Genome-Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors

Sensitivity to Boscalid and Trifloxystrobin and Fitness of Corynespora cassiicola Associated with CcSdh & CcCytb in Cucumber

The extensive use of succinate dehydrogenase inhibitors (SDHIs) and quinone outside inhibitors (QoIs) has led to the development of resistance in Corynespora cassiicola, which causes corynespora leaf spot (CLS) in cucumber. In this study, the sensitivity and the resistance phenotypes to SDHIs and QoIs were monitored, and the fitness of C. cassiicola carrying CcSdh & CcCytb mutations was measured. The average 50% effective suppressive concentration (EC50) values of C. cassiicola to boscalid from 2019 to 2021 ranged from 6.65 to 24.16 μg/mL, while the average EC50 values of C. cassiicola to trifloxystrobin from 2007 to 2021 ranged from 105.11 to 462.02 μg/mL. Ten fungicide resistance phenotypes and 19 resistance genotypes were found. The D-D95E&Cytb-G143A and B-H278L&Cytb-G143A mutants presented increased fitness, while the B-H278Y&Cytb-G143A mutant showed significant fitness costs, and the other mutants presented no or slight fitness costs. These findings provide a basis for the formulation of resistance management strategies of CLS.

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.

Endophytic strategies decoded by genome and transcriptome analysis of Fusarium nematophilum strain NQ8GII4

Introduction

Fusarium nematophilum strain NQ8GII4 is an endophytic fungus with significant potential for improving growth and disease resistance of alfalfa. However, the molecular mechanisms underlying the symbiotic relationship between NQ8GII4 and alfalfa roots remain poorly understood.

Methods

In this study, we conducted (1) a comparative genomic analysis of selected saprophytic, pathogenic, and endophytic fungi, including molecular phylogeny analysis, whole-genome alignment, and divergence date estimation positioning, and (2) transcriptomic profiling of alfalfa roots infected with NQ8GII4.

Results

Our findings reveal that NQ8GII4 is genetically closely related to F. solani, suggesting it diverged from Fusarium phytopathogens. During the early stages of symbiosis establishment, genes encoding glycosyltransferases (GTs), fungal cell wall-degrading enzymes (FCWDEs), and steroid-14α-demethylase (CYP51) were significantly downregulated, potentially suppressing hyphal growth of the fungus. Once symbiosis was established, NQ8GII4 secreted effectors that activated plant immunity, which in turn could slow growth of the fungus. Moreover, genes involved in secondary metabolite biosynthesis, such as type I polyketide synthases (T1PKS) and non-ribosomal peptide synthetases (NRPSs), were significantly downregulated. Homologs of autophagy-related genes, including ATG1, ATG2, ATG11, and others, were also downregulated, suggesting that reduced phytotoxin production and autophagy inhibition is a consequence of NQ8GII4's symbiosis.

Discussion

This study investigated the comprehensive molecular and genetic mechanisms governing the interaction between NQ8GII4 and alfalfa roots. Beyond the NQ8GII4-alfalfa system, these findings also provide a valuable molecular framework for understanding the mechanism of interactions between endophytic fungi and their host plants.

In silico analysis of secreted effectorome of the rubber tree pathogen Rigidoporus microporus highlights its potential virulence proteins

Rigidoporus microporus, the causative agent of the white root rot disease of rubber trees, poses a significant threat to natural rubber production worldwide. Understanding the molecular mechanisms facilitating its pathogenicity would be crucial for developing effective disease management strategies. The pathogen secretes effector proteins, which play pivotal roles in modulating host immune responses and infection. In this study, in silico analyses identified 357 putative secreted effector proteins from the R. microporus genome. These were then integrated into previous RNA-seq data obtained in response to rubber tree latex exposure. Annotation of putative effectors suggested the abundance of proteins in several families associated with the virulence of R. microporus, especially hydrophobin proteins and glycoside hydrolase (GH) proteins. The contribution of secreted effectors to fungal pathogenicity was discussed, particularly in response to rubber tree latex exposure. Some unknown highly expressed effectors were predicted for the protein structures, revealing their similarity to aminopeptidase, ubiquitin ligase, spherulin, and thaumatin protein. This integrative study further elucidates the molecular mechanism of R. microporus pathogenesis and offers alternative targets for developing control strategies for managing white root rot disease in rubber plantations.

Characteristics of Corynespora cassiicola, the causal agent of tobacco Corynespora leaf spot, revealed by genomic and metabolic phenomic analysis

Corynespora cassiicola is a highly diverse fungal pathogen that commonly occurs in tropical, subtropical, and greenhouse environments worldwide. In this study, the isolates were identified as C. cassiicola, and the optimum growth and sporulation were studied. The phenotypic characteristics of C. cassiicola, concerning 950 different growth conditions, were tested using Biolog PM plates 1-10. In addition, the strain of C. cassiicola DWZ from tobacco hosts was sequenced for the using Illumina PE150 and Pacbio technologies. The host resistance of tobacco Yunyan 87 with different maturity levels was investigated. In addition, the resistance evaluation of 10 common tobacco varieties was investigated. The results showed that C. cassiicola metabolized 89.47% of the tested carbon source, 100% of the nitrogen source, 100% of the phosphorus source, and 97.14% of the sulfur source. It can adapt to a variety of different osmotic pressure and pH environments, and has good decarboxylase and deaminase activities. The optimum conditions for pathogen growth and sporulation were 25-30 °C, and the growth was better on AEA and OA medium. The total length of the genome was 45.9 Mbp, the GC content was 51.23%, and a total of 13,061 protein-coding genes, 202 non-coding RNAs and 2801 and repeat sequences were predicted. Mature leaves were more susceptible than proper mature and immature leaves, and the average diameter of diseased spots reached 17.74 mm at 12 days. None of the tested ten cultivars exhibited obvious resistance to Corynespora leaf spot of tobacco, whereby all disease spot diameters reached > 10 mm and > 30 mm when at 5 and 10 days after inoculation, respectively. The phenotypic characteristics, genomic analysis of C. cassiicola and the cultivar resistance assessment of this pathogen have increased our understanding of Corynespora leaf spot of tobacco.

MinION Sequencing of Fungi in Sub-Saharan African Air and a Novel LAMP Assay for Rapid Detection of the Tropical Phytopathogenic Genus Lasiodiplodia

To date, there have been no DNA-based metabarcoding studies into airborne fungi in tropical Sub-Saharan Africa. In this initial study, 10 air samples were collected onto Vaseline-coated acrylic rods mounted on drones flown at heights of 15-50 meters above ground for 10-15 min at three sites in Ghana. Purified DNA was extracted from air samples, the internal transcribed spacer (ITS) region was amplified using fungal-specific primers, and MinION third-generation amplicon sequencing was undertaken with downstream bioinformatics analyses utilizing GAIA cloud-based software (at genus taxonomic level). Principal coordinate analyses based on Bray-Curtis beta diversity dissimilarity values found no clear evidence for the structuring of fungal air communities, nor were there significant differences in alpha diversity, based on geographic location (east vs. central Ghana), underlying vegetation type (cocoa vs. non-cocoa), or height above ground level (15-23 m vs. 25-50 m), and despite the short flight times (10-15 min), ~90 operational taxonomic units (OTUs) were identified in each sample. In Ghanaian air, fungal assemblages were skewed at the phylum taxonomic level towards the ascomycetes (53.7%) as opposed to basidiomycetes (24.6%); at the class level, the Dothideomycetes were predominant (29.8%) followed by the Agaricomycetes (21.8%). The most common fungal genus in Ghanaian air was cosmopolitan and globally ubiquitous Cladosporium (9.9% of reads). Interestingly, many fungal genera containing economically important phytopathogens of tropical crops were also identified in Ghanaian air, including Corynespora, Fusarium, and Lasiodiplodia. Consequently, a novel loop-mediated isothermal amplification (LAMP) assay, based on translation elongation factor-1α sequences, was developed and tested for rapid, sensitive, and specific detection of the fungal phytopathogenic genus Lasiodiplodia. Potential applications for improved tropical disease management are considered.

Sensitivity to 12 Fungicides and Resistance Mechanism to Trifloxystrobin, Carbendazim, and Succinate Dehydrogenase Inhibitors in Cucumber Corynespora Leaf Spot (Corynespora cassiicola)

Corynespora cassiicola is the causal agent of cucumber Corynespora leaf spot, which affects many economically important plant species. Chemical control of this disease is hampered by the common development of fungicide resistance. In this study, 100 isolates from Liaoning Province were collected, and their sensitivity to 12 fungicides was determined. All the isolates (100%) were resistant to trifloxystrobin and carbendazim, and 98% were resistant to fluopyram, boscalid, pydiflumetofen, isopyrazam, and fluxapyroxad. However, none were resistant to propiconazole, prochloraz, tebuconazole, difenoconazole, and fludioxonil. The Cytb gene of trifloxystrobin-resistant isolates encoded the G143A mutation, whereas the β-tubulin gene of carbendazim-resistant isolates encoded the E198A and E198A and M163I mutations. Mutations in SdhB-I280V, SdhC-S73P, SdhC-H134R, SdhD-D95E, and SdhD-G109V were associated with resistance to the succinate dehydrogenase inhibitors (SDHIs). Trifloxystrobin, carbendazim, and fluopyram were barely effective on the resistant isolates, whereas fludioxonil and prochloraz were effective on the isolates that were resistant to the quinone outside inhibitors (QoIs), SDHIs, and benzimidazoles. Ultimately, this study demonstrates that fungicide resistance seriously threatens the effective control of Corynespora leaf spot.

Genome-wide survey and evolutionary history of the pectin methylesterase (PME) gene family in the Dothideomycetes class of fungi

Once deposited in the plant cell wall, pectin undergoes demethylesterification by endogenous pectin methylesterases (PMEs), which play various roles in growth and development, including defense against pathogen attacks. Pathogen PMEs can alter pectin's methylesterification pattern, increasing its susceptibility to degradation by other fungal pectinases and thus playing a critical role as virulence factors during early infection stages. To investigate the evolutionary history of PMEs in the Dothideomycetes class of fungi, we obtained genomic data from 15 orders (79 species) and added genomic data from 61 isolates of Corynespora cassiicola. Our analyses involved maximum likelihood phylogenies, gene genealogies, and selection analyses. Additionally, we measured PME gene expression levels of C. cassiicola using soybean as a host through RT-qPCR assays. We recovered 145 putative effector PMEs and 57 putative non-effector PMEs from across the Dothideomycetes. The PME gene family exhibits a small size (up to 5 members per genome) and comprises three major clades. The evolutionary patterns of the PME1 and PME2 clades were largely shaped by duplications and recurring gene retention events, while biased gene loss characterized the small-sized PME3 clade. The presence of five members in the PME gene family of C. cassiicola suggests that the family may play a key role in the evolutionary success of C. cassiicola as a polyphagous plant pathogen. The haplogroups Cc_PME1.1 and Cc_PME1.2 exhibited an accelerated rate of evolution, whereas Cc_PME2.1, Cc_PME2.2, and Cc_PME2.3 seem to be under strong purifying selective constraints. All five PME genes were expressed during infection of soybean leaves, with the highest levels during from six to eight days post-inoculation. The highest relative expression level was measured for CC_29_g7533, a member of the Cc_PME2.3 clade, while the remaining four genes had relatively lower levels of expression.

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.

Case report: A case of ocular infection caused by Corynespora cassiicola

Objective

The aim of this study is to identify the pathogen causing ocular infection in a Chinese patient and to describe its morphological characteristics.

Methods

Samples from the patient's intraoperative pus were collected for microscopic examination and culture. Morphology and drug sensitivities of the isolated fungus were analyzed. Ribosomal DNA (rDNA) sequencing was performed and blasted in GenBank.

Results

A strain of fungi was repeatedly isolated from pus samples in different types of medium. No conidia were shown when the isolate cultured on normal PDA medium, whereas pseudoseptate thick-walled conidia were shown when cultured on medium containing leaf leachate. The results of BLAST and phylogenetic trees based on internal transcribed spacer, beta-tubulin, translation elongation factor 1-alpha, and RNA polymerase II gene demonstrated that the isolated fungus was Corynespora cassiicola. Minimum inhibitory concentration results of this organism were as follows: anidulafungin, 0.06 μg/ml; amphotericin B, 0.12 μg/ml; micafungin, 0.06 μg/ml; caspofungin, 0.5 μg/ml; 5-fluorocytosine, >64 μg/ml; posaconazole, 2 μg/ml; voriconazole, 0.25 μg/ml; itraconazole, 0.5 μg/ml; fluconazole, 64 μg/ml.

Conclusion

The case was infected with Corynespora cassiicola and led to eye suppurative endophthalmitis and blindness. Combined applications of morphological and molecular biology techniques facilitate accurate diagnosis of fungal infections.

The necrosis- and ethylene-inducing peptide 1-like protein (NLP) gene family of the plant pathogen Corynespora cassiicola

Effectors are secreted by plant-associated microorganisms to modify the host cell physiology. As effectors, the Necrosis- and Ethylene-inducing peptide 1-like proteins (NLPs) are involded in the early phases of plant infection and may trigger host immune responses. Corynespora cassiicola is a polyphagous plant pathogen that causes target spot on many agriculturally important crops. Using genome assembly, gene prediction, and proteome annotation tools, we retrieved 135 NLP-encoding genes from proteomes of 44 isolates. We explored the evolutionary history of NLPs using Bayesian phylogeny, gene genealogies, and selection analyses. We accessed the expression profiles of the NLP genes during the early phase of C. cassiicola-soybean interaction. Three NLP putative-effector genes (Cc_NLP1.1, Cc_NLP1.2A, and Cc_NLP1.2B) were maintained in the genomes of all isolates tested. An NLP putative-non-effector gene (Cc_NLP1.3) was found in three isolates that had been originally obtained from soybean. Putative-effector NLPs were under different selective constraints: Cc_NLP1.1 was under stronger selective pressure, while Cc_NLP1.2A was under a more relaxed constraint. Meanwhile, Cc_NLP1.2B likely evolved under either positive or balancing selection. Despite highly divergent, the putative-effector NLPs maintain conserved the residues necessary to trigger plant immune responses, suggesting they are potentially functional. Only the Cc_NLP1.1 putative-effector gene was significantly expressed at the early hours of soybean colonization, while Cc_NLP1.2A and Cc_NLP1.2B showed much lower levels of gene expression.

Comparative genomics of host-specialized populations of Corynespora cassiicola causing target spot epidemics in the southeastern United States

Numerous plant-pathogenic fungi secrete necrotrophic effectors (syn. host-selective toxins) that are important determinants of pathogenicity and virulence in species that have a necrotrophic lifestyle. Corynespora cassiicola is a necrotrophic fungus causing emerging target spot epidemics in the southeastern United States (US). Previous studies revealed that populations of C. cassiicola from cotton, soybean, and tomato are clonal, host specialized and genetically distinct. Additionally, cassiicolin - the necrotrophic effector identified in some C. cassiicola isolates - is an important toxin for virulence on rubber. It is encoded by seven Cas gene variants. Our goal was to conduct comparative genomic analyses to identify variation among putative necrotrophic effector genes and to determine if lack of one of the mating-types explained clonal populations in C. cassiicola causing outbreaks in the southeastern US and the apparent absence of sexual reproduction worldwide. A total of 12 C. cassiicola genomes, with four each from isolates from tomato, soybean, and cotton, were sequenced using an Illumina Next Seq platform. Each genome was assembled de novo, compared with the reference genome from rubber, and searched for known Cas, and other gene clusters with homologs of secondary metabolites. Cas2 and/or Cas6 were present in isolates from soybean in the southeastern US, whereas Cas1 and Cas2 were present in isolates from cotton in the southeastern US. In addition, several toxin genes, including the T-toxin biosynthetic genes were present in all C. cassiicola from cotton, soybean, and tomato. The mating-type locus was identified in all of the sequenced genomes, with the MAT1-1 idiomorph present in all cotton isolates and the rubber isolate, whereas the MAT1-2 idiomorph was present in all soybean isolates. We developed a PCR-based marker for mating-type in C. cassiicola. Both mating types were present in isolates from tomato. Thus, C. cassiicola has both mating-types necessary for sexual reproduction, but the absence of both mating-types within soybean and cotton populations could explain clonality in these populations. Variation in necrotrophic effectors may underlie host specialization and disease emergence of target spot on cotton, soybean, and tomato in the southeastern US.

Unraveling the Host-Selective Toxic Interaction of Cassiicolin with Lipid Membranes and Its Cytotoxicity

Cassiicolin (Cas), a toxin produced by Corynespora cassiicola, is responsible for Corynespora leaf fall disease in susceptible rubber trees. Currently, the molecular mechanisms of the cytotoxicity of Cas and its host selectivity have not been fully elucidated. Here, we analyzed the binding of Cas1 and Cas2 to membranes consisting of different plant lipids and their membrane disruption activities. Using high-speed atomic force microscopy and confocal microscopy, we reveal that the binding and disruption activities of Cas1 and Cas2 on lipid membranes are strongly dependent on the specific plant lipids. The negative phospholipids, glycerolipids, and sterols are more sensitive to membrane damage caused by Cas1 and Cas2 than neutral phospholipids and betaine lipids. Mature Cas1 and Cas2 play an essential role in causing membrane disruption. Cytotoxicity tests on rubber leaves of Rubber Research Institute of Vietnam (RRIV) 1, RRIV 4, and Prang Besar (PB) 255 clones suggest that the toxins cause necrosis of rubber leaves, except for the strong resistance of PB 255 against Cas2. Cryogenic scanning electron microscopy analyses of necrotic leaf tissues treated with Cas1 confirm that cytoplasmic membranes are vulnerable to the toxin. Thus, the host selectivity of Cas toxin is attained by the lipid-dependent binding activity of Cas to the membrane, and the cytotoxicity of Cas arises from its ability to form biofilm-like structures and to disrupt specific membranes.

Recent insights on gene expression studies on Hevea Brasiliensis fatal leaf fall diseases

Hevea brasiliensis is one of the most important agricultural commodities globally, heavily cultivated in Southeast Asia. Fatal leaf fall diseases cause aggressive leaf defoliation, linked to lower latex yield and death of crops before maturity. Due to the significant consequences of the disease to H. brasiliensis, the recent gene expression studies from four fall leaf diseases of H. brasiliensis were gathered; South American leaf blight, powdery mildew, Corynespora cassiicola and Phytophthora leaf fall disease. The differential analysis observed the pattern of commonly expressed genes upon fungi triggers using RT-PCR, DDRT-PCR, Real-time qRT-PCR and RNA-Seq. We have observed that RNA-Seq is the best tool to seek novel genes. Among the identified genes with defence-against fungi were pathogenesis-related genes such as β-1,3-glucanase and chitinase, the reactive oxygen species, and the phytoalexin biosynthesis. This manuscript also provided functional elaboration on the responsive genes and predicted possible biosynthetic pathways to identify and characterise novel genes in the future. At the end of the manuscript, the PCR methods and proteomic approaches were presented for future molecular and biochemical studies in the related diseases to H. brasiliensis.

Characterization of a Secretory YML079-like Cupin Protein That Contributes to Sclerotinia sclerotiorum Pathogenicity

Sclerotinia sclerotiorum causes devastating diseases in many agriculturally important crops, including oilseed rape and sunflower. However, the mechanisms of Sclerotinia sclerotiorum pathogenesis remain poorly understood. In this study, we characterized a YML079-like cupin protein (SsYCP1) from Sclerotinia sclerotiorum. We showed that SsYCP1 is strongly expressed and secreted during Sclerotinia sclerotiorum infection. Sclerotinia sclerotiorum infection was promoted by SsYCP1 overexpression and inhibited by silencing this gene with synthetic double-stranded RNA. These results collectively indicate SsYCP1 as a putative effector protein that contributes to Sclerotinia sclerotiorum pathogenicity. These findings extend our understanding of effector-mediated Sclerotinia sclerotiorum pathogenesis and suggest a novel role for YML079-like cupin proteins in plant-pathogen interactions.

Transcriptomics Analysis of Primordium Formation in Pleurotus eryngii

Primordium formation is an important stage preceding the growth and development of the Pleurotus eryngii fruiting body. However, the molecular mechanisms underlying primordium formation remain unclear. In the present study, comparative transcriptomics was performed between mature mycelia and primordium to analyze the transcriptional properties during primordium formation in P. eryngii. A total of 19,655 differentially expressed genes (10,718 upregulated genes and 8937 downregulated genes) were identified. These differentially expressed genes were involved in cell wall degradation, carbohydrate hydrolysis, light perception, and cAMP signal transduction. These results aid further understanding of the transcriptional changes and the molecular processes underlying primordium formation and differentiation, which may lay the foundation for improving the cultivation and quality control of P. eryngii.

Mitogenome-wide comparison and phylogeny reveal group I intron dynamics and intraspecific diversification within the phytopathogen Corynespora cassiicola

Corynespora cassiicola, the causal agent of an extensive range of plant diseases worldwide, is a momentous fungus with diverse lifestyles and rich in intraspecies variations. In the present study, a total of 56 mitochondrial genomes of C. cassiicola were assembled (except two available online) and analyzed, of which 16 mitogenomes were newly sequenced here. All these circular mitochondrial DNA (mtDNA) molecules, ranging from 39,223 bp to 45,786 bp in length, comprised the same set of 13 core protein-coding genes (PCGs), two rRNAs and 27 tRNAs arranged in identical order. Across the above conserved genes, nad3 had the largest genetic distance between different isolates and was possibly subjected to positive selection pressure. Comparative mitogenomic analysis indicated that seven group I (IB, IC1, and IC2) introns with a length range of 1013-1876 bp were differentially inserted in three core PCGs (cox1, nad1, and nad5), resulting in the varied mitogenome sizes among C. cassiicola isolates. In combination with dynamic distribution of the introns, a well-supported mitogenome-wide phylogeny of the 56 C. cassiicola isolates revealed eight phylogenetic groups, which only had weak correlations with host range and toxin class. Different groups of isolates exhibited obvious differences in length and GC content of some genes, while a degree of variance in codon usage and tRNA structure was also observed. This research served as the first report on mitogenomic comparisons within C. cassiicola, and could provide new insights into its intraspecific microevolution and genetic diversity.

Nanopore/Illumina Hybrid Genome Sequence Resource for Corynespora cassiicola Strain XJ Infecting Rubber Tree in China

Corynespora cassiicola is a ubiquitous pathogenic fungus that can infect a broad range of plant hosts. Corynespora leaf fall, caused by C. cassiicola, is one of the major diseases on rubber tree in China. This disease is having an increasing affect on natural rubber production worldwide. In this study, by combining the Nanopore and Illumina sequencing technologies, we present the chromosome-scale genome sequence of the rubber tree-sampled C. cassiicola strain XJ collected in the subtropical region of China. The assembly consists of 23 scaffolds (N₅₀ = 4.62 Mb) with an estimated genome size of 44.42 Mb (only 166 non-ATCG bases) and 16,108 protein-coding genes. The genome will provide a valuable resource for further research on the pathogenesis and comparative genomics of C. cassiicola on rubber tree and other hosts.

The Bioactivity and Efficacy of Benzovindiflupyr Against Corynespora cassiicola, the Causal Agent of Cucumber Corynespora Leaf Spot

Corynespora cassiicola, which causes Corynespora leaf spot, results in considerable yield loss of cucumber grown in greenhouses. Frequent reports of reduced efficacy and control failure of fungicides warrant new, efficient alternative chemistries. In this study, the sensitivity of C. cassiicola to benzovindiflupyr was evaluated using a collection of 81 isolates collected from Shandong, China. The mean EC₅₀ values for mycelial growth, spore germination, and germ tube elongation of C. cassiicola were 0.69 ± 0.44, 0.12 ± 0.063, and 0.13 ± 0.076 µg ml^-1, respectively. Benzovindiflupyr treatment led to a reduced respiration rate and ATP production of C. cassiicola and decreased spore pathogenicity by 21.9% on average. Additionally, detached cucumber leaves sprayed with fungicides before or after inoculation were used to assess the efficacy of benzovindiflupyr against C. cassiicola. Benzovindiflupyr (150 µg ml^-1) exhibited preventive and curative efficacies of 86.9 and 77.1%, respectively. Benzovindiflupyr at 150 g a.i. ha^-1 provided over 70% efficacy in field trials performed in 2018 and 2019, which was significantly higher than that of the reference fungicides fluopyram and fluxapyroxad at the same dose. Furthermore, the yield of commercial cucumber increased as disease incidence decreased. Our findings pave the way for the introduction of benzovindiflupyr in the integrated management of Corynespora leaf spot.

FunOrder: A robust and semi-automated method for the identification of essential biosynthetic genes through computational molecular co-evolution

Secondary metabolites (SMs) are a vast group of compounds with different structures and properties that have been utilized as drugs, food additives, dyes, and as monomers for novel plastics. In many cases, the biosynthesis of SMs is catalysed by enzymes whose corresponding genes are co-localized in the genome in biosynthetic gene clusters (BGCs). Notably, BGCs may contain so-called gap genes, that are not involved in the biosynthesis of the SM. Current genome mining tools can identify BGCs, but they have problems with distinguishing essential genes from gap genes. This can and must be done by expensive, laborious, and time-consuming comparative genomic approaches or transcriptome analyses. In this study, we developed a method that allows semi-automated identification of essential genes in a BGC based on co-evolution analysis. To this end, the protein sequences of a BGC are blasted against a suitable proteome database. For each protein, a phylogenetic tree is created. The trees are compared by treeKO to detect co-evolution. The results of this comparison are visualized in different output formats, which are compared visually. Our results suggest that co-evolution is commonly occurring within BGCs, albeit not all, and that especially those genes that encode for enzymes of the biosynthetic pathway are co-evolutionary linked and can be identified with FunOrder. In light of the growing number of genomic data available, this will contribute to the studies of BGCs in native hosts and facilitate heterologous expression in other organisms with the aim of the discovery of novel SMs.

The discovery and description of novel fungal secondary metabolites promises novel antibiotics, pharmaceuticals, and other useful compounds. A way to identify novel secondary metabolites is to express the corresponding genes in a suitable expression host. Consequently, a detailed knowledge or an accurate prediction of these genes is necessary. In fungi, the genes are co-localized in so-called biosynthetic gene clusters. Notably, the clusters may also contain genes that are not necessary for the biosynthesis of the secondary metabolites, so-called gap genes. We developed a method to detect co-evolved genes within the clusters and demonstrated that essential genes are co-evolving and can thus be differentiated from the gap genes. This adds an additional layer of information, which can support researchers with their decisions on which genes to study and express for the discovery of novel secondary metabolites.

Increased abundance of secreted hydrolytic enzymes and secondary metabolite gene clusters define the genomes of latent plant pathogens in the Botryosphaeriaceae

BACKGROUND

The Botryosphaeriaceae are important plant pathogens, but also have the ability to establish asymptomatic infections that persist for extended periods in a latent state. In this study, we used comparative genome analyses to shed light on the genetic basis of the interactions of these fungi with their plant hosts. For this purpose, we characterised secreted hydrolytic enzymes, secondary metabolite biosynthetic gene clusters and general trends in genomic architecture using all available Botryosphaeriaceae genomes, and selected Dothideomycetes genomes.

RESULTS

The Botryosphaeriaceae genomes were rich in carbohydrate-active enzymes (CAZymes), proteases, lipases and secondary metabolic biosynthetic gene clusters (BGCs) compared to other Dothideomycete genomes. The genomes of Botryosphaeria, Macrophomina, Lasiodiplodia and Neofusicoccum, in particular, had gene expansions of the major constituents of the secretome, notably CAZymes involved in plant cell wall degradation. The Botryosphaeriaceae genomes were shown to have moderate to high GC contents and most had low levels of repetitive DNA. The genomes were not compartmentalized based on gene and repeat densities, but genes of secreted enzymes were slightly more abundant in gene-sparse regions.

CONCLUSION

The abundance of secreted hydrolytic enzymes and secondary metabolite BGCs in the genomes of Botryosphaeria, Macrophomina, Lasiodiplodia, and Neofusicoccum were similar to those in necrotrophic plant pathogens and some endophytes of woody plants. The results provide a foundation for comparative genomic analyses and hypotheses to explore the mechanisms underlying Botryosphaeriaceae host-plant interactions.

Transcriptome profiling in susceptible and tolerant rubber tree clones in response to cassiicolin Cas1, a necrotrophic effector from Corynespora cassiicola

Corynespora cassiicola, a fungal plant pathogen with a large host range, causes important damages in rubber tree (Hevea brasiliensis), in Asia and Africa. A small secreted protein named cassiicolin was previously identified as a necrotrophic effector required for the virulence of C. cassiicola in specific rubber tree clones. The objective of this study was to decipher the cassiicolin-mediated molecular mechanisms involved in this compatible interaction. We comparatively analyzed the RNA-Seq transcriptomic profiles of leaves treated or not with the purified cassiicolin Cas1, in two rubber clones: PB260 (susceptible) and RRIM600 (tolerant). The reads were mapped against a synthetic transcriptome composed of all available transcriptomic references from the two clones. Genes differentially expressed in response to cassiicolin Cas1 were identified, in each clone, at two different time-points. After de novo annotation of the synthetic transcriptome, we analyzed GO enrichment of the differentially expressed genes in order to elucidate the main functional pathways impacted by cassiicolin. Cassiicolin induced qualitatively similar transcriptional modifications in both the susceptible and the tolerant clones, with a strong negative impact on photosynthesis, and the activation of defense responses via redox signaling, production of pathogenesis-related protein, or activation of the secondary metabolism. In the tolerant clone, transcriptional reprogramming occurred earlier but remained moderate. By contrast, the susceptible clone displayed a late but huge transcriptional burst, characterized by massive induction of phosphorylation events and all the features of a hypersensitive response. These results confirm that cassiicolin Cas1 is a necrotrophic effector triggering a hypersensitive response in susceptible rubber clones, in agreement with the necrotrophic-effector-triggered susceptibility model.

Genome sequence of Monilinia vaccinii-corymbosi sheds light on mummy berry disease infection of blueberry and mating type

Mummy berry disease, caused by the fungal pathogen Monilinia vaccinii-corymbosi (Mvc), is one of the most economically important diseases of blueberries in North America. Mvc is capable of inducing two separate blighting stages during its life cycle. Infected fruits are rendered mummified and unmarketable. Genomic data for this pathogen is lacking, but could be useful in understanding the reproductive biology of Mvc and the mechanisms it deploys to facilitate host infection. In this study, PacBio sequencing and Hi-C interaction data were utilized to create a chromosome-scale reference genome for Mvc. The genome comprises nine chromosomes with a total length of 30 Mb, an N50 length of 4.06 Mb, and an average 413X sequence coverage. A total of 9399 gene models were predicted and annotated, and BUSCO analysis revealed that 98% of 1,438 searched conserved eukaryotic genes were present in the predicted gene set. Potential effectors were identified, and the mating-type (MAT) locus was characterized. Biotrophic effectors allow the pathogen to avoid recognition by the host plant and evade or mitigate host defense responses during the early stages of fruit infection. Following locule colonization, necrotizing effectors promote the mummification of host tissues. Potential biotrophic effectors utilized by Mvc include chorismate mutase for reducing host salicylate and necrotrophic effectors include necrosis-inducing proteins and hydrolytic enzymes for macerating host tissue. The MAT locus sequences indicate the potential for homothallism in the reference genome, but a deletion allele of the MAT locus, characterized in a second isolate, indicates heterothallism. Further research is needed to verify the roles of individual effectors in virulence and to determine the role of the MAT locus in outcrossing and population genotypic diversity.

Genome sequences and in silico effector mining of Corynespora cassiicola CC_29 and Corynespora olivacea CBS 114450

The placement of Corynespora olivacea within the large genus Corynespora (Pleosporales) is controversial, because the species is distantly related to other congeners, including the type species C. cassiicola. Corynespora cassiicola is a polyphagous, cosmopolitan plant pathogen. Successful colonization of plant tissues requires the pathogen's effector repertoire to modulate host cell physiology and facilitate the infection process. We sequenced and performed functional annotations on the genomes of C. cassiicola CC_29 (genome size about 44.8 Mb; isolated from soybean leaves) and C. olivacea CBS 114450 (32.3 Mb). Our phylogenomic approach showed that C. cassiicola is distantly related to C. olivacea, which clustered among the Massarinaceae family members, supporting a hypothesis that C. olivacea was originally misclassified. The predicted sizes for the proteome and secretome of C. cassiicola (18,487 and 1327, respectively) were larger than those of C. olivacea (13,501 and 920; respectively). Corynespora cassiicola had a richer repertoire of effector proteins (CAZymes, proteases, lipases, and effectors) and genes associated with secondary metabolism than did C. olivacea.

Genomic Characteristics and Comparative Genomics Analysis of Two Chinese Corynespora cassiicola Strains Causing Corynespora Leaf Fall (CLF) Disease

Rubber tree Corynespora leaf fall (CLF) disease, caused by the fungus Corynespora cassiicola, is one of the most damaging diseases in rubber tree plantations in Asia and Africa, and this disease also threatens rubber nurseries and young rubber plantations in China. C. cassiicola isolates display high genetic diversity, and virulence profiles vary significantly depending on cultivar. Although one phytotoxin (cassicolin) has been identified, it cannot fully explain the diversity in pathogenicity between C. cassiicola species, and some virulent C. cassiicola strains do not contain the cassiicolin gene. In the present study, we report high-quality gapless genome sequences, obtained using short-read sequencing and single-molecule long-read sequencing, of two Chinese C. cassiicola virulent strains. Comparative genomics of gene families in these two stains and a virulent CPP strain from the Philippines showed that all three strains experienced different selective pressures, and metabolism-related gene families vary between the strains. Secreted protein analysis indicated that the quantities of secreted cell wall-degrading enzymes were correlated with pathogenesis, and the most aggressive CCP strain (cassiicolin toxin type 1) encoded 27.34% and 39.74% more secreted carbohydrate-active enzymes (CAZymes) than Chinese strains YN49 and CC01, respectively, both of which can only infect rubber tree saplings. The results of antiSMASH analysis showed that all three strains encode ~60 secondary metabolite biosynthesis gene clusters (SM BGCs). Phylogenomic and domain structure analyses of core synthesis genes, together with synteny analysis of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) gene clusters, revealed diversity in the distribution of SM BGCs between strains, as well as SM polymorphisms, which may play an important role in pathogenic progress. The results expand our understanding of the C. cassiicola genome. Further comparative genomic analysis indicates that secreted CAZymes and SMs may influence pathogenicity in rubber tree plantations. The findings facilitate future exploration of the molecular pathogenic mechanism of C. cassiicola.

Effectors of Plant Necrotrophic Fungi

Plant diseases caused by necrotrophic fungal pathogens result in large economic losses in field crop production worldwide. Effectors are important players of plant-pathogen interaction and deployed by pathogens to facilitate plant colonization and nutrient acquisition. Compared to biotrophic and hemibiotrophic fungal pathogens, effector biology is poorly understood for necrotrophic fungal pathogens. Recent bioinformatics advances have accelerated the prediction and discovery of effectors from necrotrophic fungi, and their functional context is currently being clarified. In this review we examine effectors utilized by necrotrophic fungi and hemibiotrophic fungi in the latter stages of disease development, including plant cell death manipulation. We define "effectors" as secreted proteins and other molecules that affect plant physiology in ways that contribute to disease establishment and progression. Studying and understanding the mechanisms of necrotrophic effectors is critical for identifying avenues of genetic intervention that could lead to improved resistance to these pathogens in plants.

Distribution of methionine sulfoxide reductases in fungi and conservation of the free-methionine-R-sulfoxide reductase in multicellular eukaryotes

Methionine, either as a free amino acid or included in proteins, can be oxidized into methionine sulfoxide (MetO), which exists as R and S diastereomers. Almost all characterized organisms possess thiol-oxidoreductases named methionine sulfoxide reductase (Msr) enzymes to reduce MetO back to Met. MsrA and MsrB reduce the S and R diastereomers of MetO, respectively, with strict stereospecificity and are found in almost all organisms. Another type of thiol-oxidoreductase, the free-methionine-R-sulfoxide reductase (fRMsr), identified so far in prokaryotes and a few unicellular eukaryotes, reduces the R MetO diastereomer of the free amino acid. Moreover, some bacteria possess molybdenum-containing enzymes that reduce MetO, either in the free or protein-bound forms. All these Msrs play important roles in the protection of organisms against oxidative stress. Fungi are heterotrophic eukaryotes that colonize all niches on Earth and play fundamental functions, in organic matter recycling, as symbionts, or as pathogens of numerous organisms. However, our knowledge on fungal Msrs is still limited. Here, we performed a survey of msr genes in almost 700 genomes across the fungal kingdom. We show that most fungi possess one gene coding for each type of methionine sulfoxide reductase: MsrA, MsrB, and fRMsr. However, several fungi living in anaerobic environments or as obligate intracellular parasites were devoid of msr genes. Sequence inspection and phylogenetic analyses allowed us to identify non-canonical sequences with potentially novel enzymatic properties. Finaly, we identified several ocurences of msr horizontal gene transfer from bacteria to fungi.

First Report of Corynespora cassiicola Causing Target Spot on Soybean in Taiwan

Soybean (Glycine max [L.] Merr.) is an important crop in Taiwan. In October 2020, an unknown leaf spot disease was counted (n = 100) to occur over 70% of soybean cultivar 'Hualien No.1' in the Shoufeng Township of Hualien County, eastern Taiwan. Initial symptoms on leaves as tiny lesions approximately 3 mm in diameter, which later enlarged and developed into round, irregular, and reddish-brown spots with concentric rings surrounded by a yellowish halo. The symptoms appeared on both young and old leaves, but rarely on the stem or pods. The lesions at the margin of healthy and infected tissues were surface-disinfested in 1% NaOCl for 30 seconds, washed twice in sterilized distilled water, dissected and plated on potato dextrose agar (PDA) to isolate the potential pathogen. Colonies on PDA exhibited light to dark brown color at 24°C with 12-hours light after 7-days incubation. The average growth rate was 3 mm per day. Conidia were light brown in color and obclavate to cylindrical in shape. The size of a conidium was measured with an average of 110.8 ± 28.2 μm in length and 15.2 ± 2.8 μm in width, typically with 3 to 18 septa (n = 50). To confirm the pathogenicity of this fungus, conidial suspension (104 conidia/mL) of two isolates, HL_GM-6 and HL_GM-7, were sprayed on the healthy leaves of 4-weeks-old soybean. Plants sprayed with sterile distilled water were used as a control. After inoculation, the plants were covered with plastic bags to maintain a high humidity for 24 hours before moving into a greenhouse with a condition of 20 to 25°C and relative humidity of 75 to 80%. After 7 days of inoculation, foliar symptoms began to appear and which were identical with the field observations. To complete the Koch's postulates, pathogen isolation was attempted and the identical fungus was retrieved from the foliar spots of the inoculated leaves. The foliar symptoms as well as the morphology of the conidiophores and conidia suggested the pathogen to be Corynespora cassiicola (Ellis et al. 1971). Molecular characterization was performed using the sequences of internal transcribed spacer (ITS) region of rDNA, actin (act1), tubulin, and translation elongation factor 1 alpha (tef1) genes after a PCR with ITS1/ITS4 (White et al. 1990), ACT-512F/ACT-783R (Carbone and Kohn, 1999), BT2a/Bt2b (Udayanga et al. 2012), EF1-728F/EF1-986R (Udayanga et al. 2012), respectively. BLASTN sequence analyses of the ITS, act1, tubulin, and tef1 genomic regions of the isolate HL_GM-7 (GenBanK accessions MW548097 MW961420, MW961419 and MW961421) showed high similarity with the isolates of C. cassiicola including 99.58% with sequence KF810854 (Deon et al. 2014), 99.11% with FJ853005 (Dixon et al. 2009), 99.34% with MH763700 (Duan et al. 2019), and 99.33% with KY112719 (Zhang et al. 2018) respectively. Based on the morphology, pathogenicity, and sequence results, this study becomes the first report of C. cassiicola causing target spot on soybean in Taiwan. C. cassiicola is known to infect a broad host range (Dixon et al. 2009; Lopezet al. 2018), and it has been found to infect tomato, cucumber, papaya, and Salvia miltiorrhiza in Taiwan (Lu et al. 2019; Tsai et al. 2015). Therefore, the emergence of soybean target spot should be aware to avoid potential damage to soybean production in Taiwan.

Proteinaceous effector discovery and characterization in filamentous plant pathogens

The complicated interplay of plant-pathogen interactions occurs on multiple levels as pathogens evolve to constantly evade the immune responses of their hosts. Many economically important crops fall victim to filamentous pathogens that produce small proteins called effectors to manipulate the host and aid infection/colonization. Understanding the effector repertoires of pathogens is facilitating an increased understanding of the molecular mechanisms underlying virulence as well as guiding the development of disease control strategies. The purpose of this review is to give a chronological perspective on the evolution of the methodologies used in effector discovery from physical isolation and in silico predictions, to functional characterization of the effectors of filamentous plant pathogens and identification of their host targets.

First Report of Target Spot on Tomato Caused by Corynespora cassiicola in Mauritius

Tomatoes (Solanum lycopersicum) represent one of the most frequently consumed vegetables in Mauritius after potatoes and onions. The value of the tomato industry is estimated to be around Rs 300 M in Mauritius, with an annual production of 18,376 t over an area of 1365 ha. (Cheung Kai Suet 2019). In August 2019, disease surveillance was conducted in the tomato cv. 'Elipida' grown in the greenhouse situated at Camp Thorel (eastern part of Mauritius), a super-humid zone where the prevailing temperature and humidity were 30°C and 70% respectively. The symptoms included numerous circular to irregular, dark brown, target like lesions on the leaves, followed by the occurrence of yellow halo and occasional defoliation. Disease incidence was estimated to be 80% in the entire greenhouse. From sampled symptomatic leaves, small pieces of infected tissue were surface-disinfected with 1% sodium hypochlorite, air dried, and placed on PDA. After 7 days incubation at 23°C under 12 hours of natural light regime, isolates with fast growing grey-brown, velvety colonies were recovered. In colonies, singly-borne or in short chains, pale brown, cylindrical, straight or slightly curved conidia with 2 - 14 pseudosepta (34 x 2 μm) were numerous. Based on morphological features, the isolates were identified as Corynespora cassiicola (Berk. and M.A. Curtis) C.T. Wei (Dixon et al. 2009). Morphological identification was confirmed by amplifying and sequencing of the ITS region (ITS1, 5.8S rDNA and ITS2 regions) of the rDNA. Total DNA was extracted directly from fungal mycelium using a DNeasy Plant Mini Kit (Qiagen, Hilden, Germany), following the manufacturer's instructions. PCR amplification and sequencing were performed with primers ITS1F and ITS4 (Takamatsu et al. 2010). The nucleotide sequence of the representative isolate 408G-19/M (575 bp) (Accession No. MN860167) was compared with those available in GenBank and shared 98 to 99.82% identity with over 100 C. cassiicola isolates (99.65% with FJ852578 from Solanum melongena, Dixon et al. 2009). Koch's postulates were confirmed by spraying 10 healthy tomato plants (four leaf phenophase) with spore suspension (1 x 103 conidia/ml) prepared from 10 days old colonies of isolate 408G-19/M in sterile water. Healthy tomato plants inoculated with sterile water served as negative control. Plants were maintained in greenhouse conditions. On all inoculated plants, characteristic target like necrotic spots were visible 7 days post inoculation. No symptoms were recorded in the negative control after 15 days. From all symptomatic tomato leaves, the original isolate was successfully recovered. So far in Mauritius, C. cassiicola had been reported on Molucella (Anon. [Director of Agriculture] 1961) and Bignonia spp. (Orieux 1959) and also as an endophyte associated with Jatropha spp. (Rampadarath et al. 2018). Although symptoms resembling target spot were previously observed on field-grown tomatoes (Vally, pers. Comm.), to our knowledge, this is the first study confirming C. cassiicola as a tomato pathogen in Mauritius. As C. cassiicola affects a wide range of hosts (Lopez et al. 2018), including tomato, cucumber, zucchini and banana which are all important for Mauritius, the occurrence of this pathogen is a potential threat. Additionally, the results will help in developing efficient disease control strategies, thus minimizing yield loss of tomatoes produced locally.

Genome sequence and spore germination-associated transcriptome analysis of Corynespora cassiicola from cucumber

BACKGROUND

Corynespora cassiicola, as a necrotrophic phytopathogenic ascomycetous fungus, can infect hundreds of species of plants and rarely causes human diseases. This pathogen infects cucumber species and causes cucumber target spot, which has recently caused large cucumber yield losses in China. Genome sequence and spore germination-associated transcriptome analysis will contribute to the understanding of the molecular mechanism of pathogenicity and spore germination of C. cassiicola.

RESULTS

First, we reported the draft genome sequences of the cucumber-sampled C. cassiicola isolate HGCC with high virulence. Although conspecific, HGCC exhibited distinct genome sequence differences from a rubber tree-sampled isolate (CCP) and a human-sampled isolate (UM591). The proportion of secreted proteins was 7.2% in HGCC. A total of 28.9% (4232) of HGCC genes, 29.5% (4298) of CCP genes and 28.6% (4214) of UM591 genes were highly homologous to experimentally proven virulence-associated genes, respectively, which were not significantly different (P = 0.866) from the average (29.7%) of 10 other phytopathogenic fungi. Thousands of putative virulence-associated genes in various pathways or families were identified in C. cassiicola. Second, a global view of the transcriptome of C. cassiicola spores during germination was evaluated using RNA sequencing (RNA-Seq). A total of 3288 differentially expressed genes (DEGs) were identified. The majority of KEGG-annotated DEGs were involved in metabolism, genetic information processing, cellular processes, the organismal system, human diseases and environmental information processing.

CONCLUSIONS

These results facilitate the exploration of the molecular pathogenic mechanism of C. cassiicola in cucumbers and the understanding of molecular and cellular processes during spore germination.

Mycoparasitism illuminated by genome and transcriptome sequencing of Coniothyrium minitans, an important biocontrol fungus of the plant pathogen Sclerotinia sclerotiorum

Coniothyrium minitans is a mycoparasite of the notorious plant pathogen Sclerotinia sclerotiorum. To further understand the parasitism of C. minitans, we assembled and analysed its genome and performed transcriptome analyses. The genome of C. minitans strain ZS-1 was assembled into 350 scaffolds and had a size of 39.8 Mb. A total of 11 437 predicted genes and proteins were annotated, and 30.8 % of the blast hits matched proteins encoded by another member of the Pleosporales, Paraphaeosphaeria sporulosa, a worldwide soilborne fungus with biocontrol ability. The transcriptome of strain ZS-1 during the early interaction with S. sclerotiorum at 0, 4 and 12 h was analysed. The detected expressed genes were involved in responses to host defenses, including cell-wall-degrading enzymes, transporters, secretory proteins and secondary metabolite productions. Seventeen differentially expressed genes (DEGs) of fungal cell-wall-degrading enzymes (FCWDs) were up-regulated during parasitism, with only one down-regulated. Most of the monocarboxylate transporter genes of the major facilitator superfamily and all the detected ABC transporters, especially the heavy metal transporters, were significantly up-regulated. Approximately 8 % of the 11 437 proteins in C. minitans were predicted to be secretory proteins with catalytic activity. In the molecular function category, hydrolase activity, peptidase activity and serine hydrolase activity were enriched. Most genes involved in serine hydrolase activity were significantly up-regulated. This genomic analysis and genome-wide expression study demonstrates that the mycoparasitism process of C. minitans is complex and a broad range of proteins are deployed by C. minitans to successfully invade its host. Our study provides insights into the mechanisms of the mycoparasitism between C. minitans and S. sclerotiorum and identifies potential secondary metabolites from C. minitans for application as a biocontrol agent.

New insights into the evolution of host specificity of three Penicillium species and the pathogenicity of P. Italicum involving the infection of Valencia orange (Citrus sinensis)

Blue and green molds, the common phenotypes of post-harvest diseases in fruits, are mainly caused by Penicillium fungal species, including P. italicum, P. digitatum, and P. expansum. We sequenced and assembled the genome of a P. italicum strain, which contains 31,034,623 bp with 361 scaffolds and 627 contigs. The mechanisms underlying the evolution of host specificity among the analyzed Penicillium species were associated with the expansion of protein families, genome restructuring, horizontal gene transfer, and positive selection pressure. A dual-transcriptome analysis following the infection of Valencia orange (Citrus sinensis) by P. italicum resulted in the annotation of 9,307 P. italicum genes and 24,591 Valencia orange genes. The pathogenicity of P. italicum may be due to the activation of effectors, including 51 small secreted cysteine-rich proteins, 110 carbohydrate-active enzymes, and 12 G protein-coupled receptors. Additionally, 211 metabolites related to the interactions between P. italicum and Valencia orange were identified by gas chromatography-time of flight mass spectrography, three of which were further confirmed by ultra-high performance liquid chromatography triple quadrupole mass spectrometry. A metabolomics analysis indicated that P. italicum pathogenicity is associated with the sphingolipid and salicylic acid signaling pathways. Moreover, a correlation analysis between the metabolite contents and gene expression levels suggested that P. italicum induces carbohydrate metabolism in Valencia orange fruits as part of its infection strategy. This study provides useful information regarding the genomic determinants that drive the evolution of host specificity in Penicillium species and clarifies the host-plant specificity during the infection of Valencia orange by P. italicum.

IMPORTANCE

P. italicum GL_Gan1, a local strain in Guangzhou, China, was sequenced. Comparison of the genome of P. italicum GL_Gan1 with other pathogenic Penicillium species, P. digitatum and P. expansum, revealed that the expansion of protein families, genome restructuring, HGT, and positive selection pressure were related to the host range expansion of the analyzed Penicillium species. Moreover, gene gains or losses might be associated with the speciation of these Penicillium species. In addition, the molecular basis of host-plant specificity during the infection of Valencia orange (Citrus sinensis) by P. italicum was also elucidated by transcriptomic and metabolomics analysis. The data presented herein may be useful for further elucidating the molecular basis of the evolution of host specificity of Penicillium species and for illustrating the host-plant specificity during the infection of Valencia orange by P. italicum.

An updated phylogenetic classification of Corynespora cassiicola isolates and a practical approach to their identification based on the nucleotide polymorphisms at the ga4 and caa5 loci

Corynespora cassiicola (Burk. & M.A. Curtis) C.T. Wei. is an anamorphic fungus that affects more than 530 plant species, including economically important crops. Several lineages of this pathogen have been recognized, but the classification of isolates into clades is time-consuming and still sometimes leads to unclear results. In this work, eight major phylogenetic clades (PhL1-PhL8) including 245 isolates of C. cassiicola from 44 plant species were established based on a Bayesian inference analysis of four combined C. cassiicola genomic loci retrieved from GenBank, i.e., rDNA internal transcribed spacer (ITS), actin-1,ga4, and caa5. The existence of PhL1-PhL5 and PhL7 as clonal lineages was further confirmed through the analysis of full-genome single-nucleotide polymorphisms of 39 isolates. Haplotypes of the caa5 locus were PhL specific and encode isoforms of the LDB19 domain of a putative α-arrestin N-terminal-like protein. Evolution of the Caa5 arrestin is in correspondence with the PhLs. ga4 and caa5 PhL consensus sequences and a cleaved amplified polymorphic sequence (CAPS) procedure were generated based on the conserved nucleotide sequences and enzyme restriction patterns observed among isolates from the same lineage, respectively. The CAPS method was validated in silico, and its practical use allowed us to differentiate between tomato and papaya isolates, as well as to reveal the prevalence of PhL1 among isolates infecting soybean in Brazil. This novel approach could be useful in the efforts to control the diseases associated with C. cassiicola.

Endophytes from Wild Rubber Trees as Antagonists of the Pathogen Corynespora cassiicola

The Corynespora leaf fall disease of rubber trees, caused by the necrotrophic fungus Corynespora cassiicola, is responsible for important yield losses in Asian and African plantations, whereas its impact is negligible in South America. The objective of this study was to identify potential antagonists of C. cassiicola among fungal endophytes (i.e., Pestalotiopsis, Colletotrichum, and Trichoderma spp.) isolated from wild and cultivated rubber trees distributed in the Peruvian Amazon. We first tested the endophytes in dual in vitro confrontation assays against a virulent C. cassiicola isolate (CCP) obtained from diseased rubber trees in the Philippines. All Trichoderma isolates overran the CCP colony, suggesting some antagonistic mechanism, while species from the other genera behaved as mutual antagonists. Trichoderma isolates were then tested through antibiosis assays for their capacity to produce growth-inhibiting molecules. One isolate (LA279), recovered as an endophyte from a wild Hevea guianensis specimen and identified as Trichoderma koningiopsis, showed significant antibiosis capacity. We demonstrated that LA279 was also able to endophytically colonize the cultivated rubber tree species (H. brasiliensis). Under controlled laboratory conditions, rubber plants were inoculated with three Trichoderma strains, including LA279, in combination with the pathogenic CCP. Results showed that 1 week preinoculation with the endophytes differentially reduced CCP mycelial development and symptoms. In conclusion, this study suggests that T. koningiopsis isolate LA279-and derivate compounds-could be a promising candidate for the biological control of the important rubber tree pathogen C. cassiicola.

Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota)

Dothideomycetes is the most diverse fungal class in Ascomycota and includes species with a wide range of lifestyles. Previous multilocus studies have investigated the taxonomic and evolutionary relationships of these taxa but often failed to resolve early diverging nodes and frequently generated inconsistent placements of some clades. Here, we use a phylogenomic approach to resolve relationships in Dothideomycetes, focusing on two genera of melanized, extremotolerant rock-inhabiting fungi, Lichenothelia and Saxomyces, that have been suggested to be early diverging lineages. We assembled phylogenomic datasets from newly sequenced (4) and previously available genomes (238) of 242 taxa. We explored the influence of tree inference methods, supermatrix vs. coalescent-based species tree, and the impact of varying amounts of genomic data. Overall, our phylogenetic reconstructions provide consistent and well-supported topologies for Dothideomycetes, recovering Lichenothelia and Saxomyces among the earliest diverging lineages in the class. In addition, many of the major lineages within Dothideomycetes are recovered as monophyletic, and the phylogenomic approach implemented strongly supports their relationships. Ancestral character state reconstruction suggest that the rock-inhabiting lifestyle is ancestral within the class.

Prevalence of Soil-borne Diseases in Kalanchoe blossfeldiana Reveals a Complex of Pathogenic and Opportunistic Fungi

Greenhouse cultivation of ornamentals is subjected to a high incidence of soil-borne fungal pathogens. In Kalanchoe, these pathogens are responsible for root and stem rot, and for infection of the vascular tissue. Well-known soil-borne pathogens are believed to cause these diseases. Yet, a systematized survey of these pathogens is lacking for Kalanchoe produced commercially. Here, we studied the occurrence of soil-borne fungal pathogens associated with cultivation of Kalanchoe in Denmark and production of cuttings and stock plants in greenhouse facilities located in Turkey and Vietnam. Molecular identification of pathogens complemented mycological identification and pathogenicity testing of the soil-borne fungal pathogens. This study revealed that the fungi Corynespora cassiicola, Thielaviopsis basicola, Fusarium solani, and F. oxysporum are the most prevalent pathogens associated with root and stem rotting and wilt of Kalanchoe under the conditions studied. Furthermore, the study showed that some of the pathogens are part of an infection complex comprising both primary and opportunistic fungal species. The fact that some of the pathogens were present in some regions, while absent in others, suggests how they move between greenhouse facilities on infected plant material. This study generated important information about the soil-borne fungal complex affecting Kalanchoe, which is useful for a better understanding of the biology of the disease and for designing control strategies.

Characterization of the complete mitochondrial genome of Corynespora cassiicola (Pleosporales: Dothideomycetes), with its phylogenetic analysis

Corynespora cassiicola is a well-known plant pathogen with a broad host range and diverse lifestyles. In this study, we presented the complete mitochondrial genome (mitogenome) of C. cassiicola for the first time. It has a total length of 40,752 bp, which encodes 17 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNA), and 27 transfer RNA (tRNA) genes. The nucleotide composition of the mitogenome is: A (36.24%), T (34.62%), G (15.74%), and C (13.39%). Phylogenetic analysis revealed that C. cassiicola has a close relationship with Didymella pinodes from Didymellaceae.

Gene deletion of Corynespora cassiicola cassiicolin Cas1 suppresses virulence in the rubber tree

Corynespora cassiicola is an ascomycete fungus causing important damages in a wide range of plant hosts, including rubber tree. The small secreted protein cassiicolin is suspected to play a role in the onset of the disease in rubber tree, based on toxicity and gene expression profiles. However, its exact contribution to virulence, compared to other putative effectors, remains unclear. We created a deletion mutant targeting the cassiicolin gene Cas1 from the highly aggressive isolate CCP. Wild-type CCP and mutant ccpΔcas1 did not differ in terms of mycelium growth, sporulation, and germination rate in vitro. Cas1 gene deletion induced a complete loss of virulence on the susceptible clones PB260 and IRCA631, as revealed by inoculation experiments on intact (non-detached) leaves. However, residual symptoms persisted when inoculations were conducted on detached leaves, notably with longer incubation times. Complementation with exogenous cassiicolin restored the mutant capacity to colonize the leaf tissues. We also compared the toxicity of CCP and ccpΔcas1 culture filtrates, through electrolyte leakage measurements on abraded detached leaves, over a range of clones as well as an F1 population derived from the cross between the clones PB260 (susceptible) and RRIM600 (tolerant). On average, filtrate toxicity was lower but not fully suppressed in ccpΔcas1 compared to CCP, with clone-dependent variations. The two QTL, previously found associated with sensitivity to CPP filtrate or to the purified cassiicolin, were no longer detected with the mutant filtrate, while new QTL were revealed. Our results demonstrate that: (1) cassiicolin is a necrotrophic effector conferring virulence to the CCP isolate in susceptible rubber clones and (2) other effectors produced by CCP contribute to residual filtrate toxicity and virulence in senescing/wounded tissues. These other effectors may be involved in saprotrophy rather than necrotrophy.

Exploitation of reverse vaccinology and immunoinformatics as promising platform for genome-wide screening of new effective vaccine candidates against Plasmodium falciparum

Background

In the current scenario, designing of world-wide effective malaria vaccine against Plasmodium falciparum remain challenging despite the significant progress has been made in last few decades. Conventional vaccinology (isolate, inactivate and inject) approaches are time consuming, laborious and expensive; therefore, the use of computational vaccinology tools are imperative, which can facilitate the design of new and promising vaccine candidates.

Results

In current investigation, initially 5548 proteins of P. falciparum genome were carefully chosen for the incidence of signal peptide/ anchor using SignalP4.0 tool that resulted into 640 surface linked proteins (SLP). Out of these SLP, only 17 were predicted to contain GPI-anchors using PredGPI tool in which further 5 proteins were considered as malarial antigenic adhesins by MAAP and VaxiJen programs, respectively. In the subsequent step, T cell epitopes of 5 genome derived predicted antigenic adhesins (GDPAA) and 5 randomly selected known malarial adhesins (RSKMA) were analysed employing MHC class I and II tools of IEDB analysis resource. Finally, VaxiJen scored T cell epitopes from each antigen were considered for prediction of population coverage (PPC) analysis in the world-wide population including malaria endemic regions. The validation of the present in silico strategy was carried out by comparing the PPC of combined (MHC class I and II) predicted epitope ensemble among GDPAA (99.97%), RSKMA (99.90%) and experimentally known epitopes (EKE) of P. falciparum (97.72%) pertaining to world-wide human population.

Conclusions

The present study systematically screened 5 potential protective antigens from P. falciparum genome using bioinformatics tools. Interestingly, these GDPAA, RSKMA and EKE of P. falciparum epitope ensembles forecasted to contain highly promiscuous T cell epitopes, which are potentially effective for most of the world-wide human population with malaria endemic regions. Therefore, these epitope ensembles could be considered in near future for novel and significantly effective vaccine candidate against malaria.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2482-x) contains supplementary material, which is available to authorized users.

Clonality and geographic structure of host-specialized populations of Corynespora cassiicola causing emerging target spot epidemics in the southeastern United States

Corynespora cassiicola is a destructive plant-pathogenic fungus causing widespread target spot epidemics, including outbreaks on cotton, soybean, and tomato in the southeastern United States. Previous studies revealed that populations from the three hosts are genetically distinct and host specialized. Although variation in aggressiveness to cotton and tomato were observed, no genetic diversity was detected within populations sampled from each of these hosts. We aimed to gain a better understanding of the emerging target spot epidemics by developing microsatellite markers for C. cassiicola to assess genetic variation, population structure, and to infer modes of reproduction and mechanisms of dispersal. Two hundred sixty-five isolates from cotton, soybean, tomato, and other host plants were genotyped with 13 microsatellite markers. Genotypic diversity revealed genetic variation within each of the populations collected from different hosts, with the population from cotton dominated by clonal genotypes and showing the least genetic diversity. In addition, C. cassiicola populations on different host species were genetically distinct and structured based on host species. No association between genetic and geographic distances was identified in the tomato populations, and the association in cotton populations was low. However, significant regional geographic structure was detected in the soybean populations of C. cassiicola. These results further support previous findings of introduced host specialized isolates or the evolution of more aggressive strains on each host. The lack of geographic structure suggests that the clones on cotton and tomato spread rapidly, or similar founder populations were established by human-mediated dispersal, and that dispersal is not limited. However, regional geographic structure of populations on soybean suggests limited dispersal among more established populations of C. cassiicola, or genetic differences in founder populations that colonized different geographic areas.