scholarly journals Accessories Make the Outfit: Accessory Chromosomes and Other Dispensable DNA Regions in Plant-Pathogenic Fungi

2018 ◽  
Vol 31 (8) ◽  
pp. 779-788 ◽  
Author(s):  
Stefania Bertazzoni ◽  
Angela H. Williams ◽  
Darcy A. Jones ◽  
Robert A. Syme ◽  
Kar-Chun Tan ◽  
...  
Keyword(s):  
Fungal Pathogen ◽  
Core Genome ◽  
Pathogenic Fungi ◽  
Gene Clusters ◽  
Fungal Species ◽  
Sequencing Technologies ◽  
Fungal Genomes ◽  
Metabolite Synthesis ◽  
Specific Virulence ◽  
Accessory Chromosomes

Fungal pathogen genomes can often be divided into core and accessory regions. Accessory regions ARs) may be comprised of either ARs (within core chromosomes (CCs) or wholly dispensable (accessory) chromosomes (ACs). Fungal ACs and ARs typically accumulate mutations and structural rearrangements more rapidly over time than CCs and many harbor genes relevant to host-pathogen interactions. These regions are of particular interest in plant pathology and include host-specific virulence factors and secondary metabolite synthesis gene clusters. This review outlines known ACs and ARs in fungal genomes, methods used for their detection, their common properties that differentiate them from the core genome, and what is currently known of their various roles in pathogenicity. Reports on the evolutionary processes generating and shaping AC and AR compartments are discussed, including repeat induced point mutation and breakage fusion bridge cycles. Previously ACs have been studied extensively within key genera, including Fusarium, Zymoseptoria, and Alternaria, but are growing in frequency of observation and perceived importance across a wider range of fungal species. Recent advances in sequencing technologies permit affordable genome assembly and resequencing of populations that will facilitate further discovery and routine screening of ACs.

scholarly journals Accessory Chromosome-Acquired Secondary Metabolism in Plant Pathogenic Fungi: The Evolution of Biotrophs Into Host-Specific Pathogens

2021 ◽  
Vol 12 ◽  
Author(s):  
Thomas E. Witte ◽  
Nicolas Villeneuve ◽  
Christopher N. Boddy ◽  
David P. Overy
Keyword(s):  
Secondary Metabolism ◽  
Secondary Metabolite ◽  
Effective Means ◽  
Pathogenic Fungi ◽  
Gene Clusters ◽  
Fungal Species ◽  
Accessory Chromosome ◽  
Peptide Synthetases ◽  
Mycotoxin Biosynthesis ◽  
Accessory Chromosomes

Accessory chromosomes are strain- or pathotype-specific chromosomes that exist in addition to the core chromosomes of a species and are generally not considered essential to the survival of the organism. Among pathogenic fungal species, accessory chromosomes harbor pathogenicity or virulence factor genes, several of which are known to encode for secondary metabolites that are involved in plant tissue invasion. Accessory chromosomes are of particular interest due to their capacity for horizontal transfer between strains and their dynamic “crosstalk” with core chromosomes. This review focuses exclusively on secondary metabolism (including mycotoxin biosynthesis) associated with accessory chromosomes in filamentous fungi and the role accessory chromosomes play in the evolution of secondary metabolite gene clusters. Untargeted metabolomics profiling in conjunction with genome sequencing provides an effective means of linking secondary metabolite products with their respective biosynthetic gene clusters that reside on accessory chromosomes. While the majority of literature describing accessory chromosome-associated toxin biosynthesis comes from studies ofAlternariapathotypes, the recent discovery of accessory chromosome-associated biosynthetic genes inFusariumspecies offer fresh insights into the evolution of biosynthetic enzymes such as non-ribosomal peptide synthetases (NRPSs), polyketide synthases (PKSs) and regulatory mechanisms governing their expression.

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 Natural products in the predatory defence of the filamentous fungal pathogen Aspergillus fumigatus

2021 ◽  
Vol 17 ◽  
pp. 1814-1827
Author(s):  
Jana M Boysen ◽  
Nauman Saeed ◽  
Falk Hillmann
Keyword(s):  
Secondary Metabolites ◽  
Aspergillus Fumigatus ◽  
Fungal Pathogen ◽  
Current Knowledge ◽  
Pathogenic Fungus ◽  
Gene Clusters ◽  
Natural Environments ◽  
Natural Habitats ◽  
Genetic Potential ◽  
Fungal Genomes

The kingdom of fungi comprises a large and highly diverse group of organisms that thrive in diverse natural environments. One factor to successfully confront challenges in their natural habitats is the capability to synthesize defensive secondary metabolites. The genetic potential for the production of secondary metabolites in fungi is high and numerous potential secondary metabolite gene clusters have been identified in sequenced fungal genomes. Their production may well be regulated by specific ecological conditions, such as the presence of microbial competitors, symbionts or predators. Here we exemplarily summarize our current knowledge on identified secondary metabolites of the pathogenic fungus Aspergillus fumigatus and their defensive function against (microbial) predators.

scholarly journals Accessory Chromosomes in Fusarium oxysporum

2020 ◽  
Vol 110 (9) ◽  
pp. 1488-1496
Author(s):  
He Yang ◽  
Houlin Yu ◽  
Li-Jun Ma
Keyword(s):  
Fusarium Oxysporum ◽  
Fungal Pathogen ◽  
Current Knowledge ◽  
Fungal Species ◽  
Gene Density ◽  
Functional Importance ◽  
The Core ◽  
Gene Functions ◽  
Epigenetic Signatures ◽  
Accessory Chromosomes

Most genomes within the species complex of Fusarium oxysporum are organized into two compartments: the core chromosomes (CCs) and accessory chromosomes (ACs). As opposed to CCs, which are conserved and vertically transmitted to carry out essential housekeeping functions, lineage- or strain-specific ACs are believed to be initially horizontally acquired through unclear mechanisms. These two genomic compartments are different in terms of gene density, the distribution of transposable elements, and epigenetic markers. Although common in eukaryotes, the functional importance of ACs is uniquely emphasized among fungal species, specifically in relationship to fungal pathogenicity and their adaptation to diverse hosts. With a focus on the cross-kingdom fungal pathogen F. oxysporum, this review provides a summary of the differences between CCs and ACs based on current knowledge of gene functions, genome structures, and epigenetic signatures, and explores the transcriptional crosstalk between the core and accessory genomes.

scholarly journals The Chemical Ecology Approach to Reveal Fungal Metabolites for Arthropod Pest Management

2021 ◽  
Vol 9 (7) ◽  
pp. 1379
Author(s):  
Alexander Berestetskiy ◽  
Qiongbo Hu
Keyword(s):  
Chemical Ecology ◽  
Insect Pests ◽  
Gene Clusters ◽  
Fungal Species ◽  
Phytopathogenic Fungi ◽  
Ecological Groups ◽  
Fungal Metabolites ◽  
Fungal Genomes ◽  
Subsequent Activation ◽  
New Compounds

Biorational insecticides (for instance, avermectins, spinosins, azadirachtin, and afidopyropen) of natural origin are increasingly being used in agriculture. The review considers the chemical ecology approach for the search for new compounds with insecticidal properties (entomotoxic, antifeedant, and hormonal) produced by fungi of various ecological groups (entomopathogens, soil saprotrophs, endophytes, phytopathogens, and mushrooms). The literature survey revealed that insecticidal metabolites of entomopathogenic fungi have not been sufficiently studied, and most of the well-characterized compounds show moderate insecticidal activity. The greatest number of substances with insecticidal properties was found to be produced by soil fungi, mainly from the genera Aspergillus and Penicillium. Metabolites with insecticidal and antifeedant properties were also found in endophytic and phytopathogenic fungi. It was noted that insect pests of stored products are mostly low sensitive to mycotoxins. Mushrooms were found to be promising producers of antifeedant compounds as well as insecticidal proteins. The expansion of the number of substances with insecticidal properties detected in prospective fungal species is possible by mining fungal genomes for secondary metabolite gene clusters and secreted proteins with their subsequent activation by various methods. The efficacy of these studies can be increased with high-throughput techniques of extraction of fungal metabolites and their analysis by various methods of chromatography and mass spectrometry.

Bacterial and fungal microbiome profiling in chilhuacle negro chili (Capsicum annuum L.) associated with fruit rot disease

Plant Disease ◽  
2021 ◽  
Author(s):  
Evelia Fajardo Rebollar ◽  
Karel Estrada ◽  
Ricardo Grande ◽  
María Julissa Ek Ramos ◽  
Gerardo Ruiz Vargas ◽  
...  
Keyword(s):  
Capsicum Annuum ◽  
Pathogenic Fungi ◽  
Fungal Species ◽  
Fruit Rot ◽  
Maturation Stage ◽  
Capsicum Annuum L ◽  
Sequencing Technologies ◽  
Fruit Decay ◽  
Microbiological Techniques ◽  
Opportunistic Pathogenic

Chilhuacle negro chili (Capsicum annuum L.) is an ancient Mexican landrace that is deeply linked to the culinary heritage of the country. Due to the high profitability and uniqueness of this crop, the “Universidad Autónoma del Estado de Morelos”, is one of the Mexican institutions exploring its production in controlled environments. In the summer of 2018, the production of chilhuacle negro plants was seriously affected by an unidentified pathogen causing fruit rot, which reduced its quality, yield and market value. Therefore, the main objective of this work was to study and characterize the fruit microbiota, which could help reveal the causal agent of this disease. Using DNA metabarcoding coupled with Illumina and nanopore sequencing technologies, both healthy and infected chili fruit, along with greenhouse bioaerosols, were collected and analyzed. We also explored the bacterial and fungal microbiota using microbiological techniques to isolate some of the culturable bacterial and fungal species. Our results suggest that the seedborne fungus Alternaria alternata is activated during the maturation stage of chilhuacle negro fruit, triggering a microbiome imbalance which may in turn enable the establishment of other opportunistic pathogenic fungi during fruit decay, such as Mucor sp. To our knowledge, this is the first study of the chilhuacle negro chili microbiome, which can shed some light on our understanding of one of the main diseases that affect this valuable crop.

scholarly journals Apicidin biosynthesis is linked to accessory chromosomes in Fusarium poae isolates

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Thomas E. Witte ◽  
Linda J. Harris ◽  
Hai D. T. Nguyen ◽  
Anne Hermans ◽  
Anne Johnston ◽  
...  
Keyword(s):  
Fusarium Head Blight ◽  
Crop Yields ◽  
High Resolution Mass Spectrometry ◽  
Gene Clusters ◽  
Biosynthetic Gene ◽  
Metabolome Analysis ◽  
Head Blight ◽  
Eastern Canada ◽  
Fusarium Poae ◽  
Accessory Chromosomes

Abstract Background Fusarium head blight is a disease of global concern that reduces crop yields and renders grains unfit for consumption due to mycotoxin contamination. Fusarium poae is frequently associated with cereal crops showing symptoms of Fusarium head blight. While previous studies have shown F. poae isolates produce a range of known mycotoxins, including type A and B trichothecenes, fusarins and beauvericin, genomic analysis suggests that this species may have lineage-specific accessory chromosomes with secondary metabolite biosynthetic gene clusters awaiting description. Methods We examined the biosynthetic potential of 38 F. poae isolates from Eastern Canada using a combination of long-read and short-read genome sequencing and untargeted, high resolution mass spectrometry metabolome analysis of extracts from isolates cultured in multiple media conditions. Results A high-quality assembly of isolate DAOMC 252244 (Fp157) contained four core chromosomes as well as seven additional contigs with traits associated with accessory chromosomes. One of the predicted accessory contigs harbours a functional biosynthetic gene cluster containing homologs of all genes associated with the production of apicidins. Metabolomic and genomic analyses confirm apicidins are produced in 4 of the 38 isolates investigated and genomic PCR screening detected the apicidin synthetase gene APS1 in approximately 7% of Eastern Canadian isolates surveyed. Conclusions Apicidin biosynthesis is linked to isolate-specific putative accessory chromosomes in F. poae. The data produced here are an important resource for furthering our understanding of accessory chromosome evolution and the biosynthetic potential of F. poae.

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 Metabolomic Analysis of The Chemical Diversity of South Africa Leaf Litter Fungal Species Using an Epigenetic Culture-Based Approach

Molecules ◽  
2021 ◽  
Vol 26 (14) ◽  
pp. 4262
Author(s):  
Rachel Serrano ◽  
Víctor González-Menéndez ◽  
Germán Martínez ◽  
Clara Toro ◽  
Jesús Martín ◽  
...  
Keyword(s):  
South Africa ◽  
Genome Mining ◽  
Fungal Species ◽  
Chemical Diversity ◽  
Fermentation Conditions ◽  
Metabolite Profiles ◽  
Different Populations ◽  
Fungal Genomes ◽  
Microbial Natural Products ◽  
Fermentation Media

Microbial natural products are an invaluable resource for the biotechnological industry. Genome mining studies have highlighted the huge biosynthetic potential of fungi, which is underexploited by standard fermentation conditions. Epigenetic effectors and/or cultivation-based approaches have successfully been applied to activate cryptic biosynthetic pathways in order to produce the chemical diversity suggested in available fungal genomes. The addition of Suberoylanilide Hydroxamic Acid to fermentation processes was evaluated to assess its effect on the metabolomic diversity of a taxonomically diverse fungal population. Here, metabolomic methodologies were implemented to identify changes in secondary metabolite profiles to determine the best fermentation conditions. The results confirmed previously described effects of the epigenetic modifier on the metabolism of a population of 232 wide diverse South Africa fungal strains cultured in different fermentation media where the induction of differential metabolites was observed. Furthermore, one solid-state fermentation (BRFT medium), two classic successful liquid fermentation media (LSFM and YES) and two new liquid media formulations (MCKX and SMK-II) were compared to identify the most productive conditions for the different populations of taxonomic subgroups.

scholarly journals New Method for Identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences

2021 ◽  
Vol 7 (3) ◽  
pp. 207
Author(s):  
Lene Lange ◽  
Kristian Barrett ◽  
Anne S. Meyer
Keyword(s):  
Fungal Species ◽  
Fungal Genome ◽  
Sequencing Data ◽  
Carbohydrate Active Enzymes ◽  
New Approach ◽  
Fungal Enzyme ◽  
Biomass Processing ◽  
Fungal Genomes ◽  
Robust Prediction ◽  
Fungal Kingdom

Fungal genome sequencing data represent an enormous pool of information for enzyme discovery. Here, we report a new approach to identify and quantitatively compare biomass-degrading capacity and diversity of fungal genomes via integrated function-family annotation of carbohydrate-active enzymes (CAZymes) encoded by the genomes. Based on analyses of 1932 fungal genomes the most potent hotspots of fungal biomass processing CAZymes are identified and ranked according to substrate degradation capacity. The analysis is achieved by a new bioinformatics approach, Conserved Unique Peptide Patterns (CUPP), providing for CAZyme-family annotation and robust prediction of molecular function followed by conversion of the CUPP output to lists of integrated “Function;Family” (e.g., EC 3.2.1.4;GH5) enzyme observations. An EC-function found in several protein families counts as different observations. Summing up such observations allows for ranking of all analyzed genome sequenced fungal species according to richness in CAZyme function diversity and degrading capacity. Identifying fungal CAZyme hotspots provides for identification of fungal species richest in cellulolytic, xylanolytic, pectinolytic, and lignin modifying enzymes. The fungal enzyme hotspots are found in fungi having very different lifestyle, ecology, physiology and substrate/host affinity. Surprisingly, most CAZyme hotspots are found in enzymatically understudied and unexploited species. In contrast, the most well-known fungal enzyme producers, from where many industrially exploited enzymes are derived, are ranking unexpectedly low. The results contribute to elucidating the evolution of fungal substrate-digestive CAZyme profiles, ecophysiology, and habitat adaptations, and expand the knowledge base for novel and improved biomass resource utilization.

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