scholarly journals Spontaneous and Fungicide-Induced Genomic Variation in Sclerotinia sclerotiorum

2020 ◽  
pp. PHYTO-10-20-047
Author(s):  
Nikita Gambhir ◽  
Zhian N. Kamvar ◽  
Rebecca Higgins ◽  
B. Sajeewa Amaradasa ◽  
Sydney E. Everhart
Keyword(s):  
Sclerotinia Sclerotiorum ◽  
Plant Pathogens ◽  
Management Strategies ◽  
Genomic Variation ◽  
Sublethal Dose ◽  
P Value ◽  
Nucleotide Polymorphisms ◽  
In Planta ◽  
Induced Mutations ◽  
Fungal Plant Pathogens

Stress from exposure to sublethal fungicide doses may cause genomic instability in fungal plant pathogens, which may accelerate the emergence of fungicide resistance or other adaptive traits. In a previous study, five strains of Sclerotinia sclerotiorum were exposed to sublethal doses of four fungicides with different modes of action, and genotyping showed that such exposure induced mutations. The goal of the present study was to characterize genome-wide mutations in response to sublethal fungicide stress in S. sclerotiorum and study the effect of genomic background on the mutational repertoire. The objectives were to determine the effect of sublethal dose exposure and genomic background on mutation frequency/type, distribution of mutations, and fitness costs. Fifty-five S. sclerotiorum genomes were sequenced and aligned to the reference genome. Variants were called and quality filtered to obtain high confidence calls for single nucleotide polymorphisms (SNPs), insertions/deletions (INDELs), copy number variants, and transposable element (TE) insertions. Results suggest that sublethal fungicide exposure significantly increased the frequency of INDELs in two strains from one genomic background (P value ≤ 0.05), while TE insertions were generally repressed for all genomic backgrounds and under all fungicide exposures. The frequency and/or distribution of SNPs, INDELs, and TE insertions varied with genomic background. A propensity for large duplications on chromosome 7 and aneuploidy of this chromosome were observed in the S. sclerotiorum genome. Mutation accumulation did not significantly affect the overall in planta strain aggressiveness (P value > 0.05). Understanding factors that affect pathogen mutation rates can inform disease management strategies that delay resistance evolution.

scholarly journals Evaluation of in-vitro methods to select effective streptomycetes against toxigenic fusaria

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6905 ◽  
Author(s):  
Elena Maria Colombo ◽  
Cristina Pizzatti ◽  
Andrea Kunova ◽  
Claudio Gardana ◽  
Marco Saracchi ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Culture Media ◽  
Screening Methods ◽  
Dual Culture ◽  
In Planta ◽  
In Vitro Method ◽  
In Vitro Methods ◽  
Strain Diversity ◽  
Fungal Plant Pathogens

Biocontrol microorganisms are emerging as an effective alternative to pesticides. Ideally, biocontrol agents (BCAs) for the control of fungal plant pathogens should be selected by an in vitro method that is high-throughput and is predictive of in planta efficacy, possibly considering environmental factors, and the natural diversity of the pathogen. The purpose of our study was (1) to assess the effects ofFusariumstrain diversity (N= 5) and culture media (N= 6) on the identification of biological control activity ofStreptomycesstrains (N= 20) againstFusariumpathogens of wheat in vitro and (2) to verify the ability of our in vitro screening methods to simulate the activity in planta. Our results indicate that culture media,Fusariumstrain diversity, and their interactions affect the results of an in vitro selection by dual culture assay. The results obtained on the wheat-based culture media resulted in the highest correlation score (r= 0.5) with the in planta root rot (RR) inhibition, suggesting that this in vitro method was the best predictor of in planta performance of streptomycetes against Fusarium RR of wheat assessed as extension of the necrosis on the root. Contrarily, none of the in vitro plate assays using the media tested could appropriately predict the activity of the streptomycetes against Fusarium foot rot symptoms estimated as the necrosis at the crown level. Considering overall data of correlation, the activity in planta cannot be effectively predicted by dual culture plate studies, therefore improved in vitro methods are needed to better mimic the activity of biocontrol strains in natural conditions. This work contributes to setting up laboratory standards for preliminary screening assays ofStreptomycesBCAs against fungal pathogens.

scholarly journals Histone modification dynamics at H3K27 are associated with altered transcription of in planta induced genes in Magnaporthe oryzae

PLoS Genetics ◽  
2021 ◽  
Vol 17 (2) ◽  
pp. e1009376 ◽  
Author(s):  
Wei Zhang ◽  
Jun Huang ◽  
David E. Cook
Keyword(s):  
Histone Modification ◽  
Transcriptional Repression ◽  
Plant Pathogens ◽  
Fungal Genome ◽  
In Planta ◽  
Fungal Plant Pathogens ◽  
Repressive Histone Modification ◽  
Induced Genes ◽  
Host Infection ◽  
Genomic Locations

Transcriptional dynamic in response to environmental and developmental cues are fundamental to biology, yet many mechanistic aspects are poorly understood. One such example is fungal plant pathogens, which use secreted proteins and small molecules, termed effectors, to suppress host immunity and promote colonization. Effectors are highly expressed in planta but remain transcriptionally repressed ex planta, but our mechanistic understanding of these transcriptional dynamics remains limited. We tested the hypothesis that repressive histone modification at H3-Lys27 underlies transcriptional silencing ex planta, and that exchange for an active chemical modification contributes to transcription of in planta induced genes. Using genetics, chromatin immunoprecipitation and sequencing and RNA-sequencing, we determined that H3K27me3 provides significant local transcriptional repression. We detail how regions that lose H3K27me3 gain H3K27ac, and these changes are associated with increased transcription. Importantly, we observed that many in planta induced genes were marked by H3K27me3 during axenic growth, and detail how altered H3K27 modification influences transcription. ChIP-qPCR during in planta growth suggests that H3K27 modifications are generally stable, but can undergo dynamics at specific genomic locations. Our results support the hypothesis that dynamic histone modifications at H3K27 contributes to fungal genome regulation and specifically contributes to regulation of genes important during host infection.

scholarly journals Transfection of Sclerotinia sclerotiorum withIn VitroTranscripts of a Naturally Occurring Interspecific Recombinant of Sclerotinia sclerotiorum Hypovirus 2 Significantly Reduces Virulence of the Fungus

2015 ◽  
Vol 89 (9) ◽  
pp. 5060-5071 ◽  
Author(s):  
Shin-Yi Lee Marzano ◽  
Houston A. Hobbs ◽  
Berlin D. Nelson ◽  
Glen L. Hartman ◽  
Darin M. Eastburn ◽  
...  
Keyword(s):  
Sclerotinia Sclerotiorum ◽  
Plant Pathogens ◽  
High Throughput Sequencing ◽  
Infectious Clone ◽  
White Mold ◽  
Content Type ◽  
Fungal Plant Pathogens ◽  
Rapid Amplification ◽  
Valsa Ceratosperma

ABSTRACTA recombinant strain ofSclerotinia sclerotiorumhypovirus 2 (SsHV2) was identified from a North AmericanSclerotinia sclerotiorumisolate (328) from lettuce (Lactuca sativaL.) by high-throughput sequencing of total RNA. The 5′- and 3′-terminal regions of the genome were determined by rapid amplification of cDNA ends. The assembled nucleotide sequence was up to 92% identical to two recently reported SsHV2 strains but contained a deletion near its 5′ terminus of more than 1.2 kb relative to the other SsHV2 strains and an insertion of 524 nucleotides (nt) that was distantly related toValsa ceratospermahypovirus 1. This suggests that the new isolate is a heterologous recombinant of SsHV2 with a yet-uncharacterized hypovirus. We named the new strainSclerotinia sclerotiorumhypovirus 2 Lactuca (SsHV2L) and deposited the sequence in GenBank with accession numberKF898354.Sclerotinia sclerotiorumisolate 328 was coinfected with a strain ofSclerotinia sclerotiorumendornavirus 1 and was debilitated compared to cultures of the same isolate that had been cured of virus infection by cycloheximide treatment and hyphal tipping. To determine whether SsHV2L alone could induce hypovirulence inS. sclerotiorum, a full-length cDNA of the 14,538-nt viral genome was cloned. Transcripts corresponding to the viral RNA were synthesizedin vitroand transfected into a virus-free isolate ofS. sclerotiorum, DK3. Isolate DK3 transfected with SsHV2L was hypovirulent on soybean and lettuce and exhibited delayed maturation of sclerotia relative to virus-free DK3, completing Koch's postulates for the association of hypovirulence with SsHV2L.IMPORTANCEA cosmopolitan fungus,Sclerotinia sclerotioruminfects more than 400 plant species and causes a plant disease known as white mold that produces significant yield losses in major crops annually. Mycoviruses have been used successfully to reduce losses caused by fungal plant pathogens, but definitive relationships between hypovirus infections and hypovirulence inS. sclerotiorumwere lacking. By establishing a cause-and-effect relationship betweenSclerotinia sclerotiorumhypovirus Lactuca (SsHV2L) infection and the reduction in host virulence, we showed direct evidence that hypoviruses have the potential to reduce the severity of white mold disease. In addition to intraspecific recombination, this study showed that recent interspecific recombination is an important factor shaping viral genomes. The construction of an infectious clone of SsHV2L allows future exploration of the interactions between SsHV2L andS. sclerotiorum, a widespread fungal pathogen of plants.

scholarly journals Population Genomics Trace Clonal Diversification and Intercontinental Migration of an Emerging Fungal Pathogen of Boxwood

2020 ◽  
pp. PHYTO-06-20-021
Author(s):  
Nicholas LeBlanc ◽  
Marc A. Cubeta ◽  
Jo Anne Crouch
Keyword(s):  
United States ◽  
Plant Pathogens ◽  
Population Genomics ◽  
The United States ◽  
Sister Species ◽  
Evolutionary Divergence ◽  
Nucleotide Polymorphisms ◽  
Disease Emergence ◽  
Fungal Plant Pathogens ◽  
Genetic Clusters

Boxwood blight was first documented in Europe, prior to its recent colonization of North America, where it continues to have significant negative impacts on the ornamental industry. Due to near genetic uniformity in the two sister species of fungal plant pathogens that cause boxwood blight, understanding historical disease emergence and predicting future outbreaks is limited. The goal of this research was to apply population genomics to understand the role of pathogen diversification and migration in disease emergence. Specifically, we tested whether the primary pathogen species Calonectria pseudonaviculata has remained genetically isolated from its European-limited sister species C. henricotiae, while diversifying into clonal lineages that have migrated among continents. Whole-genome sequencing identified 1,608 single-nucleotide polymorphisms (SNPs) in 67 C. pseudonaviculata isolates from four continents and 1,017 SNPs in 13 C. henricotiae isolates from Europe. Interspecific genetic differentiation and an absence of shared polymorphisms indicated lack of gene flow between the sister species. Tests for intraspecific genetic structure in C. pseudonaviculata identified four genetic clusters, three of which corresponded to monophyletic phylogenetic clades. Comparison of evolutionary divergence scenarios among the four genetic clusters using approximate Bayesian computation indicated that the two C. pseudonaviculata genetic clusters currently found in the United States were derived from different sources, one from the first genetic cluster found in Europe and the second from an unidentified population. Evidence for multiple introductions of this pathogen into the United States and intercontinental migration indicates that future introductions are likely to occur and should be considered in plant disease quarantine regulation.

scholarly journals Population Structure and Aggressiveness of Sclerotinia sclerotiorum From Rapeseed (Brassica napus) in Chongqing City

Plant Disease ◽  
2020 ◽  
Vol 104 (4) ◽  
pp. 1201-1206
Author(s):  
Yang Yu ◽  
Junsong Cai ◽  
Linhao Ma ◽  
Zhiqiang Huang ◽  
Yabo Wang ◽  
...  
Keyword(s):  
Population Structure ◽  
Sclerotinia Sclerotiorum ◽  
Plant Pathogens ◽  
Gene Diversity ◽  
Sclerotinia Stem Rot ◽  
Pair Group ◽  
Fungal Plant Pathogens ◽  
Chongqing City ◽  
Mycelial Compatibility ◽  
Rapeseed Production

Sclerotinia sclerotiorum is one of the most devastating fungal plant pathogens of oilseed Brassica and is distributed worldwide. In particular, Sclerotinia stem rot has always been a serious threat to rapeseed production in Chongqing City, China. In this study, simple sequence repeat (SSR) markers and mycelial compatibility groups (MCGs) were used to characterize the population structure of 90 geographic isolates of S. sclerotiorum collected from rapeseed in nine counties of Chongqing. A total of 52 microsatellite haplotypes were identified, and a few haplotypes were found with high frequency. Gene diversity ranged from 0.1570 to 0.4700 in nine populations. A constructed unweighted pair group with arithmetic mean dendrogram based on Nei genetic distance and a STRUCTURE analysis revealed that the genetic composition of the isolates collected in the five counties located in western Chongqing are different from those collected in the two eastern counties, suggesting that breed lines should be cultivated in both the western and eastern regions to effectively evaluate resistance levels. A total of 47 MCGs were identified, and 72% of the MCGs was represented by single isolates. Seven of 13 MCGs that included at least two isolates contained isolates from only one county. SSR haplotypes were not correlated with MCGs. A subset of 34 isolates were inoculated on rapeseed stems, and the aggressiveness showed variation. This research revealed the population genetic structure and aggressiveness of this pathogen in Chongqing, and the results will help to develop disease management and resistance screening strategies.

scholarly journals Genomic Characterization, Formulation and Efficacy in Planta of a Siphoviridae and Podoviridae Protection Cocktail against the Bacterial Plant Pathogens Pectobacterium spp.

Viruses ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 150
Author(s):  
Maja A. Zaczek-Moczydłowska ◽  
Gillian K. Young ◽  
James Trudgett ◽  
Colin C. Fleming ◽  
Katrina Campbell ◽  
...  
Keyword(s):  
Crop Production ◽  
Plant Pathogens ◽  
Management Strategies ◽  
Soft Rot ◽  
Field Trials ◽  
Control Measures ◽  
In Planta ◽  
Sustainable Food ◽  
Phage Cocktail ◽  
Causative Agents

In the face of global human population increases, there is a need for efficacious integrated pest management strategies to improve agricultural production and increase sustainable food production. To counteract significant food loses in crop production, novel, safe and efficacious measures should be tested against bacterial pathogens. Pectobacteriaceae species are one of the causative agents of the bacterial rot of onions ultimately leading to crop losses due to ineffective control measures against these pathogens. Therefore, the aim of this study was to isolate and characterize bacteriophages which could be formulated in a cocktail and implemented in planta under natural environmental conditions. Transmission electron microscopy (TEM) and genome analysis revealed Siphoviridae and Podoviridae family bacteriophages. To test the protective effect of a formulated phage cocktail against soft rot disease, three years of field trials were performed, using three different methods of treatment application. This is the first study to show the application of a phage cocktail containing Podoviridae and Siphoviridae bacteriophages capable of protecting onions against soft rot in field conditions.

scholarly journals Phosphorylative Transduction of Developmental and Pathogenicity-Related Cues in Sclerotinia Sclerotiorum

2004 ◽  
Author(s):  
Martin B. Dickman ◽  
Oded Yarden
Keyword(s):  
Sclerotinia Sclerotiorum ◽  
Plant Pathogens ◽  
Expression Patterns ◽  
Fungal Growth ◽  
Detailed Examination ◽  
Dry Bean ◽  
Fungal Pathogenicity ◽  
Regulatory Subunits ◽  
Fungal Plant Pathogens ◽  
Dependent Protein

Sclerotinia sclerotiorum (Lib.) de Bary is among the world's most successful and omnivorous fungal plant pathogens. Included in the more than 400 species of plants reported as hosts to this fungus are canola, alfalfa, soybean, sunflower, dry bean, and potato. The general inability to develop resistant germplasm with these economically important crops to this pathogen has focused attention on the need for a more detailed examination of the pathogenic determinants involved in disease development. This proposal involved experiments that examined the involvement of protein phosphorylation during morphogenesis (hyphal elongation and sclerotia formation) and pathogenesis (oxalic acid). Data obtained from our laboratories during the course of this project substantiates the fact that kinases and phosphatases are involved and important for these processes. A mechanistic understanding of the successful strategy(ies) used by S . sclerotiorum in infecting and proliferating in host plants and this linkage to fungal development will provide targets and/or novel approaches with which to design resistant crop plants including interference with fungal pathogenic development. The original objectives of this grant included: I. Clone the cyclic AMP-dependent protein kinase A (PKA) catalytic subunit gene from S.sclerotiorum and determine its role in fungal pathogenicity, OA production (OA) and/or morphogenesis (sclerotia formation). II. Clone and characterize the catalytic and regulatory subunits of the protein phosphatase PP2A holoenzyme complex and determine their role in fungal pathogenicity and/or morphogenesis as well as linkage with PKA-regulation of OA production and sclerotia formation. III. Clone and characterize the adenylate cyclase-encoding gene from S . sclerotiorum and detennine its relationship to the PKA/PP2A-regulated pathway. IV. Analyze the expression patterns of the above-mentioned genes and their products during pathogenesis and determine their linkage with infection and fungal growth.  

scholarly journals Interspecific Transmission of Double-Stranded RNA and Hypovirulence from Sclerotinia sclerotiorum to S. minor

2002 ◽  
Vol 92 (7) ◽  
pp. 780-784 ◽  
Author(s):  
M. S. Melzer ◽  
S. S. Ikeda ◽  
G. J. Boland
Keyword(s):  
Sclerotinia Sclerotiorum ◽  
Plant Pathogens ◽  
Dna Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Cdna Probe ◽  
Romaine Lettuce ◽  
Double Stranded Rna ◽  
Fungal Plant Pathogens ◽  
Detached Leaves ◽  
Slow Growing

Interspecific transmission of a hypovirulence-associated double-stranded RNA (dsRNA) and hypovirulent phenotype was attempted from hypovirulent isolate Ss275 of Sclerotinia sclerotiorum to five virulent isolates of S. minor. dsRNA and the hypovirulent phenotype were successfully transmitted to one of the five isolates, Sm10. Three putative converted isolates of Sm10 were slow growing and developed atypical colony morphologies characteristic of the hypovirulent phenotype. These isolates were assayed for virulence and produced significantly smaller lesions than isolate Sm10 on detached leaves of Romaine lettuce. One of these putative converted isolates, designated Sm10T, was tested to confirm interspecific transmission of dsRNA. In northern hybridizations, dsRNA isolated from Sm10T hybridized with a digoxigenin-labeled cDNA probe prepared from dsRNA isolated from Ss275. Random amplified polymorphic DNA analysis confirmed that isolate Sm10T was derived from Sm10 and not from Ss275 or a hybrid of the two species. The dsRNA and hypovirulent phenotype were subsequently transmitted intraspecifically from Sm10T to Sm8. To our knowledge, this is the first report of interspecific transmission of dsRNA and an associated hypovirulent phenotype between fungal plant pathogens by hyphal anastomosis.

Antifungal activities of cytochalasins produced byDiaporthe miriciae, an endophytic fungus associated with tropical medicinal plants

2018 ◽  
Vol 64 (11) ◽  
pp. 835-843 ◽  
Author(s):  
C.R. de Carvalho ◽  
A. Ferreira-D’Silva ◽  
D.E. Wedge ◽  
C.L. Cantrell ◽  
L.H. Rosa
Keyword(s):  
Medicinal Plants ◽  
Plant Pathogens ◽  
Phytopathogenic Fungi ◽  
Colletotrichum Acutatum ◽  
In Planta ◽  
Phomopsis Viticola ◽  
H Nmr ◽  
Crude Extracts ◽  
Fungal Plant Pathogens ◽  
Microdilution Broth

In the present study, we evaluated the antifungal potential of cytochalasins produced by Diaporthe taxa against phytopathogenic fungi. Using molecular methods, seven endophytic fungal strains from the medicinal plants Copaifera pubiflora and Melocactus ernestii were identified as Diaporthe miriciae, while two isolates were identified to the genus level (Diaporthe sp.). All crude extracts of Diaporthe species produced via solid-state fermentation were evaluated by1H NMR analyses. Crude extracts of the isolates D. miriciae UFMGCB 6350, 7719, 7646, 7653, 7701, 7772, and 7770 and Diaporthe sp. UFMGCB 7696 and 7720 were demonstrated to produce highly functionalized compounds. The extracts of D. miriciae UFMGCB 7719 and 6350 were selected as representative Diaporthe samples and subjected to bioassay-directed fractionation to isolate cytochalasins H and J. Cytochalasins H and J were evaluated for activities against the fungal plant pathogens Colletotrichum fragariae, Colletotrichum gloeosporioides, Colletotrichum acutatum, Botrytis cinerea, Fusarium oxysporum, Phomopsis obscurans, and Phomopsis viticola using microdilution broth assays. Cytochalasins H and J exhibited the most potent activities against the Phomopsis species tested. Our results showed that Diaporthe species were potential producers of different cytochalasins, which exhibit potential for controlling fungal diseases in planta and (or) maintaining antagonism.

scholarly journals Pathogenicity and Sclerotial Development of Sclerotinia sclerotiorum: Involvement of Oxalic Acid and Chitin Synthesis

1995 ◽  
Author(s):  
Martin B. Dickman ◽  
Oded Yarden
Keyword(s):  
Oxalic Acid ◽  
Sclerotinia Sclerotiorum ◽  
Plant Pathogens ◽  
Detailed Examination ◽  
Genetically Engineered ◽  
Molecular Techniques ◽  
Chitin Synthesis ◽  
Dry Bean ◽  
Fungal Plant Pathogens ◽  
Sclerotial Development

Sclerotinia sclerotiorum (Lib.) de Bary is among the world's most successful and omnivorous fungal plant pathogens. Included in the nearly 400 species of plants reported as hosts to this fungus are canola, alfalfa, soybean, sunflower, dry bean and potato. The general inability to develop resistant germplasm with these economically important crops to this pathogen has focused attention on the need for a more detailed examination of the pathogenic determinants involved in disease development. A mechanistic understanding of the successful strategy(ies) used by S. sclerotiorum in colonizing host plants and their linkage to fungal development may provide targets and/or novel approaches with which to design resistant crop plants. This proposal involved experiments which were successful in generating genetically-engineered plants harboring resistance to S. sclerotiorum, the establishment and improvement of molecular tools for the study of this pathogen and the analysis of the linkage between pathogenicity, sclerotial morphogenesis and two biosynthetic pathways: oxalic acid production and chitin synthesis. The highly collaborative project has improved our understanding of S. sclerotiorum pathogenicity, established reliable molecular techniques to facilitate experimental manipilation and generated transgenic plants which are resistant to this econimically important fungus.

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