scholarly journals Comparative Genomic and Phenotypic Analyses of Pathogenic Fungi Neoscytalidium Dimidiatum and Bipolaris Papendorfii, Isolated From Human Skin Scraping

2020 ◽  
Author(s):  
Chee Sian Kuan ◽  
Kee Peng Ng ◽  
Su Mei Yew ◽  
Hadiza Umar Meleh ◽  
Heng Fong Seow ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Plant Pathogens ◽  
Pathogenic Fungi ◽  
Gene Clusters ◽  
Comparative Genomic ◽  
Broad Host Range ◽  
Neoscytalidium Dimidiatum ◽  
Functional Studies ◽  
Ph Tolerance ◽  
Fungal Plant Pathogens

Abstract Background: Neoscytalidium dimidiatum and Bipolaris species are fungal plant pathogens that have been reported to cause human diseases. Recently, we have isolated numerous N. dimidiatum and Bipolaris species from the skin scrapings and nails of different patients. In this work, we have sequenced the genome of one strain of N. dimidiatum. The sequenced genome was compared to that of a previously reported Bipolaris papendorfii genome for a better understanding of their complex lifestyle and broad host-range pathogenicity. Results: Their 33-43 Mb genomes include 11,015-12,320 putative coding DNA sequences, of which 0.51-2.49 are predicted transposable elements. Analysis of secondary metabolism gene clusters revealed several melanin biosynthetic genes and genes involved in fungal iron uptake. The arsenal of CAZymes related to plants pathogenicity is comparable between the species, including genes involved in hemicellulose and pectin decomposition. Several important genes-encoding keratinolytic peptidases were identified in N. dimidiatum and B. papendorfii, reflecting their potential pathogenic role in causing skin and nail infections. In this study, additional information on the metabolic features of these two species, such as nutritional profiling, pH tolerance, and osmotolerant are revealed. Conclusions: The genomic characterization of N. dimidiatum and B. papendorfii provides the basis for the future functional studies to gain further insights as to what makes these fungi persist in plants and why they are pathogenic to humans.

scholarly journals The Pattern and Function of DNA Methylation in Fungal Plant Pathogens

2020 ◽  
Vol 8 (2) ◽  
pp. 227 ◽  
Author(s):  
Chang He ◽  
Zhanquan Zhang ◽  
Boqiang Li ◽  
Shiping Tian
Keyword(s):  
Dna Methylation ◽  
Dna Sequences ◽  
Plant Pathogens ◽  
Epigenetic Modification ◽  
Gene Promoter ◽  
Pathogenic Fungi ◽  
Dna Methyltransferases ◽  
Phytopathogenic Fungi ◽  
Fungal Plant Pathogens ◽  
Wide Range

To successfully infect plants and trigger disease, fungal plant pathogens use various strategies that are dependent on characteristics of their biology and genomes. Although pathogenic fungi are different from animals and plants in the genomic heritability, sequence feature, and epigenetic modification, an increasing number of phytopathogenic fungi have been demonstrated to share DNA methyltransferases (MTases) responsible for DNA methylation with animals and plants. Fungal plant pathogens predominantly possess four types of DNA MTase homologs, including DIM-2, DNMT1, DNMT5, and RID. Numerous studies have indicated that DNA methylation in phytopathogenic fungi mainly distributes in transposable elements (TEs), gene promoter regions, and the repetitive DNA sequences. As an important and heritable epigenetic modification, DNA methylation is associated with silencing of gene expression and transposon, and it is responsible for a wide range of biological phenomena in fungi. This review highlights the relevant reports and insights into the important roles of DNA methylation in the modulation of development, pathogenicity, and secondary metabolism of fungal plant pathogens. Recent evidences prove that there are massive links between DNA and histone methylation in fungi, and they commonly regulate fungal development and mycotoxin biosynthesis.

scholarly journals The Ustilago hordei–Barley Interaction is a Versatile System for Characterization of Fungal Effectors

2021 ◽  
Vol 7 (2) ◽  
pp. 86
Author(s):  
Bilal Ökmen ◽  
Daniela Schwammbach ◽  
Guus Bakkeren ◽  
Ulla Neumann ◽  
Gunther Doehlemann
Keyword(s):  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Expression System ◽  
Pathogenic Fungi ◽  
Effector Proteins ◽  
Mating Partner ◽  
Fungal Virulence ◽  
Functional Studies ◽  
Infection Structures ◽  
Ustilago Hordei

Obligate biotrophic fungal pathogens, such as Blumeria graminis and Puccinia graminis, are amongst the most devastating plant pathogens, causing dramatic yield losses in many economically important crops worldwide. However, a lack of reliable tools for the efficient genetic transformation has hampered studies into the molecular basis of their virulence or pathogenicity. In this study, we present the Ustilago hordei–barley pathosystem as a model to characterize effectors from different plant pathogenic fungi. We generate U. hordei solopathogenic strains, which form infectious filaments without the presence of a compatible mating partner. Solopathogenic strains are suitable for heterologous expression system for fungal virulence factors. A highly efficient Crispr/Cas9 gene editing system is made available for U. hordei. In addition, U. hordei infection structures during barley colonization are analyzed using transmission electron microscopy, showing that U. hordei forms intracellular infection structures sharing high similarity to haustoria formed by obligate rust and powdery mildew fungi. Thus, U. hordei has high potential as a fungal expression platform for functional studies of heterologous effector proteins in barley.

scholarly journals Spray-induced gene silencing for disease control is dependent on the efficiency of pathogen RNA uptake

2021 ◽  
Author(s):  
Lulu Qiao ◽  
Chi Lan ◽  
Luca Capriotti ◽  
Audrey Ah-Fong ◽  
Jonatan Nino Sanchez ◽  
...  
Keyword(s):  
Disease Management ◽  
Plant Disease ◽  
Plant Pathogens ◽  
Developmental Stages ◽  
Pathogenic Fungi ◽  
Cell Types ◽  
Uptake Efficiency ◽  
Fungal Plant Pathogens ◽  
Plant Disease Management ◽  
Fungal Genes

AbstractRecent discoveries show that fungi can take up environmental RNA, which can then silence fungal genes through environmental RNA interference. This discovery prompted the development of Spray-Induced Gene Silencing (SIGS) for plant disease management. In this study, we aimed to determine the efficacy of SIGS across a variety of eukaryotic microbes. We first examined the efficiency of RNA uptake in multiple pathogenic and non-pathogenic fungi, and an oomycete pathogen. We observed efficient double-stranded RNA (dsRNA) uptake in the fungal plant pathogens Botrytis cinerea, Sclerotinia sclerotiorum, Rhizoctonia solani, Aspergillus niger, and Verticillium dahliae, but no uptake in Colletotrichum gloeosporioides, and weak uptake in a beneficial fungus, Trichoderma virens. For the oomycete plant pathogen, Phytophthora infestans, RNA uptake was limited, and varied across different cell types and developmental stages. Topical application of dsRNA targeting virulence-related genes in the pathogens with high RNA uptake efficiency significantly inhibited plant disease symptoms, whereas the application of dsRNA in pathogens with low RNA uptake efficiency did not suppress infection. Our results have revealed that dsRNA uptake efficiencies vary across eukaryotic microbe species and cell types. The success of SIGS for plant disease management can largely be determined by the pathogen RNA uptake efficiency.

scholarly journals Preliminary Study on the Activity of Phycobiliproteins against Botrytis cinerea

Marine Drugs ◽  
2020 ◽  
Vol 18 (12) ◽  
pp. 600
Author(s):  
Hillary Righini ◽  
Ornella Francioso ◽  
Michele Di Foggia ◽  
Antera Martel Quintana ◽  
Roberta Roberti
Keyword(s):  
Spore Germination ◽  
Plant Pathogens ◽  
Disease Incidence ◽  
Fungal Growth ◽  
Pathogenic Fungi ◽  
Gray Mold ◽  
Fungal Plant Pathogens ◽  
Ft Ir ◽  
Preliminary Study ◽  
Ft Raman

Phycobiliproteins (PBPs) are proteins of cyanobacteria and some algae such as rhodophytes. They have antimicrobial, antiviral, antitumor, antioxidative, and anti-inflammatory activity at the human level, but there is a lack of knowledge on their antifungal activity against plant pathogens. We studied the activity of PBPs extracted from Arthrospiraplatensis and Hydropuntiacornea against Botrytiscinerea, one of the most important worldwide plant-pathogenic fungi. PBPs were characterized by using FT-IR and FT-Raman in order to investigate their structures. Their spectra differed in the relative composition in the amide bands, which were particularly strong in A. platensis. PBP activity was tested on tomato fruits against gray mold disease, fungal growth, and spore germination at different concentrations (0.3, 0.6, 1.2, 2.4, and 4.8 mg/mL). Both PBPs reduced fruit gray mold disease. A linear dose–response relationship was observed for both PBPs against disease incidence and H. cornea against disease severity. Pathogen mycelial growth and spore germination were reduced significantly by both PBPs. In conclusion, PBPs have the potential for being also considered as natural compounds for the control of fungal plant pathogens in sustainable agriculture.

scholarly journals Conservation of a gene cluster reveals novel cercosporin biosynthetic mechanisms and extends production to the genus Colletotrichum

2017 ◽  
Author(s):  
Ronnie de Jonge ◽  
Malaika K. Ebert ◽  
Callie R. Huitt-Roehl ◽  
Paramita Pal ◽  
Jeffrey C. Suttle ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Gene Cluster ◽  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Pathogenic Fungi ◽  
Gene Clusters ◽  
Phylogenomic Analysis ◽  
First Case ◽  
Horizontal Transfers ◽  
Fungal Genus

AbstractSpecies in the genus Cercospora cause economically devastating diseases in sugar beet, maize, rice, soy bean and other major food crops. Here we sequenced the genome of the sugar beet pathogen C. beticola and found it encodes 63 putative secondary metabolite gene clusters, including the cercosporin toxin biosynthesis (CTB) cluster. We show that the CTB gene cluster has experienced multiple duplications and horizontal transfers across a spectrum of plant pathogenic fungi, including the wide host range Colletotrichum genus as well as the rice pathogen Magnaporthe oryzae. Although cercosporin biosynthesis has been thought to-date to rely on an eight gene CTB cluster, our phylogenomic analysis revealed gene collinearity adjacent to the established cluster in all CTB cluster-harboring species. We demonstrate that the CTB cluster is larger than previously recognized and includes cercosporin facilitator protein (CFP) previously shown to be involved with cercosporin auto-resistance, and four additional genes required for cercosporin biosynthesis including the final pathway enzymes that install the unusual cercosporin methylenedioxy bridge. Finally, we demonstrate production of cercosporin by Colletotrichum fioriniae, the first known cercosporin producer within this agriculturally important genus. Thus, our results provide new insight into the intricate evolution and biology of a toxin critical to agriculture and broaden the production of cercosporin to another fungal genus containing many plant pathogens of important crops worldwide.Significance StatementSpecies in the fungal genus Cercospora cause diseases in many important crops worldwide. Their success as pathogens is largely due to the secretion of cercosporin during infection. We report that the cercosporin toxin biosynthesis (CTB) cluster is ancient and was horizontally transferred to diverse fungal pathogens on an unprecedented scale. Since these analyses revealed genes adjacent to the established CTB cluster, we evaluated their role in C. beticola to show that four are necessary for cercosporin biosynthesis. Finally, we confirmed that the apple pathogen Colletotrichum fioriniae produces cercosporin, the first case outside the family Mycosphaerellaceae. Other Colletotrichum plant pathogens also harbor the CTB cluster, which points to a wider concern that this toxin may play in virulence and human health.

scholarly journals Complex evolutionary origins of specialized metabolite gene cluster diversity among the plant pathogenic fungi of theFusarium graminearumspecies complex

2019 ◽  
Author(s):  
Sabina Moser Tralamazza ◽  
Liliana Oliveira Rocha ◽  
Ursula Oggenfuss ◽  
Benedito Corrêa ◽  
Daniel Croll
Keyword(s):  
Gene Cluster ◽  
Plant Pathogens ◽  
De Novo ◽  
Chromosomal Rearrangements ◽  
Pathogenic Fungi ◽  
Gene Clusters ◽  
Death Process ◽  
Head Blight ◽  
Fungal Genomes ◽  
Gain Loss

AbstractFungal genomes encode highly organized gene clusters that underlie the production of specialized (or secondary) metabolites. Gene clusters encode key functions to exploit plant hosts or environmental niches. Promiscuous exchange among species and frequent reconfigurations make gene clusters some of the most dynamic elements of fungal genomes. Despite evidence for high diversity in gene cluster content among closely related strains, the microevolutionary processes driving gene cluster gain, loss and neofunctionalization are largely unknown. We analyzed theFusarium graminearumspecies complex (FGSC) composed of plant pathogens producing potent mycotoxins and causing Fusarium head blight on cereals. Wede novoassembled genomes of previously uncharacterized FGSC members (two strains ofF. austroamericanum,F. cortaderiaeandF. meridionale). Our analyses of eight species of the FGSC in addition to 15 otherFusariumspecies identified a pangenome of 54 gene clusters within FGSC. We found that multiple independent losses were a key factor generating extant cluster diversity within the FGSC and theFusariumgenus. We identified a modular gene cluster conserved among distantly related fungi, which was likely reconfigured to encode different functions. We also found strong evidence that a rare cluster in FGSC was gained through an ancient horizontal transfer between bacteria and fungi. Chromosomal rearrangements underlying cluster loss were often complex and were likely facilitated by an enrichment in specific transposable elements. Our findings identify important transitory stages in the birth and death process of specialized metabolism gene clusters among very closely related species.

scholarly journals A detailed in silico analysis of secondary metabolite biosynthesis clusters in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum

2019 ◽  
Author(s):  
Carolyn Graham-Taylor ◽  
Lars G Kamphuis ◽  
Mark Derbyshire
Keyword(s):  
Secondary Metabolites ◽  
Host Range ◽  
Secondary Metabolite ◽  
Sclerotinia Sclerotiorum ◽  
Plant Pathogens ◽  
Pathogenic Fungus ◽  
Gene Clusters ◽  
Sequence Diversity ◽  
Broad Host Range ◽  
Data Set

Abstract Background The broad host range pathogen Sclerotinia sclerotiorum infects over 400 plant species and causes substantial yield losses in crops worldwide. Secondary metabolites are known to play important roles in the virulence of plant pathogens, but little is known about the secondary metabolite repertoire of S. sclerotiorum. In this study, we predicted secondary metabolite biosynthetic gene clusters in the genome of S. sclerotiorum and analysed their expression during infection of Brassica napus using an existing transcriptome data set. We also investigated their sequence diversity among a panel of 25 previously published S. sclerotiorum isolate genomes.Results We identified 80 putative secondary metabolite clusters. Over half of the clusters contained at least three transcriptionally coregulated genes. Comparative genomics revealed clusters homologous to clusters in the closely related plant pathogen Botrytis cinerea for production of carotenoids, hydroxamate siderophores, DHN melanin and botcinic acid. We also identified putative phytotoxin clusters that can potentially produce the polyketide sclerin and an epipolythiodioxopiperazine. Secondary metabolite clusters were enriched in subtelomeric genomic regions, and those containing paralogues showed a particularly strong association with repeats. The positional bias we identified was borne out by intraspecific comparisons that revealed putative secondary metabolite genes suffered more presence / absence polymorphisms and exhibited a significantly higher sequence diversity than other genes.Conclusions These data suggest that S. sclerotiorum produces numerous secondary metabolites during plant infection and that their gene clusters undergo enhanced rates of mutation, duplication and recombination in subtelomeric regions. The microevolutionary regimes leading to S. sclerotiorum secondary metabolite diversity have yet to be elucidated. Several potential phytotoxins documented in this study provide the basis for future functional analyses.

scholarly journals The Conserved Colletotrichum spp. Effector Candidate CEC3 Induces Nuclear Expansion and Cell Death in Plants

2021 ◽  
Vol 12 ◽  
Author(s):  
Ayako Tsushima ◽  
Mari Narusaka ◽  
Pamela Gan ◽  
Naoyoshi Kumakura ◽  
Ryoko Hiroyama ◽  
...  
Keyword(s):  
Cell Death ◽  
Plant Pathogens ◽  
Host Cells ◽  
Comparative Genomic ◽  
Broad Host Range ◽  
Functional Conservation ◽  
Host Cell Death ◽  
Two Phases ◽  
Nuclear Expansion ◽  
Core Effectors

Plant pathogens secrete proteins, known as effectors, that promote infection by manipulating host cells. Members of the phytopathogenic fungal genus Colletotrichum collectively have a broad host range and generally adopt a hemibiotrophic lifestyle that includes an initial biotrophic phase and a later necrotrophic phase. We hypothesized that Colletotrichum fungi use a set of conserved effectors during infection to support the two phases of their hemibiotrophic lifestyle. This study aimed to examine this hypothesis by identifying and characterizing conserved effectors among Colletotrichum fungi. Comparative genomic analyses using genomes of ascomycete fungi with different lifestyles identified seven effector candidates that are conserved across the genus Colletotrichum. Transient expression assays showed that one of these putative conserved effectors, CEC3, induces nuclear expansion and cell death in Nicotiana benthamiana, suggesting that CEC3 is involved in promoting host cell death during infection. Nuclear expansion and cell death induction were commonly observed in CEC3 homologs from four different Colletotrichum species that vary in host specificity. Thus, CEC3 proteins could represent a novel class of core effectors with functional conservation in the genus Colletotrichum.

scholarly journals Genome, Transcriptome, and Functional Analyses of Penicillium expansum Provide New Insights Into Secondary Metabolism and Pathogenicity

2015 ◽  
Vol 28 (3) ◽  
pp. 232-248 ◽  
Author(s):  
Ana-Rosa Ballester ◽  
Marina Marcet-Houben ◽  
Elena Levin ◽  
Noa Sela ◽  
Cristina Selma-Lázaro ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Secondary Metabolism ◽  
Plant Pathogens ◽  
Citrus Fruit ◽  
Genomic Analysis ◽  
Pathogenic Fungi ◽  
Gene Clusters ◽  
Penicillium Expansum ◽  
Pome Fruit ◽  
Penicillium Species

The relationship between secondary metabolism and infection in pathogenic fungi has remained largely elusive. The genus Penicillium comprises a group of plant pathogens with varying host specificities and with the ability to produce a wide array of secondary metabolites. The genomes of three Penicillium expansum strains, the main postharvest pathogen of pome fruit, and one Pencillium italicum strain, a postharvest pathogen of citrus fruit, were sequenced and compared with 24 other fungal species. A genomic analysis of gene clusters responsible for the production of secondary metabolites was performed. Putative virulence factors in P. expansum were identified by means of a transcriptomic analysis of apple fruits during the course of infection. Despite a major genome contraction, P. expansum is the Penicillium species with the largest potential for the production of secondary metabolites. Results using knockout mutants clearly demonstrated that neither patulin nor citrinin are required by P. expansum to successfully infect apples. Li et al. ( MPMI-12-14-0398-FI ) reported similar results and conclusions in MPMI's June 2015 issue.

scholarly journals Isolation, Identification, and Complete Genome Assembly of an Endophytic Bacillus velezensis YB-130, Potential Biocontrol Agent Against Fusarium graminearum

2020 ◽  
Vol 11 ◽  
Author(s):  
Wen Xu ◽  
Liyong Zhang ◽  
Paul H. Goodwin ◽  
Mingcong Xia ◽  
Jie Zhang ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Biological Control Agent ◽  
Gene Clusters ◽  
Whole Genome Sequence ◽  
Yield Reduction ◽  
Rrna Gene ◽  
Whole Genome ◽  
Bacillus Velezensis ◽  
Fungal Plant Pathogens ◽  
Dual Cultures

Wheat scab caused by F. graminearum is a highly destructive disease that leads to yield reduction and mycotoxin contamination of grains. In this study, an endophytic bacterium of strain YB-130 was isolated from surface sterilized wheat spikes with scab symptoms and identified as Bacillus velezensis by whole genome annotation, 16S rRNA gene and average nucleotide identities analysis. The whole-genome sequence of strain YB-130 was obtained by PacBio sequencing. 88 putative Carbohydrate-Active Enzymes and 12 gene clusters encoding for secondary metabolites were identified in the YB-130 genome, including one gene cluster for the synthesis of lanthipeptide only found in strain YB-130 genome. In dual cultures, strain YB-130 significantly inhibited the growth of F. graminearum PH-1 and other eight fungal plant pathogens, indicating a broad antifungal activity. Furthermore, strain YB-130 was able to significantly inhibit spore morphology and hyphal development of F. graminearum PH-1. Strain YB-130 also reduced deoxynivalenol production by F. graminearum PH-1 in dual cultures, possibly due to its ability to suppress the expression of tri5, tri3, and tri8 that are required for deoxynivalenol production in F. graminearum. Overall, B. velezensis YB-130 is a promising biological control agent of both F. graminearum infection and mycotoxin production.

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