fijiensis P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis fimbriata P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis fuzhouensis P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis guangxiensis P. Razaghi, F. Liu, M. Raza & L. Cai, Neopestalotiopsis guizhouensis P. Razaghi, F. Liu, M. Raza & L. Cai, Neopestalotiopsis jiangxiensis P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis liquidambaris P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis machili P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis megabetaspora P. Razaghi, F. Liu, M. Raza & L. Cai, Neopestalotiopsis moniliformis P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis nanningensis P. Razaghi, F. Liu, M. Raza & L. Cai, Neopestalotiopsis phyllostachydis P. Razaghi, F. Liu, M. Raza & L. Cai, Neopestalotiopsis poae P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis smilacis P. Razaghi, F. Liu, M. Raza & L. Cai, Pestalotiopsis alloschemones P. Razaghi, F. Liu & L. Cai, Pestalotiopsis americana P. Razaghi, F. Liu & L. Cai, Pestalotiopsis biappendiculata P. Razaghi, F. Liu & L. Cai, Pestalotiopsis cratoxyli P. Razaghi, F. Liu, M. Raza & L. Cai, Pestalotiopsis exudata P. Razaghi, F. Liu & L. Cai, Pestalotiopsis fusiformis P. Razaghi, F. Liu & L. Cai, Pestalotiopsis ganzhouensis P. Razaghi, F. Liu & L. Cai, Pestalotiopsis leucospermi P. Razaghi, F. Liu & L. Cai, Pestalotiopsis lobata P. Razaghi, F. Liu & L. Cai, Pestalotiopsis machili P. Razaghi, F. Liu & L. Cai, Pestalotiopsis multiappendiculata P. Razaghi, F. Liu & L. Cai, Pestalotiopsis pruni P. Razaghi, F. Liu & L. Cai, Pestalotiopsis rubrae P. Razaghi, F. Liu, M. Raza & L. Cai, Pestalotiopsis wulichongensis P. Razaghi, F. Liu, M. Raza & L. Cai, Seimatosporium tibetense P. Razaghi, F. Liu & L. Cai, Seiridium rhododendri P. Razaghi, F. Liu & L. Cai, Sporocadus cavernicola P. Razaghi, F. Liu & L. Cai, Sporocadus hyperici P. Razaghi, F. Liu & L. Cai, Sporocadus tibetensis P. Razaghi, F. Liu & L. Cai. New combinations: Discosia kaki (Kaz. Tanaka et al.) P. Razaghi, F. Liu & L. Cai, Monochaetia bulbophylli (S.F. Ran & Yong Wang bis) P. Razaghi, F. Liu & L. Cai, Neopestalotiopsis keteleeriae (Y. Song et al.) P. Razaghi, F. Liu & L. Cai. Citation: Razaghi P, Raza M, Han SL, Ma ZY, Cai L, Zhao P, Chen Q, Phurbu D, Liu F (2024). Sporocadaceae revisited. Studies in Mycology 109: 155-272. doi: 10.3114/sim.2024.109.03.

Transcriptomics reveal a mechanism of niche defense: two beneficial root endophytes deploy an antimicrobial GH18-CBM5 chitinase to protect their hosts

Effector secretion is crucial for root endophytes to establish and protect their ecological niche. We used time-resolved transcriptomics to monitor effector gene expression dynamics in two closely related Sebacinales, Serendipita indica and Serendipita vermifera, during symbiosis with three plant species, competition with the phytopathogenic fungus Bipolaris sorokiniana, and cooperation with root-associated bacteria. We observed increased effector gene expression in response to biotic interactions, particularly with plants, indicating their importance in host colonization. Some effectors responded to both plants and microbes, suggesting dual roles in intermicrobial competition and plant-microbe interactions. A subset of putative antimicrobial effectors, including a GH18-CBM5 chitinase, was induced exclusively by microbes. Functional analyses of this chitinase revealed its antimicrobial and plant-protective properties. We conclude that dynamic effector gene expression underpins the ability of Sebacinales to thrive in diverse ecological niches with a single fungal chitinase contributing substantially to niche defense.

Use of the Puccinia sorghi haustorial transcriptome to identify and characterize AvrRp1-D recognized by the maize Rp1-D resistance protein

The common rust disease of maize is caused by the obligate biotrophic fungus Puccinia sorghi. The maize Rp1-D allele imparts resistance against the P. sorghi IN2 isolate by initiating a defense response that includes a rapid localized programmed cell death process, the hypersensitive response (HR). In this study, to identify AvrRp1-D from P. sorghi IN2, we employed the isolation of haustoria, facilitated by a biotin-streptavidin interaction, as a powerful approach. This method proves particularly advantageous in cases where the genome information for the fungal pathogen is unavailable, enhancing our ability to explore and understand the molecular interactions between maize and P. sorghi. The haustorial transcriptome generated through this technique, in combination with bioinformatic analyses such as SignalP and TMHMM, enabled the identification of 251 candidate effectors. We ultimately identified two closely related genes, AvrRp1-D.1 and AvrRp1-D.2, which triggered an Rp1-D-dependent defense response in Nicotiana benthamiana. AvrRp1-D-induced Rp1-D-dependent HR was further confirmed in maize protoplasts. We demonstrated that AvrRp1-D.1 interacts directly and specifically with the leucine-rich repeat (LRR) domain of Rp1-D through yeast two-hybrid assay. We also provide evidence that, in the absence of Rp1-D, AvrRp1-D.1 plays a role in suppressing the plant immune response. Our research provides valuable insights into the molecular interactions driving resistance against common rust in maize.

Comparative secretome analysis unveils species-specific virulence factors in Elsinoe perseae, the causative agent of the scab disease of avocado (Persea americana)

The scab disease, caused by Elsinoe perseae, poses a significant risk to avocado (Persea americana) production in countries with warm and humid climates. Although the genome has been published, the precise virulence factors accountable for the pathogenicity of E. perseae have not yet been determined. The current study employed an in silico approach to identify and functionally characterize the secretory proteins of E. perseae. A total of 654 potential secretory proteins were identified, of which 190 were classified as carbohydrate-active enzymes (CAZymes), 49 as proteases, and 155 as potential effectors. A comparison to six other closely related species identified 40 species-specific putative effectors in E. perseae, indicating their specific involvement in the pathogenicity of E. perseae on avocado. The data presented in this study might be valuable for further research focused on understanding the molecular mechanisms that contribute to the pathogenicity of E. perseae on avocado.

Whole-Genome Sequencing of the Entomopathogenic Fungus Fusarium solani KMZW-1 and Its Efficacy Against Bactrocera dorsalis

Fusarium solani KMZW-1 is recognized for its potential as a biocontrol agent against agricultural and forestry pests, particularly due to its compatibility with integrated pest management (IPM) strategies. This study aimed to investigate the complete genome of F. solani KMZW-1 and assess its pathogenicity against Bactrocera dorsalis. Whole-genome sequencing revealed a genome size of 47,239,278 bp, comprising 27 contigs, with a GC content of 51.16% and fungus identified as F. solani KMZW-1. The genome completeness was assessed as 97.93% using BUSCO analysis, the DFVF sequence identifier was Fusarium 0G092560.1, and AntiSMASH analysis identified 35 gene clusters associated with secondary metabolite biosynthesis, providing insights into the genetic basis of its pathogenic mechanisms and biocontrol potential. Comparative genomic analysis found 269 unique genes for F. solani KMZW-1, and collinearity analysis exhibited a high degree of synteny with Fusarium solani-melongenae. The pathogenicity of F. solani KMZW-1 was assessed using concentrations ranging from 1 × 104 to 1 × 1011 conidia/mL. Higher concentrations (1 × 1010 to 1 × 1011 conidia/mL) resulted in significantly increased cumulative mortality rates of B. dorsalis adults compared to the control group. Notably, the pathogenicity was higher in male adults than in females. Probit analysis yielded LC50 (50% lethal concentration) values of 5.662 for female and 4.486 for male B. dorsalis adults. In summary, F. solani, KMZW-1 exhibits strong insecticidal activity against B. dorsalis and shows potential as a biocontrol agent with IPM strategies. These findings provide robust genomic evidence supporting the use of F. solani KMZW-1 in managing against B. dorsalis populations.

Comparative genomics and transcriptomics reveal differences in effector complement and expression between races of Fusarium oxysporum f.sp. lactucae

This study presents the first genome and transcriptome analyses for Fusarium oxysporum f. sp. lactucae (Fola) which causes Fusarium wilt disease of lettuce. Long-read genome sequencing of three race 1 (Fola1) and three race 4 (Fola4) isolates revealed key differences in putative effector complement between races and with other F. oxysporum ff. spp. following mimp-based bioinformatic analyses. Notably, homologues of Secreted in Xylem (SIX) genes, also present in many other F. oxysporum ff. spp, were identified in Fola, with both SIX9 and SIX14 (multiple copies with sequence variants) present in both Fola1 and Fola4. All Fola4 isolates also contained an additional single copy of SIX8. RNAseq of lettuce following infection with Fola1 and Fola4 isolates identified highly expressed effectors, some of which were homologues of those reported in other F. oxysporum ff. spp. including several in F. oxysporum f. sp. apii. Although SIX8, SIX9 and SIX14 were all highly expressed in Fola4, of the two SIX genes present in Fola1, only SIX9 was expressed as further analysis revealed that SIX14 gene copies were disrupted by insertion of a transposable element. Two variants of Fola4 were also identified based on different genome and effector-based analyses. This included two different SIX8 sequence variants which were divergently transcribed from a shared promoter with either PSE1 or PSL1 respectively. In addition, there was evidence of two independent instances of HCT in the different Fola4 variants. The involvement of helitrons in Fola genome rearrangement and gene expression is discussed.

Uncovering the Mechanisms: The Role of Biotrophic Fungi in Activating or Suppressing Plant Defense Responses

This paper discusses the mechanisms by which fungi manipulate plant physiology and suppress plant defense responses by producing effectors that can target various host proteins. Effector-triggered immunity and effector-triggered susceptibility are pivotal elements in the complex molecular dialogue underlying plant-pathogen interactions. Pathogen-produced effector molecules possess the ability to mimic pathogen-associated molecular patterns or hinder the binding of pattern recognition receptors. Effectors can directly target nucleotide-binding domain, leucine-rich repeat receptors, or manipulate downstream signaling components to suppress plant defense. Interactions between these effectors and receptor-like kinases in host plants are critical in this process. Biotrophic fungi adeptly exploit the signaling networks of key plant hormones, including salicylic acid, jasmonic acid, abscisic acid, and ethylene, to establish a compatible interaction with their plant hosts. Overall, the paper highlights the importance of understanding the complex interplay between plant defense mechanisms and fungal effectors to develop effective strategies for plant disease management.

Virulent Effector Hasp155 of Puccinia striiformis f. sp. tritici Suppresses Plant Immunity and Promotes Fungus Infection

As a kind of obligate biotrophic fungus, Puccinia striiformis f. sp. tritici (Pst) secretes vast effectors via haustoria to host cells during the infection to inhibit host defense responses and promote fungal invasion. In this study, based on the completion of genome sequencing and haustorial transcriptome sequencing of Pst, we identified a Pst effector (Hasp155) that is significantly induced in the early stage of Pst infection to wheat. The 18 N-terminal amino acids of Hasp155 encoded a signal peptide with a secretory function. Transient expression of Hasp155 in Nicotiana benthamiana inhibited Bax-induced cell death as well as chitin-triggered callose deposition and defense-related gene expression. Moreover, delivery of the Hasp155 protein into wheat cells via type three secretion systems (TTSS) led to reduced plant immunity to nonpathogenic bacteria and to the avirulent Pst race with decreased H2O2 accumulation and promoted Pst development. Furthermore, transgenic overexpression of Hasp155 significantly renders wheat resistance susceptible, resulting in a decreased defense response and increased Pst pathogenicity. Overall, these results indicate that Hasp155 is an important effector of Pst pathogenicity by suppressing plant immunity.

A Genomic Sequence Resource of Diaporthe mahothocarpus GZU-Y2 Causing Leaf Spot Blight in Camellia oleifera

Diaporthe mahothocarpus GZU-Y2, a new pathogen responsible for leaf spot blight disease, leads to significant damage and economic losses in some Camellia oleifera plantations. The current study annotated the genome of the D. mahothocarpus isolate GZU-Y2 to advance our knowledge of the pathogen and facilitate improved disease management of leaf spot blight. The initial Pacbio-Illumina hybrid draft genome for GZU-Y2 resulted in a high-quality assembly with 62 contigs, characterized by an N50 length of 7.07 Mb. The complete genome of isolate GZU-Y2 was 58.97 Mbp, with a GC content of 50.65%. Importantly, the assembly exhibits remarkable integrity, with 97.93% of complete BUSCO validating genome completeness. The prediction results showed that a total of 15,918 protein-coding genes were annotated using multiple bioinformatics databases. The genome assembly and annotation resource reported here will be useful for the further study of fungal infection mechanisms and pathogen-host interaction.

Fungtion: A Server for Predicting and Visualizing Fungal Effector Proteins

Fungal pathogens pose significant threats to plant health by secreting effectors that manipulate plant-host defences. However, identifying effector proteins remains challenging, in part because they lack common sequence motifs. Here, we introduce Fungtion (Fungal effector prediction), a toolkit leveraging a hybrid framework to accurately predict and visualize fungal effectors. By combining global patterns learned from pretrained protein language models with refined information from known effectors, Fungtion achieves state-of-the-art prediction performance. Additionally, the interactive visualizations we have developed enable researchers to explore both sequence- and high-level relationships between the predicted and known effectors, facilitating effector function discovery, annotation, and hypothesis formulation regarding plant-pathogen interactions. We anticipate Fungtion to be a valuable resource for biologists seeking deeper insights into fungal effector functions and for computational biologists aiming to develop future methodologies for fungal effector prediction: https://step3.erc.monash.edu/Fungtion/.

Whole-genome sequence of Sclerotium delphinii, a pathogenic fungus of Dendrobium officinale southern blight

Dendrobium officinale is a rare and precious medicinal plant. Southern blight is a destructive disease in the artificial cultivation of D. officinale, and one of its pathogens is Sclerotium delphinii. S. delphinii is a phytopathogenic fungus with a wide host range with extremely strong pathogenicity. In this study, S. delphinii was isolated from D. officinale with southern blight. Subsequently, this specific strain underwent thorough whole-genome sequencing using the PacBio Sequel II platform, which employed single-molecule real-time (SMRT) technology. Comprehensive annotations were obtained through functional annotation of protein sequences using various publicly available databases. The genome of S. delphinii measures 73.66 Mb, with an N90 contig size of 2,707,110 bp, and it contains 18,506 putative predictive genes. This study represents the first report on the genome size assembly and annotation of S. delphinii, making it the initial species within the Sclerotium genus to undergo whole-genome sequencing, which can provide solid data and a theoretical basis for further research on the pathogenesis, omics of S. delphinii.

Definition of the effector landscape across 13 phytoplasma proteomes with LEAPH and EffectorComb

'Candidatus Phytoplasma' genus, a group of fastidious phloem-restricted bacteria, can infect a wide variety of both ornamental and agro-economically important plants. Phytoplasmas secrete effector proteins responsible for the symptoms associated with the disease. Identifying and characterizing these proteins is of prime importance for expanding our knowledge of the molecular bases of the disease. We faced the challenge of identifying phytoplasma's effectors by developing LEAPH, a machine learning ensemble predictor composed of four models. LEAPH was trained on 479 proteins from 53 phytoplasma species, described by 30 features. LEAPH achieved 97.49% accuracy, 95.26% precision and 98.37% recall, ensuring a low false-positive rate and outperforming available state-of-the-art methods. The application of LEAPH to 13 phytoplasma proteomes yields a comprehensive landscape of 2089 putative pathogenicity proteins. We identified three classes according to different secretion models: 'classical', 'classical-like' and 'non-classical'. Importantly, LEAPH identified 15 out of 17 known experimentally validated effectors belonging to the three classes. Furthermore, to help the selection of novel candidates for biological validation, we applied the Self-Organizing Maps algorithm and developed a Shiny app called EffectorComb. LEAPH and the EffectorComb app can be used to boost the characterization of putative effectors at both computational and experimental levels, and can be employed in other phytopathological models.

Identification of novel toxins associated with the extracellular contractile injection system using machine learning

Secretion systems play a crucial role in microbe-microbe or host-microbe interactions. Among these systems, the extracellular contractile injection system (eCIS) is a unique bacterial and archaeal extracellular secretion system that injects protein toxins into target organisms. However, the specific proteins that eCISs inject into target cells and their functions remain largely unknown. Here, we developed a machine learning classifier to identify eCIS-associated toxins (EATs). The classifier combines genetic and biochemical features to identify EATs. We also developed a score for the eCIS N-terminal signal peptide to predict EAT loading. Using the classifier we classified 2,194 genes from 950 genomes as putative EATs. We validated four new EATs, EAT14-17, showing toxicity in bacterial and eukaryotic cells, and identified residues of their respective active sites that are critical for toxicity. Finally, we show that EAT14 inhibits mitogenic signaling in human cells. Our study provides insights into the diversity and functions of EATs and demonstrates machine learning capability of identifying novel toxins. The toxins can be employed in various applications dependently or independently of eCIS.

The origin, deployment, and evolution of a plant-parasitic nematode effectorome

Plant-parasitic nematodes constrain global food security. During parasitism, they secrete effectors into the host plant from two types of pharyngeal gland cells. These effectors elicit profound changes in host biology to suppress immunity and establish a unique feeding organ from which the nematode draws nutrition. Despite the importance of effectors in nematode parasitism, there has been no comprehensive identification and characterisation of the effector repertoire of any plant-parasitic nematode. To address this, we advance techniques for gland cell isolation and transcriptional analysis to define a stringent annotation of putative effectors for the cyst nematode Heterodera schachtii at three key life-stages. We define 717 effector gene loci: 269 "known" high-confidence homologs of plant-parasitic nematode effectors, and 448 "novel" effectors with high gland cell expression. In doing so we define the most comprehensive "effectorome" of a plant-parasitic nematode to date. Using this effector definition, we provide the first systems-level understanding of the origin, deployment and evolution of a plant-parasitic nematode effectorome. The robust identification of the effector repertoire of a plant-parasitic nematode will underpin our understanding of nematode pathology, and hence, inform strategies for crop protection.

Decoding the Arsenal: Protist Effectors and Their Impact on Photosynthetic Hosts

Interactions between various microbial pathogens including viruses, bacteria, fungi, oomycetes, and their plant hosts have traditionally been the focus of phytopathology. In recent years, a significant and growing interest in the study of eukaryotic microorganisms not classified among fungi or oomycetes has emerged. Many of these protists establish complex interactions with photosynthetic hosts, and understanding these interactions is crucial in understanding the dynamics of these parasites within traditional and emerging types of farming, including marine aquaculture. Many phytopathogenic protists are biotrophs with complex polyphasic life cycles, which makes them difficult or impossible to culture, a fact reflected in a wide gap in the availability of comprehensive genomic data when compared to fungal and oomycete plant pathogens. Furthermore, our ability to use available genomic resources for these protists is limited by the broad taxonomic distance that these organisms span, which makes comparisons with other genomic datasets difficult. The current rapid progress in genomics and computational tools for the prediction of protein functions and interactions is revolutionizing the landscape in plant pathology. This is also opening novel possibilities, specifically for a deeper understanding of protist effectors. Tools like AlphaFold2 enable structure-based function prediction of effector candidates with divergent protein sequences. In turn, this allows us to ask better biological questions and, coupled with innovative experimental strategies, will lead into a new era of effector research, especially for protists, to expand our knowledge on these elusive pathogens and their interactions with photosynthetic hosts. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

The massive 340 megabase genome of Anisogramma anomala, a biotrophic ascomycete that causes eastern filbert blight of hazelnut

BACKGROUND

The ascomycete fungus Anisogramma anomala causes Eastern Filbert Blight (EFB) on hazelnut (Corylus spp.) trees. It is a minor disease on its native host, the American hazelnut (C. americana), but is highly destructive on the commercially important European hazelnut (C. avellana). In North America, EFB has historically limited commercial production of hazelnut to west of the Rocky Mountains. A. anomala is an obligately biotrophic fungus that has not been grown in continuous culture, rendering its study challenging. There is a 15-month latency before symptoms appear on infected hazelnut trees, and only a sexual reproductive stage has been observed. Here we report the sequencing, annotation, and characterization of its genome.

RESULTS

The genome of A. anomala was assembled into 108 scaffolds totaling 342,498,352 nt with a GC content of 34.46%. Scaffold N50 was 33.3 Mb and L50 was 5. Nineteen scaffolds with lengths over 1 Mb constituted 99% of the assembly. Telomere sequences were identified on both ends of two scaffolds and on one end of another 10 scaffolds. Flow cytometry estimated the genome size of A. anomala at 370 Mb. The genome exhibits two-speed evolution, with 93% of the assembly as AT-rich regions (32.9% GC) and the other 7% as GC-rich (57.1% GC). The AT-rich regions consist predominantly of repeats with low gene content, while 90% of predicted protein coding genes were identified in GC-rich regions. Copia-like retrotransposons accounted for more than half of the genome. Evidence of repeat-induced point mutation (RIP) was identified throughout the AT-rich regions, and two copies of the rid gene and one of dim-2, the key genes in the RIP mutation pathway, were identified in the genome. Consistent with its homothallic sexual reproduction cycle, both MAT1-1 and MAT1-2 idiomorphs were found. We identified a large suite of genes likely involved in pathogenicity, including 614 carbohydrate active enzymes, 762 secreted proteins and 165 effectors.

CONCLUSIONS

This study reveals the genomic structure, composition, and putative gene function of the important pathogen A. anomala. It provides insight into the molecular basis of the pathogen's life cycle and a solid foundation for studying EFB.

Template-Based Modelling of the Structure of Fungal Effector Proteins

The discovery of new fungal effector proteins is necessary to enable the screening of cultivars for disease resistance. Sequence-based bioinformatics methods have been used for this purpose, but only a limited number of functional effector proteins have been successfully predicted and subsequently validated experimentally. A significant obstacle is that many fungal effector proteins discovered so far lack sequence similarity or conserved sequence motifs. The availability of experimentally determined three-dimensional (3D) structures of a number of effector proteins has recently highlighted structural similarities amongst groups of sequence-dissimilar fungal effectors, enabling the search for similar structural folds amongst effector sequence candidates. We have applied template-based modelling to predict the 3D structures of candidate effector sequences obtained from bioinformatics predictions and the PHI-BASE database. Structural matches were found not only with ToxA- and MAX-like effector candidates but also with non-fungal effector-like proteins-including plant defensins and animal venoms-suggesting the broad conservation of ancestral structural folds amongst cytotoxic peptides from a diverse range of distant species. Accurate modelling of fungal effectors were achieved using RaptorX. The utility of predicted structures of effector proteins lies in the prediction of their interactions with plant receptors through molecular docking, which will improve the understanding of effector-plant interactions.

Characterization of Microbotryum lychnidis-dioicae Secreted Effector Proteins, Their Potential Host Targets, and Localization in a Heterologous Host Plant

Microbotryum lychnidis-dioicae is an obligate fungal species colonizing the plant host, Silene latifolia. The fungus synthesizes and secretes effector proteins into the plant host during infection to manipulate the host for completion of the fungal lifecycle. The goal of this study was to continue functional characterization of such M. lychnidis-dioicae effectors. Here, we identified three putative effectors and their putative host-plant target proteins. MVLG_02245 is highly upregulated in M. lychnidis-dioicae during infection; yeast two-hybrid analysis suggests it targets a tubulin α-1 chain protein ortholog in the host, Silene latifolia. A potential plant protein interacting with MVLG_06175 was identified as CASP-like protein 2C1 (CASPL2C1), which facilitates the polymerization of the Casparian strip at the endodermal cells. Proteins interacting with MVLG_05122 were identified as CSN5a or 5b, involved in protein turnover. Fluorescently labelled MVLG_06175 and MVLG_05122 were expressed in the heterologous plant, Arabidopsis thaliana. MVLG_06175 formed clustered granules at the tips of trichomes on leaves and in root caps, while MVLG_05122 formed a band structure at the base of leaf trichomes. Plants expressing MVLG_05122 alone were more resistant to infection with Fusarium oxysporum. These results indicate that the fungus might affect the formation of the Casparian strip in the roots and the development of trichomes during infection as well as alter plant innate immunity.

A review of artificial intelligence-assisted omics techniques in plant defense: current trends and future directions

Plants intricately deploy defense systems to counter diverse biotic and abiotic stresses. Omics technologies, spanning genomics, transcriptomics, proteomics, and metabolomics, have revolutionized the exploration of plant defense mechanisms, unraveling molecular intricacies in response to various stressors. However, the complexity and scale of omics data necessitate sophisticated analytical tools for meaningful insights. This review delves into the application of artificial intelligence algorithms, particularly machine learning and deep learning, as promising approaches for deciphering complex omics data in plant defense research. The overview encompasses key omics techniques and addresses the challenges and limitations inherent in current AI-assisted omics approaches. Moreover, it contemplates potential future directions in this dynamic field. In summary, AI-assisted omics techniques present a robust toolkit, enabling a profound understanding of the molecular foundations of plant defense and paving the way for more effective crop protection strategies amidst climate change and emerging diseases.

Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers?

Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.

Analysis of five near-complete genome assemblies of the tomato pathogen Cladosporium fulvum uncovers additional accessory chromosomes and structural variations induced by transposable elements effecting the loss of avirulence genes

BACKGROUND

Fungal plant pathogens have dynamic genomes that allow them to rapidly adapt to adverse conditions and overcome host resistance. One way by which this dynamic genome plasticity is expressed is through effector gene loss, which enables plant pathogens to overcome recognition by cognate resistance genes in the host. However, the exact nature of these loses remains elusive in many fungi. This includes the tomato pathogen Cladosporium fulvum, which is the first fungal plant pathogen from which avirulence (Avr) genes were ever cloned and in which loss of Avr genes is often reported as a means of overcoming recognition by cognate tomato Cf resistance genes. A recent near-complete reference genome assembly of C. fulvum isolate Race 5 revealed a compartmentalized genome architecture and the presence of an accessory chromosome, thereby creating a basis for studying genome plasticity in fungal plant pathogens and its impact on avirulence genes.

RESULTS

Here, we obtained near-complete genome assemblies of four additional C. fulvum isolates. The genome assemblies had similar sizes (66.96 to 67.78 Mb), number of predicted genes (14,895 to 14,981), and estimated completeness (98.8 to 98.9%). Comparative analysis that included the genome of isolate Race 5 revealed high levels of synteny and colinearity, which extended to the density and distribution of repetitive elements and of repeat-induced point (RIP) mutations across homologous chromosomes. Nonetheless, structural variations, likely mediated by transposable elements and effecting the deletion of the avirulence genes Avr4E, Avr5, and Avr9, were also identified. The isolates further shared a core set of 13 chromosomes, but two accessory chromosomes were identified as well. Accessory chromosomes were significantly smaller in size, and one carried pseudogenized copies of two effector genes. Whole-genome alignments further revealed genomic islands of near-zero nucleotide diversity interspersed with islands of high nucleotide diversity that co-localized with repeat-rich regions. These regions were likely generated by RIP, which generally asymmetrically affected the genome of C. fulvum.

CONCLUSIONS

Our results reveal new evolutionary aspects of the C. fulvum genome and provide new insights on the importance of genomic structural variations in overcoming host resistance in fungal plant pathogens.

POOE: predicting oomycete effectors based on a pre-trained large protein language model

Oomycetes are fungus-like eukaryotic microorganisms which can cause catastrophic diseases in many plants. Successful infection of oomycetes depends highly on their effector proteins that are secreted into plant cells to subvert plant immunity. Thus, systematic identification of effectors from the oomycete proteomes remains an initial but crucial step in understanding plant-pathogen relationships. However, the number of experimentally identified oomycete effectors is still limited. Currently, only a few bioinformatics predictors exist to detect potential effectors, and their prediction performance needs to be improved. Here, we used the sequence embeddings from a pre-trained large protein language model (ProtTrans) as input and developed a support vector machine-based method called POOE for predicting oomycete effectors. POOE could achieve a highly accurate performance with an area under the precision-recall curve of 0.804 (area under the receiver operating characteristic curve = 0.893, accuracy = 0.874, precision = 0.777, recall = 0.684, and specificity = 0.936) in the fivefold cross-validation, considerably outperforming various combinations of popular machine learning algorithms and other commonly used sequence encoding schemes. A similar prediction performance was also observed in the independent test. Compared with the existing oomycete effector prediction methods, POOE provided very competitive and promising performance, suggesting that ProtTrans effectively captures rich protein semantic information and dramatically improves the prediction task. We anticipate that POOE can accelerate the identification of oomycete effectors and provide new hints to systematically understand the functional roles of effectors in plant-pathogen interactions. The web server of POOE is freely accessible at http://zzdlab.com/pooe/index.php. The corresponding source codes and data sets are also available at https://github.com/zzdlabzm/POOE.IMPORTANCEIn this work, we use the sequence representations from a pre-trained large protein language model (ProtTrans) as input and develop a Support Vector Machine-based method called POOE for predicting oomycete effectors. POOE could achieve a highly accurate performance in the independent test set, considerably outperforming existing oomycete effector prediction methods. We expect that this new bioinformatics tool will accelerate the identification of oomycete effectors and further guide the experimental efforts to interrogate the functional roles of effectors in plant-pathogen interaction.

Genome-Wide Identification and Characterization of Effector Candidates with Conserved Motif in Falciphora oryzae

Microbes employ effectors to disrupt immune responses and promote host colonization. Conserved motifs including RXLR, LFLAK-HVLVxxP (CRN), Y/F/WxC, CFEM, LysM, Chitin-bind, DPBB_1 (PNPi), and Cutinase have been discovered to play crucial roles in the functioning of effectors in filamentous fungi. Nevertheless, little is known about effectors with conserved motifs in endophytes. This research aims to discover the effector genes with conserved motifs in the genome of rice endophyte Falciphora oryzae. SignalP identified a total of 622 secreted proteins, out of which 227 were predicted as effector candidates by EffectorP. By utilizing HMM features, we discovered a total of 169 effector candidates with conserved motifs and three novel motifs. Effector candidates containing LysM, CFEM, DPBB_1, Cutinase, and Chitin_bind domains were conserved across species. In the transient expression assay, it was observed that one CFEM and one LysM activated cell death in tobacco leaves. Moreover, two CFEM and one Chitin_bind inhibited cell death induced by Bax protein. At various points during the infection, the genes' expression levels were increased. These results will help to identify functional effector proteins involving omics methods using new bioinformatics tools, thus providing a basis for the study of symbiosis mechanisms.

The genomes of Scedosporium between environmental challenges and opportunism

Emerging fungal pathogens are a global challenge for humankind. Many efforts have been made to understand the mechanisms underlying pathogenicity in bacteria, and OMICs techniques are largely responsible for those advancements. By contrast, our limited understanding of opportunism and antifungal resistance is preventing us from identifying, limiting and interpreting the emergence of fungal pathogens. The genus Scedosporium (Microascaceae) includes fungi with high tolerance to environmental pollution, whilst some species can be considered major human pathogens, such as Scedosporium apiospermum and Scedosporium boydii. However, unlike other fungal pathogens, little is known about the genome evolution of these organisms. We sequenced two novel genomes of Scedosporium aurantiacum and Scedosporium minutisporum isolated from extreme, strongly anthropized environments. We compared all the available Scedosporium and Microascaceae genomes, that we systematically annotated and characterized ex novo in most cases. The genomes in this family were integrated in a Phylum-level comparison to infer the presence of putative, shared genomic traits in filamentous ascomycetes with pathogenic potential. The analysis included the genomes of 100 environmental and clinical fungi, revealing poor evolutionary convergence of putative pathogenicity traits. By contrast, several features in Microascaceae and Scedosporium were detected that might have a dual role in responding to environmental challenges and allowing colonization of the human body, including chitin, melanin and other cell wall related genes, proteases, glutaredoxins and magnesium transporters. We found these gene families to be impacted by expansions, orthologous transposon insertions, and point mutations. With RNA-seq, we demonstrated that most of these anciently impacted genomic features responded to the stress imposed by an antifungal compound (voriconazole) in the two environmental strains S. aurantiacum MUT6114 and S. minutisporum MUT6113. Therefore, the present genomics and transcriptomics investigation stands on the edge between stress resistance and pathogenic potential, to elucidate whether fungi were pre-adapted to infect humans. We highlight the strengths and limitations of genomics applied to opportunistic human pathogens, the multifactoriality of pathogenicity and resistance to drugs, and suggest a scenario where pressures other than anthropic contributed to forge filamentous human pathogens.

A chromosome-scale genome assembly of the grape powdery mildew pathogen Erysiphe necator reveals its genomic architecture and previously unknown features of its biology

Erysiphe necator is an obligate fungal pathogen that causes grape powdery mildew, globally the most important disease on grapevines. Previous attempts to obtain a quality genome assembly for this pathogen were hindered by its high repetitive DNA content. Here, chromatin conformation capture (Hi-C) with long-read PacBio sequencing was combined to obtain a chromosome-scale assembly and a high-quality annotation for E. necator isolate EnFRAME01. The resulting 81.1 Mb genome assembly is 98% complete and consists of 34 scaffolds, 11 of which represent complete chromosomes. All chromosomes contain large centromeric-like regions and lack synteny to the 11 chromosomes of the cereal PM pathogen Blumeria graminis. Further analysis of their composition showed that repeats and transposable elements (TEs) occupy 62.7% of their content. TEs were almost evenly interspersed outside centromeric and telomeric regions and massively overlapped with regions of annotated genes, suggesting that they could have a significant functional impact. Abundant gene duplicates were observed as well, particularly in genes encoding candidate secreted effector proteins. Moreover, younger in age gene duplicates exhibited more relaxed selection pressure and were more likely to be located physically close in the genome than older duplicates. A total of 122 genes with copy number variations among six isolates of E. necator were also identified and were enriched in genes that were duplicated in EnFRAME01, indicating they may reflect an adaptive variation. Taken together, our study illuminates higher-order genomic architectural features of E. necator and provides a valuable resource for studying genomic structural variations in this pathogen. IMPORTANCE Grape powdery mildew caused by the ascomycete fungus Erysiphe necator is economically the most important and recurrent disease in vineyards across the world. The obligate biotrophic nature of E. necator hinders the use of typical genetic methods to elucidate its pathogenicity and adaptation to adverse conditions, and thus comparative genomics has been a major method to study its genome biology. However, the current reference genome of E. necator isolate C-strain is highly fragmented with many non-coding regions left unassembled. This incompleteness prohibits in-depth comparative genomic analyses and the study of genomic structural variations (SVs) that are known to affect several aspects of microbial life, including fitness, virulence, and host adaptation. By obtaining a chromosome-scale genome assembly and a high-quality gene annotation for E. necator, we reveal the organization of its chromosomal content, unearth previously unknown features of its biology, and provide a reference for studying genomic SVs in this pathogen.

Crop-saving with AI: latest trends in deep learning techniques for plant pathology

Plant diseases pose a major threat to agricultural production and the food supply chain, as they expose plants to potentially disruptive pathogens that can affect the lives of those who are associated with it. Deep learning has been applied in a range of fields such as object detection, autonomous vehicles, fraud detection etc. Several researchers have tried to implement deep learning techniques in precision agriculture. However, there are pros and cons to the approaches they have opted for disease detection and identification. In this survey, we have made an attempt to capture the significant advancements in machine-learning based disease detection. We have discussed prevalent datasets and techniques that have been employed as well as highlighted emerging approaches being used for plant disease detection. By exploring these advancements, we aim to present a comprehensive overview of the prominent approaches in precision agriculture, along with their associated challenges and potential improvements. This paper delves into the challenges associated with the implementation and briefly discusses the future trends. Overall, this paper presents a bird's eye view of plant disease datasets, deep learning techniques, their accuracies and the challenges associated with them. Our insights will serve as a valuable resource for researchers and practitioners in the field. We hope that this survey will inform and inspire future research efforts, ultimately leading to improved precision agriculture practices and enhanced crop health management.

EffectorO: Motif-Independent Prediction of Effectors in Oomycete Genomes Using Machine Learning and Lineage Specificity

Oomycete plant pathogens cause a wide variety of diseases, including late blight of potato, sudden oak death, and downy mildews of plants. These pathogens are major contributors to loss in numerous food crops. Oomycetes secrete effector proteins to manipulate their hosts to the advantage of the pathogen. Plants have evolved to recognize effectors, resulting in an evolutionary cycle of defense and counter-defense in plant-microbe interactions. This selective pressure results in highly diverse effector sequences that can be difficult to computationally identify using only sequence similarity. We developed a novel effector prediction tool, EffectorO, that uses two complementary approaches to predict effectors in oomycete pathogen genomes: i) a machine learning-based pipeline that predicts effector probability based on the biochemical properties of the N-terminal amino-acid sequence of a protein and ii) a pipeline based on lineage specificity to find proteins that are unique to one species or genus, a sign of evolutionary divergence due to adaptation to the host. We tested EffectorO on Bremia lactucae, which causes lettuce downy mildew, and Phytophthora infestans, which causes late blight of potato and tomato, and predicted many novel effector candidates while recovering the majority of known effector candidates. EffectorO will be useful for discovering novel families of oomycete effectors without relying on sequence similarity to known effectors. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

The Phantom Menace: latest findings on effector biology in the rice blast fungus

Magnaporthe oryzae is a hemibiotrophic fungus responsible for the economically devastating and recalcitrant rice blast disease. However, the blast fungus is not only restricted to rice plants as it can also infect wheat, millet, and other crops. Despite previous outstanding discoveries aimed to understand and control the disease, the fungus remains one of the most important pathogens that threatens global food security. To cause disease, M. oryzae initiates morphological changes to attach, penetrate, and colonize rice cells, all while suppressing plant immune defenses that would otherwise hinder its proliferation. As such, M. oryzae actively secretes a battery of small proteins called "effectors" to manipulate host machinery. In this review, we summarize the latest findings in effector identification, expression, regulation, and functionality. We review the most studied effectors and their roles in pathogenesis. Additionally, we discern the current methodologies to structurally catalog effectors, and we highlight the importance of climate change and its impact on the future of rice blast disease.

Characterization of Arbuscular Mycorrhizal Effector Proteins

Plants are colonized by various fungi with both pathogenic and beneficial lifestyles. One type of colonization strategy is through the secretion of effector proteins that alter the plant's physiology to accommodate the fungus. The oldest plant symbionts, the arbuscular mycorrhizal fungi (AMF), may exploit effectors to their benefit. Genome analysis coupled with transcriptomic studies in different AMFs has intensified research on the effector function, evolution, and diversification of AMF. However, of the current 338 predicted effector proteins from the AM fungus Rhizophagus irregularis, only five have been characterized, of which merely two have been studied in detail to understand which plant proteins they associate with to affect the host physiology. Here, we review the most recent findings in AMF effector research and discuss the techniques used for the functional characterization of effector proteins, from their in silico prediction to their mode of action, with an emphasis on high-throughput approaches for the identification of plant targets of the effectors through which they manipulate their hosts.

Comparative proteome analysis identifies species-specific signature proteins in Aspergillus pathogens

Aspergillus flavus and Aspergillus fumigatus are important human pathogens that can infect the lung and cornea. During infection, Aspergillus dormant conidia are the primary morphotype that comes in contact with the host. As the conidial surface-associated proteins (CSPs) and the extracellular proteins during the early stages of growth play a crucial role in establishing infection, we profiled and compared these proteins between a clinical strain of A. flavus and a clinical strain of A. fumigatus. We identified nearly 100 CSPs in both Aspergillus, and these non-covalently associated surface proteins were able to stimulate the neutrophils to secrete interleukin IL-8. Mass spectrometry analysis identified more than 200 proteins in the extracellular space during the early stages of conidial growth and germination (early exoproteome). The conidial surface proteins and the early exoproteome of A. fumigatus were enriched with immunoreactive proteins and those with pathogenicity-related functions while that of the A. flavus were primarily enzymes involved in cell wall reorganization and binding. Comparative proteome analysis of the CSPs and the early exoproteome between A. flavus and A. fumigatus enabled the identification of a common core proteome and potential species-specific signature proteins. Transcript analysis of selected proteins indicate that the transcript-protein level correlation does not exist for all proteins and might depend on factors such as membrane-anchor signals and protein half-life. The probable signature proteins of A. flavus and A. fumigatus identified in this study can serve as potential candidates for developing species-specific diagnostic tests. KEY POINTS: • CSPs and exoproteins could differentiate A. flavus and A. fumigatus. • A. fumigatus conidial surface harbored more antigenic proteins than A. flavus. • Identified species-specific signature proteins of A. flavus and A. fumigatus.

Natural variation in Avr3D1 from Zymoseptoria sp. contributes to quantitative gene-for-gene resistance and to host specificity

Successful host colonization by plant pathogens requires the circumvention of host defense responses, frequently through sequence modifications in secreted pathogen proteins known as avirulence factors (Avrs). Although Avr sequences are often polymorphic, the contribution of these polymorphisms to virulence diversity in natural pathogen populations remains largely unexplored. We used molecular genetic tools to determine how natural sequence polymorphisms of the avirulence factor Avr3D1 in the wheat pathogen Zymoseptoria tritici contributed to adaptive changes in virulence. We showed that there is a continuous distribution in the magnitude of resistance triggered by different Avr3D1 isoforms and demonstrated that natural variation in an Avr gene can lead to a quantitative resistance phenotype. We further showed that homologues of Avr3D1 in two nonpathogenic sister species of Z. tritici are recognized by some wheat cultivars, suggesting that Avr-R gene-for-gene interactions can contribute to nonhost resistance. We suggest that the mechanisms underlying host range, qualitative resistance, and quantitative resistance are not exclusive.

A Novel Effector FlSp1 Inhibits the Colonization of Endophytic Fusarium lateritium and Increases the Resistance to Ralstonia solanacearum in Tobacco

Effectors are crucial for the interaction between endophytes and their host plants. However, limited attention has been paid to endophyte effectors, with only a few reports published. This work focuses on an effector of Fusarium lateritium, namely FlSp1 (Fusarium-lateritium-Secreted-Protein), a typical unknown secreted protein. The transcription of FlSp1 was up-regulated after 48 h following fungal inoculation in the host plant, i.e., tobacco. The inactivation of FlSp1 with the inhibition rate decreasing by 18% (p < 0.01) resulted in a remarkable increase in the tolerance of F. lateritium to oxidative stress. The transient expression of FlSp1 stimulated the accumulation of reactive oxygen species (ROS) without causing plant necrosis. In comparison with the wild type of F. lateritium (WT), the FlSp1 mutant of the F. lateritium plant (ΔFlSp1) reduced the ROS accumulation and weakened the plant immune response, which resulted in significantly higher colonization in the host plants. Meanwhile, the resistance of the ΔFlSp1 plant to the pathogenic Ralstonia solanacearum, which causes bacterial wilt, was increased. These results suggest that the novel secreted protein FlSp1 might act as an immune-triggering effector to limit fungal proliferation by stimulating the plant immune system through ROS accumulation and thus balance the interaction between the endophytic fungi and their host plants.

Extracellular Vesicles of the Plant Pathogen Botrytis cinerea

Fungal secretomes are known to contain a multitude of components involved in nutrition, cell growth or biotic interactions. Recently, extra-cellular vesicles have been identified in a few fungal species. Here, we used a multidisciplinary approach to identify and characterize extracellular vesicles produced by the plant necrotroph Botrytis cinerea. Transmission electron microscopy of infectious hyphae and hyphae grown in vitro revealed extracellular vesicles of various sizes and densities. Electron tomography showed the co-existence of ovoid and tubular vesicles and pointed to their release via the fusion of multi-vesicular bodies with the cell plasma membrane. The isolation of these vesicles and exploration of their protein content using mass spectrometry led to the identification of soluble and membrane proteins involved in transport, metabolism, cell wall synthesis and remodeling, proteostasis, oxidoreduction and traffic. Confocal microscopy highlighted the capacity of fluorescently labeled vesicles to target cells of B. cinerea, cells of the fungus Fusarium graminearum, and onion epidermal cells but not yeast cells. In addition, a specific positive effect of these vesicles on the growth of B. cinerea was quantified. Altogether, this study broadens our view on the secretion capacity of B. cinerea and its cell-to-cell communication.

A Complete Genome Sequence of Podosphaera xanthii Isolate YZU573, the Causal Agent of Powdery Mildew Isolated from Cucumber in China

Podosphaera xanthii is a well-known obligate biotrophic pathogen that causes powdery mildew (PM) disease on cucurbitaceous plants and is one of the most important limiting factors for cucumber production worldwide. To better understand the avirulence effector proteins in this species that are known to be involved in host-pathogen interaction, the draft genome assembly of P. xanthii isolate YZU573 from cucumber leaves with symptoms of PM was obtained with a hybrid approach, combining nanopore long-read and llumina paired-end sequencing. The final P. xanthii YZU573 genome assembly of 152.7 Mb consists of 58 contigs, with an N50 value of 0.75 Mb and 6491 predicted protein-coding genes. The effector analysis using the whole-genome sequence information revealed a total of 87 putative effector candidates, and 65 of them had their analogs, whereas the remaining 22 were novel ones. The new P. xanthii genome provides valuable resources to better understand plant-microbe interaction in cucumber PM disease.

Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi

With >7000 species the order of rust fungi has a disproportionately large impact on agriculture, horticulture, forestry and foreign ecosystems. The infectious spores are typically dikaryotic, a feature unique to fungi in which two haploid nuclei reside in the same cell. A key example is Phakopsora pachyrhizi, the causal agent of Asian soybean rust disease, one of the world's most economically damaging agricultural diseases. Despite P. pachyrhizi's impact, the exceptional size and complexity of its genome prevented generation of an accurate genome assembly. Here, we sequence three independent P. pachyrhizi genomes and uncover a genome up to 1.25 Gb comprising two haplotypes with a transposable element (TE) content of ~93%. We study the incursion and dominant impact of these TEs on the genome and show how they have a key impact on various processes such as host range adaptation, stress responses and genetic plasticity.

Insights on Novel Effectors and Characterization of Metacaspase (RS107_6) as a Potential Cell Death-Inducing Protein in Rhizoctonia solani

Effectors play an important role in host–pathogen interactions. Though an economically significant disease in rice, knowledge regarding the infection strategy of Rhizoctonia solani is obscure. In this study, we performed a genome-wide identification of the effectors in R. solani based on the characteristics of previously reported effector proteins. A total of seven novel effectors (designated as RS107_1 to RS107_7) in the disease mechanism of R. solani were identified and were predicted to be non-classically secreted proteins with functionally conserved domains. The function, reactivity, and stability of these proteins were evaluated through physiochemical characterization. The target proteins involved in the regulation of rice defense mechanisms were identified. Furthermore, the effector genes were cloned and RS107_6 (metacaspase) was heterologously expressed in Escherichia coli to obtain a purified protein of ~36.5 kDa. The MALD-TOF characterization confirmed that the protein belonged to a metacaspase of the Peptidase_C14 protein family, 906 bp in size, and encoded a polypeptide of 301 amino acids. These findings suggest that the identified effectors can potentially serve as a virulence factor and can be targeted for the management of sheath blight in rice.