scholarly journals Remote homology clustering identifies lowly conserved families of effector proteins in plant-pathogenic fungi

2021 ◽  
Vol 7 (9) ◽  
Author(s):  
Darcy A. B. Jones ◽  
Paula M. Moolhuijzen ◽  
James K. Hane
Keyword(s):  
Fungal Pathogens ◽  
Pathogenic Fungi ◽  
Comparison Method ◽  
Fungal Species ◽  
Effector Proteins ◽  
Plant Diseases ◽  
Plant Host ◽  
Homology Inference ◽  
Developing Area ◽  
Inference Methods

Plant diseases caused by fungal pathogens are typically initiated by molecular interactions between ‘effector’ molecules released by a pathogen and receptor molecules on or within the plant host cell. In many cases these effector-receptor interactions directly determine host resistance or susceptibility. The search for fungal effector proteins is a developing area in fungal-plant pathology, with more than 165 distinct confirmed fungal effector proteins in the public domain. For a small number of these, novel effectors can be rapidly discovered across multiple fungal species through the identification of known effector homologues. However, many have no detectable homology by standard sequence-based search methods. This study employs a novel comparison method (RemEff) that is capable of identifying protein families with greater sensitivity than traditional homology-inference methods, leveraging a growing pool of confirmed fungal effector data to enable the prediction of novel fungal effector candidates by protein family association. Resources relating to the RemEff method and data used in this study are available from https://figshare.com/projects/Effector_protein_remote_homology/87965.

Biodiversity of pathogenic wood fungi isolated from Xylotrechus arvicola (Olivier) galleries in vine shoots

OENO One ◽  
2013 ◽  
Vol 47 (2) ◽  
pp. 73 ◽  
Author(s):  
Pablo García Benavides ◽  
Pedro Martin Zamorano ◽  
Carlos Alvar Ocete ◽  
Lara Maistrello ◽  
Rafael Ocete
Keyword(s):  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Pathogenic Fungi ◽  
Fungal Species ◽  
Its2 Sequence ◽  
Plant Diseases ◽  
Northern Spain ◽  
Grapevine Decline ◽  
La Rioja

<p style="text-align: justify;"><strong>Aim</strong>: Grapevine decline caused by wood fungi seriously threatens viticulture worldwide. In Spain, the polyphagous borer <em>Xylotrechus</em> <em>arvicola</em> (Coleoptera, Cerambycidae) is becoming a serious pest in different Qualified Designation of Origin (DOC) wine regions. The aim of the present work was to identify the fungal species growing in the galleries excavated by <em>X. arvicola</em> larvae inside the vine branches and investigate the possible relationship between wood pathogenic fungi and this borer.</p><p style="text-align: justify;"><strong>Methods and results</strong>: Wood samples from branches of Tempranillo vines and <em>Prunus pisardi</em> trees affected by the borer <em>X. arvicola</em> were collected in La Rioja DOC vineyards (Northern Spain) and analyzed for the presence of fungi using both morphological techniques and genetic tools based on Internal Transcribed Spacer 2 (ITS2) sequence. Among the 20 different fungal species/isolates identified, 7 belonged to fungi associated with grapevine decline (esca, Petri disease, and <em>Eutypa</em> dieback), 6 were plant pathogens, 6 were saprophytic and one was entomopathogenic (<em>Beauveria bassiana</em>).</p><p style="text-align: justify;"><strong>Conclusion</strong>: The fact that 65 % of the fungi detected inside <em>X. arvicola</em> galleries belong to species recognized as plant pathogens suggests that this borer, in addition to causing a progressive decay of the branches, could facilitate the transmission of plant diseases, further threatening the vineyards by spreading grapevine decline pathogens.</p><p style="text-align: justify;"><strong>Significance and impact of the study</strong>: The present work represents a first step in recognizing the association between the fungal pathogens associated with grapevine decline and the borer <em>X. arvicola</em>, suggesting a possible role of this insect as a vector in the transmission of these fungi.</p>

scholarly journals Global food and fibre security threatened by current inefficiencies in fungal identification

2016 ◽  
Vol 371 (1709) ◽  
pp. 20160024 ◽  
Author(s):  
Pedro W. Crous ◽  
Johannes Z. Groenewald ◽  
Bernard Slippers ◽  
Michael J. Wingfield
Keyword(s):  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Animal Health ◽  
Pathogenic Fungi ◽  
Fungal Species ◽  
Plant Diseases ◽  
Health Food ◽  
Natural Ecosystems ◽  
New Guidelines ◽  
Global Food

Fungal pathogens severely impact global food and fibre crop security. Fungal species that cause plant diseases have mostly been recognized based on their morphology. In general, morphological descriptions remain disconnected from crucially important knowledge such as mating types, host specificity, life cycle stages and population structures. The majority of current fungal species descriptions lack even the most basic genetic data that could address at least some of these issues. Such information is essential for accurate fungal identifications, to link critical metadata and to understand the real and potential impact of fungal pathogens on production and natural ecosystems. Because international trade in plant products and introduction of pathogens to new areas is likely to continue, the manner in which fungal pathogens are identified should urgently be reconsidered. The technologies that would provide appropriate information for biosecurity and quarantine already exist, yet the scientific community and the regulatory authorities are slow to embrace them. International agreements are urgently needed to enforce new guidelines for describing plant pathogenic fungi (including key DNA information), to ensure availability of relevant data and to modernize the phytosanitary systems that must deal with the risks relating to trade-associated plant pathogens. This article is part of the themed issue ‘Tackling emerging fungal threats to animal health, food security and ecosystem resilience’.

scholarly journals The Role of Fungi in the Cocoa Production Chain and the Challenge of Climate Change

2021 ◽  
Vol 7 (3) ◽  
pp. 202
Author(s):  
Johannes Delgado-Ospina ◽  
Junior Bernardo Molina-Hernández ◽  
Clemencia Chaves-López ◽  
Gianfranco Romanazzi ◽  
Antonello Paparella
Keyword(s):  
Climate Change ◽  
Fungal Infections ◽  
Close Association ◽  
Pathogenic Fungi ◽  
Fungal Species ◽  
Mitigation Strategies ◽  
Plant Diseases ◽  
Production Chain ◽  
Cocoa Production

Background: The role of fungi in cocoa crops is mainly associated with plant diseases and contamination of harvest with unwanted metabolites such as mycotoxins that can reach the final consumer. However, in recent years there has been interest in discovering other existing interactions in the environment that may be beneficial, such as antagonism, commensalism, and the production of specific enzymes, among others. Scope and approach: This review summarizes the different fungi species involved in cocoa production and the cocoa supply chain. In particular, it examines the presence of fungal species during cultivation, harvest, fermentation, drying, and storage, emphasizing the factors that possibly influence their prevalence in the different stages of production and the health risks associated with the production of mycotoxins in the light of recent literature. Key findings and conclusion: Fungi associated with the cocoa production chain have many different roles. They have evolved in a varied range of ecosystems in close association with plants and various habitats, affecting nearly all the cocoa chain steps. Reports of the isolation of 60 genera of fungi were found, of which only 19 were involved in several stages. Although endophytic fungi can help control some diseases caused by pathogenic fungi, climate change, with increased rain and temperatures, together with intensified exchanges, can favour most of these fungal infections, and the presence of highly aggressive new fungal genotypes increasing the concern of mycotoxin production. For this reason, mitigation strategies need to be determined to prevent the spread of disease-causing fungi and preserve beneficial ones.

scholarly journals Mitotic Recombination and Adaptive Genomic Changes in Human Pathogenic Fungi

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 901 ◽  
Author(s):  
Asiya Gusa ◽  
Sue Jinks-Robertson
Keyword(s):  
Fungal Pathogens ◽  
Repetitive Sequences ◽  
Pathogenic Fungi ◽  
Genetic Alterations ◽  
Fungal Species ◽  
Chronic Infections ◽  
Yeast Saccharomyces Cerevisiae ◽  
Genomic Changes ◽  
Break Site ◽  
Repair Mechanisms

Genome rearrangements and ploidy alterations are important for adaptive change in the pathogenic fungal species Candida and Cryptococcus, which propagate primarily through clonal, asexual reproduction. These changes can occur during mitotic growth and lead to enhanced virulence, drug resistance, and persistence in chronic infections. Examples of microevolution during the course of infection were described in both human infections and mouse models. Recent discoveries defining the role of sexual, parasexual, and unisexual cycles in the evolution of these pathogenic fungi further expanded our understanding of the diversity found in and between species. During mitotic growth, damage to DNA in the form of double-strand breaks (DSBs) is repaired, and genome integrity is restored by the homologous recombination and non-homologous end-joining pathways. In addition to faithful repair, these pathways can introduce minor sequence alterations at the break site or lead to more extensive genetic alterations that include loss of heterozygosity, inversions, duplications, deletions, and translocations. In particular, the prevalence of repetitive sequences in fungal genomes provides opportunities for structural rearrangements to be generated by non-allelic (ectopic) recombination. In this review, we describe DSB repair mechanisms and the types of resulting genome alterations that were documented in the model yeast Saccharomyces cerevisiae. The relevance of similar recombination events to stress- and drug-related adaptations and in generating species diversity are discussed for the human fungal pathogens Candida albicans and Cryptococcus neoformans.

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.

Small talk and large impact: the importance of small RNA molecules in the fight against plant diseases.

2021 ◽  
pp. 86-93
Author(s):  
Zhen Liao ◽  
Kristian Persson Hodén ◽  
Christina Dixelius
Keyword(s):  
Small Rnas ◽  
Crop Production ◽  
Pathogenic Fungi ◽  
Plant Diseases ◽  
Communication Process ◽  
Plant Host ◽  
Small Talk ◽  
Rna Molecules ◽  
General Chapter ◽  
Late Blight Pathogen

Abstract This short and general chapter summarizes how plants and pathogens communicate using not only proteins for recognition and signal transduction or other metabolites but also RNA molecules where small RNAs with sizes between 21 to 40 nt are most important. These small RNAs can move between plants and a range of interacting pathogenic organisms in both directions, that is, a 'cross-kingdom' communication process. The first reports on RNA-based communications between plants and plant pathogenic fungi appeared about 10 years ago. Since that time, we have learnt much about sRNA biology in plants and their function in different parasitic organisms. However, many questions on the processes involved remain unanswered. Such information is crucial in order to sustain high crop production. Besides giving a brief background, we highlight the interactions between the potato late blight pathogen and its plant host potato.

scholarly journals Fungal Pathogens Affecting the Production and Quality of Medical Cannabis in Israel

Plants ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 882
Author(s):  
Shachar Jerushalmi ◽  
Marcel Maymon ◽  
Aviv Dombrovsky ◽  
Stanley Freeman
Keyword(s):  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Pathogenic Fungi ◽  
Plant Diseases ◽  
Soilborne Pathogens ◽  
Medical Cannabis ◽  
Plant Parts ◽  
Commercial Cultivation

The use of and research on medical cannabis (MC) is becoming more common, yet there are still many challenges regarding plant diseases of this crop. For example, there is a lack of formal and professional knowledge regarding fungi that infect MC plants, and practical and effective methods for managing the casual agents of disease are limited. The purpose of this study was to identify foliar, stem, and soilborne pathogens affecting MC under commercial cultivation in Israel. The predominant major foliage pathogens were identified as Alternaria alternata and Botrytis cinerea, while the common stem and soilborne pathogens were identified as Fusarium oxysporum and F. solani. Other important fungi that were isolated from foliage were those producing various mycotoxins that can directly harm patients, such as Aspergillus spp. and Penicillium spp. The sampling and characterization of potential pathogenic fungi were conducted from infected MC plant parts that exhibited various disease symptoms. Koch postulates were conducted by inoculating healthy MC tissues and intact plants with fungi isolated from infected commercially cultivated symptomatic plants. In this study, we report on the major and most common plant pathogens of MC found in Israel, and determine the seasonal outbreak of each fungus.

Small talk and large impact: the importance of small RNA molecules in the fight against plant diseases.

2021 ◽  
pp. 86-93
Author(s):  
Zhen Liao ◽  
Kristian Persson Hodén ◽  
Christina Dixelius
Keyword(s):  
Small Rnas ◽  
Crop Production ◽  
Pathogenic Fungi ◽  
Plant Diseases ◽  
Communication Process ◽  
Plant Host ◽  
Small Talk ◽  
Rna Molecules ◽  
General Chapter ◽  
Late Blight Pathogen

Abstract This short and general chapter summarizes how plants and pathogens communicate using not only proteins for recognition and signal transduction or other metabolites but also RNA molecules where small RNAs with sizes between 21 to 40 nt are most important. These small RNAs can move between plants and a range of interacting pathogenic organisms in both directions, that is, a 'cross-kingdom' communication process. The first reports on RNA-based communications between plants and plant pathogenic fungi appeared about 10 years ago. Since that time, we have learnt much about sRNA biology in plants and their function in different parasitic organisms. However, many questions on the processes involved remain unanswered. Such information is crucial in order to sustain high crop production. Besides giving a brief background, we highlight the interactions between the potato late blight pathogen and its plant host potato.

scholarly journals Volatile Organic Compound from Trichoderma asperelloides TSU1: Impact on Plant Pathogenic Fungi

2021 ◽  
Vol 7 (3) ◽  
pp. 187
Author(s):  
On-Uma Ruangwong ◽  
Prisana Wonglom ◽  
Nakarin Suwannarach ◽  
Jaturong Kumla ◽  
Narit Thaochan ◽  
...  
Keyword(s):  
Antifungal Activity ◽  
Fungal Pathogens ◽  
Solid Phase ◽  
Sclerotium Rolfsii ◽  
Soil Fungus ◽  
Pathogenic Fungi ◽  
Emerging Diseases ◽  
Plant Diseases ◽  
Gas Chromatography Mass Spectrometry ◽  
Volatile Organic

Soil microorganisms are well studied for their beneficial effects on plant growth and their impact on biocontrol agents. The production of volatile antifungal compounds emitted from soil fungi is considered to be an effective ability that can be applied in biofumigants in the control of plant diseases. A soil fungus, Trichoderma asperelloides TSU1, was isolated from flamingo flower cultivated soil and identified on the basis of the morphology and molecular analysis of the internal transcribed spacer (ITS), rpb2, and tef1-α genes. To test T. asperelloides TSU1-produced volatile organic compounds (VOCs) with antifungal activity, the sealed plate method was used. The VOCs of T. asperelloides TSU1 inhibited the mycelial growth of fungal pathogens that were recently reported as emerging diseases in Thailand, namely, Corynespora cassiicola, Fusarium incarnatum, Neopestalotiopsis clavispora, N. cubana, and Sclerotium rolfsii, with a percentage inhibition range of 38.88–68.33%. Solid-phase microextraction (SPME) was applied to trap VOCs from T. asperelloides TSU1 and tentatively identify them through gas chromatography–mass spectrometry (GC/MS). A total of 17 compounds were detected in the VOCs of T. asperelloides TSU1, and the dominant compounds were identified as fluoro(trinitro)methane (18.192% peak area) and 2-phenylethanol (9.803% peak area). Interestingly, the commercial 2-phenyethanol showed antifungal activity against fungal pathogens that were similar to the VOCs of T. asperelloides TSU1 by bioassay. On the basis of our study’s results, T. asperelloides TSU1 isolated from soil displayed antifungal abilities via the production of VOCs responsible for restricting pathogen growth.

scholarly journals Fungal pathogens of the genus Fusarium in winter wheat Triticum aestivum L. protected with fungicides in north-eastern Poland

2013 ◽  
Vol 66 (2) ◽  
pp. 95-106 ◽  
Author(s):  
Agnieszka Pszczółkowska ◽  
Adam Okorski ◽  
Jacek Olszewski ◽  
Joanna Jarmołkowicz
Keyword(s):  
Winter Wheat ◽  
Fungal Pathogens ◽  
Crop Protection ◽  
Pathogenic Fungi ◽  
Triticum Aestivum L ◽  
Fungal Species ◽  
Diagnostic Methods ◽  
Growth Stages ◽  
Monthly Precipitation ◽  
Wheat Grain

Various diagnostic methods were used to evaluate the effect of fungicide protection on the prevalence of pathogenic fungi in wheat grain. Winter wheat cv. Nutka and Zyta was grown during a field experiment established in the Production and Experimental Station in Bałcyny in 2006–2007. The experimental factor was chemical crop protection: epoxiconazole, kresoxim-methyl and fenpropimorph applied at growth stages BBCH 33–35 as well as dimoxystrobin and epoxiconazole applied at BBCH 51–53. In this experiment, microscopic observations and conventional PCR assays were used as complementary methods. The quantification of <em>Fusarium</em> <em>poae</em> DNA by qPCR demonstrated the effectiveness of chemical protection against the analyzed fungal species. Lower monthly precipitation levels and higher daily temperatures intensified grain infections, in particular those caused by <em>F</em>. <em>poae</em>. A significant correlation was determined between the number of <em>F</em>. <em>poae</em> cultures isolated from winter wheat grain and the quantity of pathogenic DNA in grain identified by qPCR. Grain infections caused by <em>F</em>.<em> poae</em> lowered yield and thousand seed weight.

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