Evidence that a secondary metabolic biosynthetic gene cluster has grown by gene relocation during evolution of the filamentous fungus Fusarium

FunFEA: an R package for fungal functional enrichment analysis

BACKGROUND

The functional annotation of fungal genomes is critical for understanding their biological processes and ecological roles. While existing tools support functional enrichment analysis from publicly available annotations of well-established model organisms, few are tailored to the specific needs of the fungal research community. Furthermore, many tools struggle with processing functional annotations of novel species, for which no publicly available functional annotations are yet available.

RESULTS

FunFEA is an R package designed for functional enrichment analysis of fungal genomes. It supports COG/KOG (Clusters of Orthologous Genes), GO (Gene Ontology), and KEGG (Kyoto Encyclopedia of Genes and Genomes) annotations, and generates background frequency models from publicly available annotations for overrepresentation analysis, within a set of experimentally defined genes or proteins. Additionally, FunFEA can process eggNOG-mapper annotations, thus enabling functional enrichment analysis of novel genomes. The package offers a suite of tools for generation of background frequency models, functional enrichment analysis, as well as visualization of enriched functional categories. On release, the package includes precomputed models for 65 commonly used fungal strains in academic research and strains listed on the WHO fungal priority pathogens list.

CONCLUSIONS

FunFEA fills a critical need for a specialized tool in fungal genomics, providing valuable insights into fungal biology. Additionally, its ability to process eggNOG-mapper annotations makes it an essential resource for researchers, helping to drive further exploration of fungal functional diversity and pathways and derive biological insights from novel genomes.

Fusarium graminearum in Wheat-Management Strategies in Central Europe

The main aim of this study was to discuss and compare the threats associated with F. graminearum in wheat production in Poland and in other Central European countries. Wheat is one of the most widely cultivated crops in the world, and pathogens causing Fusarium head blight (FHB) pose the greatest threat to wheat production. Our knowledge of FHB has to be regularly expanded in order to explore the impacts of climate change, new wheat cultivars, and new fungicides on the prevalence of this disease. The pathogen's resistance to fungicides was analyzed in a global context due to the relative scarcity of studies examining this problem in Central Europe (excluding Germany). This is an interesting research perspective because, despite a relatively large number of Polish studies on FHB, F. graminearum genotypes and the pathogen's resistance to fungicides remain insufficiently investigated. The hemibiotrophic pathogen Fusarium graminearum causes particularly high losses in wheat cultivation due to its ability to produce mycotoxins that are dangerous to human health (mainly deoxynivalenol, DON), colonize plant residues in soil in the saprotrophic phase, and produce spores that infect the stem base and spikes throughout the growing season. The infection process is highly dynamic, and it is facilitated by DON. The synthesis of DON (trichothecene) is encoded by Tri genes located in four loci. In Poland, the F. graminearum population is mainly composed of the 15ADON genotype, and the spread of FHB cannot effectively be managed with fungicides during epidemic years. Dynamic gene flows in field populations enable the pathogen to rapidly adapt to environmental changes and overcome wheat resistance to FHB. The emergence of fungicide-resistant F. graminearum strains significantly compromises the quality of wheat crops, but the associated mechanisms have not been sufficiently investigated to date. In addition, although some biopreparations are promising and effective in small-scale field trials, very few have been commercialized. Extensive research into pathogen populations, the development of new resistant wheat varieties, and the use of effective fungicides and biopreparations are required to produce wheat grain that is free of mycotoxins.

Debunking the Myth of Fusarium poae T-2/HT-2 Toxin Production

Fusarium poae is commonly detected in field surveys of Fusarium head blight (FHB) of cereal crops and can produce a range of trichothecene mycotoxins. Although experimentally validated reports of F. poae strains producing T-2/HT-2 trichothecenes are rare, F. poae is frequently generalized in the literature as a producer of T-2/HT-2 toxins due to a single study from 2004 in which T-2/HT-2 toxins were detected at low levels from six out of forty-nine F. poae strains examined. To validate/substantiate the observations reported from the 2004 study, the producing strains were acquired and phylogenetically confirmed to be correctly assigned as F. poae; however, no evidence of T-2/HT-2 toxin production was observed from axenic cultures. Moreover, no evidence for a TRI16 ortholog, encoding a key acyltransferase shown to be necessary for T-2 toxin production in other Fusarium species, was observed in any of the de novo assembled genomes of the F. poae strains. Our findings corroborate multiple field-based and in vitro studies on FHB-associated Fusarium populations which also do not support the production of T-2/HT-2 toxins with F. poae and therefore conclude that F. poae should not be generalized as a T-2/HT-2 toxin producing species of Fusarium.

Regulation of TRI5 expression and deoxynivalenol biosynthesis by a long non-coding RNA in Fusarium graminearum

Deoxynivalenol (DON) is the most frequently detected mycotoxin in cereal grains and processed food or feed. Two transcription factors, Tri6 and Tri10, are essential for DON biosynthesis in Fusarium graminearum. In this study we conduct stranded RNA-seq analysis with tri6 and tri10 mutants and show that Tri10 acts as a master regulator controlling the expression of sense and antisense transcripts of TRI6 and over 450 genes with diverse functions. TRI6 is more specific for regulating TRI genes although it negatively regulates TRI10. Two other TRI genes, including TRI5 that encodes a key enzyme for DON biosynthesis, also have antisense transcripts. Both Tri6 and Tri10 are essential for TRI5 expression and for suppression of antisense-TRI5. Furthermore, we identify a long non-coding RNA (named RNA5P) that is transcribed from the TRI5 promoter region and is also regulated by Tri6 and Tri10. Deletion of RNA5P by replacing the promoter region of TRI5 with that of TRI12 increases TRI5 expression and DON biosynthesis, indicating that RNA5P suppresses TRI5 expression. However, ectopic constitutive overexpression of RNA5P has no effect on DON biosynthesis and TRI5 expression. Nevertheless, elevated expression of RNA5P in situ reduces TRI5 expression and DON production. Our results indicate that TRI10 and TRI6 regulate each other's expression, and both are important for suppressing the expression of RNA5P, a long non-coding RNA with cis-acting inhibitory effects on TRI5 expression and DON biosynthesis in F. graminearum.

Phylogenetic Variation of Tri1 Gene and Development of PCR-RFLP Analysis for the Identification of NX Genotypes in Fusarium graminearum Species Complex

NX toxins have been described as a novel group of type A trichothecenes produced by members of the Fusarium graminearum species complex (FGSC). Differences in structure between NX toxins and the common type B trichothecenes arise from functional variation in the trichothecene biosynthetic enzyme Tri1 in the FGSC. The identified highly conserved changes in the Tri1 gene can be used to develop specific PCR-based assays to identify the NX-producing strains. In this study, the sequences of the Tri1 gene from type B trichothecene- and NX-producing strains were analyzed to identify DNA polymorphisms between the two different kinds of trichothecene producers. Four sets of Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methods were successfully developed to distinguish the common type B trichothecene producers and NX producers within FGSC. These promising diagnostic methods can be used for high-throughput genotype detection of Fusarium strains as a step forward for crop disease management and mycotoxin control in agriculture. Additionally, it was found that the Tri1 gene phylogeny differs from the species phylogeny, which is consistent with the previous studies.

The Fusarium graminearum Transporters Abc1 and Abc6 Are Important for Xenobiotic Resistance, Trichothecene Accumulation, and Virulence to Wheat

The plant pathogenic fungus Fusarium graminearum is the causal agent of Fusarium head blight (FHB) disease on small-grain cereals. F. graminearum produces trichothecene mycotoxins such as deoxynivalenol (DON) that are required for full virulence. DON must be exported outside the cell to cause FHB disease, a process that may require the involvement of membrane-bound transporters. In this study, we show that the deletion of membrane-bound transporters results in reduced DON accumulation as well as reduced FHB symptoms on wheat. Deletion of the ATP-binding cassette (ABC) transporter gene Abc1 results in the greatest reduction in DON accumulation and virulence. Deletion of another ABC transporter gene, Abc6, also reduces FHB symptoms to a lesser degree. Combining deletions fails to reduce DON accumulation or virulence in an additive fashion, even when a ∆abc1 deletion is included. Heterologous expression of F. graminearum transporters in a DON-sensitive strain of yeast confirms Abc1 as a major DON resistance mechanism; furthermore, it suggests that Abc1 is directly participating in DON transport rather than facilitating DON transport though other means. Yeast expression further indicates that multiple transporters, including Abc1, play an important role in resistance to the wheat phytoalexin 2-benzoxazolinone (BOA) and other xenobiotics. Thus, Abc1 may contribute to virulence on wheat both by facilitating export of DON and by providing resistance to the wheat phytoalexin BOA. This research provides useful information that may aid in designing novel management techniques of FHB or other destructive plant diseases.

A Mycovirus VIGS Vector Confers Hypovirulence to a Plant Pathogenic Fungus to Control Wheat FHB

Mycovirus-mediated hypovirulence has the potential to control fungal diseases. However, the availability of hypovirulence-conferring mycoviruses for plant fungal disease control is limited as most fungal viruses are asymptomatic. In this study, the virus-induced gene silencing (VIGS) vector p26-D4 of Fusarium graminearum gemytripvirus 1 (FgGMTV1), a tripartite circular single-stranded DNA mycovirus, is successfully constructed to convert the causal fungus of cereal Fusarium head blight (FHB) into a hypovirulent strain. p26-D4, with an insert of a 75-150 bp fragment of the target reporter transgene transcript in both sense and antisense orientations, efficiently triggered gene silencing in Fusarium graminearum. Notably, the two hypovirulent strains, p26-D4-Tri101, and p26-D4-FgPP1, obtained by silencing the virulence-related genes Tri101 and FgPP1 with p26-D4, can be used as biocontrol agents to protect wheat from a fungal disease FHB and mycotoxin contamination at the field level. This study not only describes the first mycovirus-derived VIGS system but also proves that the VIGS vector can be used to establish multiple hypovirulent strains to control pathogenic fungi.

Type A Trichothecene Metabolic Profile Differentiation, Mechanisms, Biosynthetic Pathways, and Evolution in Fusarium Species-A Mini Review

Trichothecenes are the most common Fusarium toxins detected in grains and related products. Type A trichothecenes are among the mycotoxins of greatest concern to food and feed safety due to their high toxicity. Recently, two different trichothecene genotypes within Fusarium species were reported. The available information showed that Tri1 and Tri16 genes are the key determinants of the trichothecene profiles of T-2 and DAS genotypes. In this review, polymorphisms in the Tri1 and Tri16 genes in the two genotypes were investigated. Meanwhile, the functions of genes involved in DAS and NEO biosynthesis are discussed. The possible biosynthetic pathways of DAS and NEO are proposed in this review, which will facilitate the understanding of the synthesis process of trichothecenes in Fusarium strains and may also inspire researchers to design and conduct further research. Together, the review provides insight into trichothecene profile differentiation and Tri gene evolutionary processes responsible for the structural diversification of trichothecene produced by Fusarium.

Paralogous FgIDO genes with differential roles in tryptophan catabolism, fungal development and virulence in Fusarium graminearum

Indoleamine 2,3-dioxygenase (Ido) is a tryptophan-degrading enzyme that is widely distributed across species. Ido catalyzes the first step of tryptophan (TRP) degradation and drives the de novo synthesis of nicotinamide adenine dinucleotide (NAD⁺) coenzymes via the kynurenine (KYN) pathway. The budding yeast Saccharomyces cerevisiae possesses a single IDO gene (BNA2) that is responsible for NAD⁺ synthesis, whereas a number of fungal species contain multiple IDO genes. However, the biological roles of IDO paralogs in plant pathogens remain unclear. In the current study, we identified three FgIDOs from the wheat head blight fungus Fusarium graminearum. FgIDOA/B/C expression was significantly induced upon TRP treatment. Targeted disruption of FgIDOA and/or FgIDOB caused different levels of NAD⁺ auxotrophy, thus resulting in pleotropic phenotypic defects. Loss of FgIDOA resulted in abnormal conidial morphology, reduced mycelial growth, decreased virulence in wheat heads and reduced deoxynivalenol accumulation. Exogenous addition of KYN or various intermediates involved in the KYN pathway rescued auxotrophy of the mutants. Metabolomics analysis revealed shifts toward alternative TRP degradation pathways to melatonin and indole derivatives in mutants lacking FgIDOB. Upregulation of partner genes in auxotrophic mutants and the capacity to rescue the auxotroph by overexpressing a partner gene indicated functional complementation among FgIDOA/B/C. Taken together, the results of this study provide insights into differential roles in paralogous FgIDOs and how fungal TRP catabolism modulates fungal development and virulence.

Detection of fungicide resistance to fludioxonil and tebuconazole in Fusarium pseudograminearum, the causal agent of Fusarium crown rot in wheat

Fusarium crown rot (FCR) on wheat is a soil-borne disease that affects the yield and quality of the produce. In 2020, 297 Fusarium pseudograminearum isolates were isolated from diseased FCR wheat samples from eight regional areas across Hebei Province in China. Baseline sensitivity of F. pseudograminearum to fludioxonil (0.0613 ± 0.0347 μg/mL) and tebuconazole (0.2328 ± 0.0840 μg/mL) were constructed based on the in vitro tests of 71 and 83 isolates, respectively. The resistance index analysis showed no resistance isolate to fludioxonil but two low-resistance isolates to tebuconazole in 2020. There was an increased frequency of resistant isolates from 2021 to 2022 based on the baseline sensitivity for tebuconazole. There was no cross-resistance between fludioxonil and tebuconazole. This study provides a significant theoretical and practical basis for monitoring the resistance of F. pseudograminearum to fungicides, especially the control of FCR.

First report of Fusarium meridionale causing Fusarium head blight of wheat in Henan Province, China

Fusarium graminearum and F. asiaticum have been found as a major cause of Fusarium head blight (FHB) of wheat (Triticum aestivum L.), especially in Henan Province of China (Zhang et al. 2014; Xu et al. 2021). In May 2021, a survey to determine the composition of Fusarium species infecting wheat heads was conducted in commercial fields in Henan. A total of 395 diseased spikes with premature whitening symptom were collected from 31 commercial fields in Henan. Symptomatic spikelets were excised, surface-sterilized for 10 s in 70% ethanol followed by 1 min in 3% sodium hypochlorite, rinsed three times with autoclaved distilled water, and then plated onto potato dextrose agar (PDA) medium. Isolated colonies that resembled Fusarium species were transferred to fresh PDA plates and purified using a single spore method. Species were identified based on sequence analysis of the translation elongation factor-1α (TEF) and trichothecene 3-Oacetyltransferase (Tri 101) gene (Proctor et al. 2009). The results indicated that F. graminearum (43.3%), F. asiaticum (47.8%), F. pseudograminearum (6.6%) were the main causal agents of FHB in Henan. However, nine isolates (2.3%) were found to be identical to F. meridionale by sequence comparison in GenBank, and eight isolates of which came from three fields with 1% to 2% diseased spikes near Reservoir Luhun (34.1255° N, 112.1111° E, altitude: 388 m above sea level), Songxian County of Henan. The isolates of F. meridionale were transferred onto carnation leaf agar (CLA) and incubated at 20℃ under black light blue illumination. Macroconidia were abundant, relatively slender, curved to almost straight, commonly six- to seven-septate, and 27.0 to 61.0 (average 44.0) μm × 3.2 to 6.8 (average 5.3) μm. Microconidia were not observed. The TEF sequences (Accession nos. OM460748 to OM460756) and the Tri 101 sequences (OM460759 to OM460767) of the nine isolates showed 99 to 100% similarity with the TEF and Tri 101 sequences of F. meridionale NRRL 28436 and NRRL 28723 (AF212435 and AF212436 (TEF); AF212582 and AF212683 (Tri 101)). To complete Koch's postulates, the pathogenicity of the fungus was tested by using the single floret inoculation method by injecting 20-μl conidial suspension (5 × 105 conidia per milliliter) into healthy inflorescences of wheat cultivar Bainong 207 at anthesis in the field. Another 30 healthy inflorescences were injected with sterile distilled water. The heads were covered with polyethylene bags that were removed after 2 days. Twenty days after inoculation, while control inflorescences were asymptomatic, the F. meridionale-inoculated inflorescences showed 12% bleached spikelets per spike. By using the methodology described above, the fungus was re-isolated from infected spikelets of inoculated wheat heads but not from the controls. Although F. meridionale has frequently been reported in association with Fusarium ear rot (FER) of maize in Chongqing City and Gansu Province (Zhang et al. 2014; Zhou et al. 2018), and rice FER in Sichuan Province (Dong et al. 2020), to our knowledge, this is the first report of F. meridionale from diseased wheat heads in Henan, China. Further investigation is needed to gain a better understanding of this species by collecting isolates from different cropping system in Henan, which maize-wheat and rice-wheat rotation fields have coexisted in the region.

A Novel Trichothecene Toxin Phenotype Associated with Horizontal Gene Transfer and a Change in Gene Function in Fusarium

Fusarium trichothecenes are among the mycotoxins of most concern to food and feed safety. Production of these mycotoxins and presence of the trichothecene biosynthetic gene (TRI) cluster have been confirmed in only two multispecies lineages of Fusarium: the Fusarium incarnatum-equiseti (Incarnatum) and F. sambucinum (Sambucinum) species complexes. Here, we identified and characterized a TRI cluster in a species that has not been formally described and is represented by Fusarium sp. NRRL 66739. This fungus is reported to be a member of a third Fusarium lineage: the F. buharicum species complex. Cultures of NRRL 66739 accumulated only two trichothecenes, 7-hydroxyisotrichodermin and 7-hydroxyisotrichodermol. Although these are not novel trichothecenes, the production profile of NRRL 66739 is novel, because in previous reports 7-hydroxyisotrichodermin and 7-hydroxyisotrichodermol were components of mixtures of 6-8 trichothecenes produced by several Fusarium species in Sambucinum. Heterologous expression analysis indicated that the TRI13 gene in NRRL 66739 confers trichothecene 7-hydroxylation. This contrasts the trichothecene 4-hydroxylation function of TRI13 in other Fusarium species. Phylogenetic analyses suggest that NRRL 66739 acquired the TRI cluster via horizontal gene transfer from a close relative of Incarnatum and Sambucinum. These findings provide insights into evolutionary processes that have shaped the distribution of trichothecene production among Fusarium species and the structural diversity of the toxins.

Characterization of Host-Specific Genes from Pine- and Grass-Associated Species of the Fusarium fujikuroi Species Complex

The Fusarium fujikuroi species complex (FFSC) includes socioeconomically important pathogens that cause disease for numerous crops and synthesize a variety of secondary metabolites that can contaminate feedstocks and food. Here, we used comparative genomics to elucidate processes underlying the ability of pine-associated and grass-associated FFSC species to colonize tissues of their respective plant hosts. We characterized the identity, possible functions, evolutionary origins, and chromosomal positions of the host-range-associated genes encoded by the two groups of fungi. The 72 and 47 genes identified as unique to the respective genome groups were potentially involved in diverse processes, ranging from transcription, regulation, and substrate transport through to virulence/pathogenicity. Most genes arose early during the evolution of Fusarium/FFSC and were only subsequently retained in some lineages, while some had origins outside Fusarium. Although differences in the densities of these genes were especially noticeable on the conditionally dispensable chromosome of F. temperatum (representing the grass-associates) and F. circinatum (representing the pine-associates), the host-range-associated genes tended to be located towards the subtelomeric regions of chromosomes. Taken together, these results demonstrate that multiple mechanisms drive the emergence of genes in the grass- and pine-associated FFSC taxa examined. It also highlighted the diversity of the molecular processes potentially underlying niche-specificity in these and other Fusarium species.

The First Annotated Genome Assembly of Macrophomina tecta Associated with Charcoal Rot of Sorghum

Charcoal rot is an important soilborne disease caused by a range of Macrophomina species, which affects a broad range of commercially important crops worldwide. Even though Macrophomina species are fungal pathogens of substantial economic importance, their mechanism of pathogenicity and host spectrum are poorly understood. There is an urgent need to better understand the biology, epidemiology, and evolution of Macrophomina species, which, in turn, will aid in improving charcoal rot management strategies. Here, we present the first high-quality genome assembly and annotation of Macrophomina tecta strain BRIP 70781 associated with charcoal rot symptoms on sorghum. Hybrid assembly integrating long reads generated by Oxford Nanopore Technology and short Illumina paired-end reads resulted in 43 contigs with a total assembly size of ∼54 Mb, and an N50 of 3.4 Mb. In total, 12,926 protein-coding genes and 7,036 repeats were predicted. Genome comparisons detected accumulation of DNA transposons in Macrophomina species associated with sorghum. The first reference genome of M. tecta generated in this study will contribute to more comparative and population genomics studies of Macrophomina species.

Dynamics of Deoxynivalenol and Nivalenol Glucosylation in Wheat Cultivars Infected with Fusarium culmorum in Field Conditions─A 3 Year Study (2018-2020)

Fusarium head blight (FHB) caused by pathogenic species of Fusarium fungi is one of the most important diseases of cereal plants and a factor contributing to losses in plant production. The growth of FHB-associated species is often accompanied by biosynthesis of secondary metabolites─mycotoxins, which serve as a virulence factor. The aim of the study was to evaluate the ratios between deoxynivalenol (DON) and nivalenol (NIV) and their derivatives in the ears of six cultivars of winter wheat with varying resistance to FHB, taking into account a range of factors (weather conditions, location, cultivar, and year) after inoculation with Fusarium culmorum, during a 3 year field experiment, 2018-2020. The presence of toxins in the ears was measured within 21 days of inoculation. The toxins were found in the ears as soon as on the third day from the start of the experiment, whereas relative humidity higher than 80% was a decisive factor for FHB incidence. All wheat cultivars showed the ability to biotransform DON and NIV present in the ears to glucosides, that is, deoxynivalenol-3-glucoside (DON-3G) and nivalenol-3-glucoside (NIV-3G). The levels of these metabolites showed significant correlation with the levels of their basic analogues. In most cases, higher levels of DON and NIV in wheat ears and higher levels of their metabolites were observed, but the relative levels of DON-3G/DON and NIV-3G/NIV at relatively high levels of toxins were lower compared to the ear samples with relatively low toxin levels. The presented results are the first studies, which systematically correlate a variety of wheat cultivars with their extent to glucosylate trichothecenes.

Trichothecene Genotype Profiling of Wheat Fusarium graminearum Species Complex in Paraguay

Paraguay is a non-traditional wheat-producing country in one of the warmest regions in South America. Fusarium Head Blight (FHB) is a critical disease affecting this crop, caused by the Fusarium graminearum species complex (FGSC). A variety of these species produce trichothecenes, including deoxynivalenol (DON) and its acetylated forms (3-ADON and 15-ADON) or nivalenol (NIV). This study characterized the phylogenetic relationships, and chemotype diversity of 28 strains within FGSC collected from wheat fields across different country regions. Phylogenetic analysis based on the sequence of elongation factor-1α gene (EF-1α) from 28 strains revealed the presence of four species in the FGSC: F. graminearum sensu stricto, F. asiaticum, F. meridionale and F. cortaderiae. Ten strains selected for further analysis revealed that all F. graminearum strains were 15-ADON chemotype, while the two strains of F. meridionale and one strain of F. asiaticum were NIV chemotype. Thus, the 15-ADON chemotype of F. graminearum sensu stricto was predominant within the Fusarium strains isolated in the country. This work is the first report of phylogenetic relationships and chemotype diversity among Fusarium strains which will help understand the population diversity of this pathogen in Paraguay.

The Evolution of the Satratoxin and Atranone Gene Clusters of Stachybotrys chartarum

Stachybotrys chartarum is frequently isolated from damp building materials or improperly stored animal forage. Human and animal exposure to the secondary metabolites of this mold is linked to severe health effects. The mutually exclusive production of either satratoxins or atranones defines the chemotypes A and S. Based upon the genes (satratoxin cluster, SC1-3, sat or atranone cluster, AC1, atr) that are supposed to be essential for satratoxin and atranone production, S. chartarum can furthermore be divided into three genotypes: the S-type possessing all sat- but no atr-genes, the A-type lacking the sat- but harboring all atr-genes, and the H-type having only certain sat- and all atr-genes. We analyzed the above-mentioned gene clusters and their flanking regions to shed light on the evolutionary relationship. Furthermore, we performed a deep re-sequencing and LC-MS/MS (Liquid chromatography-mass spectrometry) analysis. We propose a first model for the evolution of the S. chartarum genotypes. We assume that genotype H represents the most ancient form. A loss of the AC1 and the concomitant acquisition of the SC2 led to the emergence of the genotype S. According to our model, the genotype H also developed towards genotype A, a process that was accompanied by a loss of SC1 and SC3.

Diacetoxyscirpenol, a Fusarium exometabolite, prevents efficiently the incidence of the parasitic weed Striga hermonthica

BACKGROUND

Certain Fusarium exometabolites have been reported to inhibit seed germination of the cereal-parasitizing witchweed, Striga hermonthica, in vitro. However, it is unknown if these exometabolites will consistently prevent S. hermonthica incidence in planta. The study screened a selection of known, highly phytotoxic Fusarium exometabolites, in identifying the most potent/efficient candidate (i.e., having the greatest effect at minimal concentration) to completely hinder S. hermonthica seed germination in vitro and incidence in planta, without affecting the host crop development and yield.

RESULTS

In vitro germination assays of the tested Fusarium exometabolites (i.e., 1,4-naphthoquinone, equisetin, fusaric acid, hymeglusin, neosolaniol (Neo), T-2 toxin (T-2) and diacetoxyscirpenol (DAS)) as pre-Striga seed conditioning treatments at 1, 5, 10, 20, 50 and 100 µM, revealed that only DAS, out of all tested exometabolites, completely inhibited S. hermonthica seed germination at each concentration. It was followed by T-2 and Neo, as from 10 to 20 µM respectively. The remaining exometabolites reduced S. hermonthica seed germination as from 20 µM (P < 0. 0001). In planta assessment (in a S. hermonthica-sorghum parasitic system) of the exometabolites at 20 µM showed that, although, none of the tested exometabolites affected sorghum aboveground dry biomass (P > 0.05), only DAS completely prevented S. hermonthica incidence. Following a 14-d incubation of DAS in the planting soil substrate, bacterial 16S ribosomal RNA (rRNA) and fungal 18S rRNA gene copy numbers of the soil microbial community were enhanced; which coincided with complete degradation of DAS in the substrate. Metabolic footprinting revealed that the S. hermonthica mycoherbicidal agent, Fusarium oxysporum f. sp. strigae (isolates Foxy-2, FK3), did not produce DAS; a discovery that corresponded with underexpression of key genes (Tri5, Tri4) necessary for Fusarium trichothecene biosynthesis (P < 0.0001).

CONCLUSIONS

Among the tested Fusarium exometabolites, DAS exhibited the most promising herbicidal potential against S. hermonthica. Thus, it could serve as a new biocontrol agent for efficient S. hermonthica management. Further examination of DAS specific mode of action against the target weed S. hermonthica at low concentrations (≤ 20 µM), as opposed to non-target soil organisms, is required.

Distribution, Function, and Evolution of a Gene Essential for Trichothecene Toxin Biosynthesis in Trichoderma

Trichothecenes are terpenoid toxins produced by species in 10 fungal genera, including species of Trichoderma. The trichothecene biosynthetic gene (tri) cluster typically includes the tri5 gene, which encodes a terpene synthase that catalyzes formation of trichodiene, the parent compound of all trichothecenes. The two Trichoderma species, Trichoderma arundinaceum and T. brevicompactum, that have been examined are unique in that tri5 is located outside the tri cluster in a genomic region that does not include other known tri genes. In the current study, analysis of 35 species representing a wide range of the phylogenetic diversity of Trichoderma revealed that 22 species had tri5, but only 13 species had both tri5 and the tri cluster. tri5 was not located in the cluster in any species. Using complementation analysis of a T. arundinaceum tri5 deletion mutant, we demonstrated that some tri5 homologs from species that lack a tri cluster are functional, but others are not. Phylogenetic analyses suggest that Trichoderma tri5 was under positive selection following its divergence from homologs in other fungi but before Trichoderma species began diverging from one another. We propose two models to explain these diverse observations. One model proposes that the location of tri5 outside the tri cluster resulted from loss of tri5 from the cluster in an ancestral species followed by reacquisition via horizontal transfer. The other model proposes that in species that have a functional tri5 but lack the tri cluster, trichodiene production provides a competitive advantage.

Fusarium chaquense, sp. nov, a novel type A trichothecene-producing species from native grasses in a wetland ecosystem in Argentina

The Chaco wetland is among the most biologically diverse regions in Argentina. In collections of fungi from asymptomatic native grasses (Poaceae) from the wetlands, we identified isolates of Fusarium that were morphologically similar to F. armeniacum, but distinct from it by their production of abundant microconidia. All the isolates had identical, or nearly identical, partial sequences of TEF1 and RPB2. But they were distinct from reference sequences from F. armeniacum and Fusarium species closely related to it. Phylogenetic analysis of 34 full-length housekeeping gene sequences retrieved from whole genome sequences of three Chaco wetland isolates, 29 genes resolved the isolates as an exclusive clade within the F. sambucinum species complex. Based on results of the morphological and phylogenetic analysis, we concluded that the Chaco wetland isolates are a distinct and novel species, herein described as Fusarium chaquense, sp. nov., which is closely related to F. armeniacum. F. chaquense in culture can produce the trichothecenes T-2 and HT-2 toxin, neosolaniol, diacetoxyscirpenol, and monoacetoxyscirpenol, as well as beauvericin and the pigment aurofusarin. Genome sequence analysis also revealed the presence of three previously described loci required for trichothecene biosynthesis. This research represents the first study of Fusarium in a natural ecosystem in Argentina.

The Distribution of Fusarium graminearum and Fusarium asiaticum Causing Fusarium Head Blight of Wheat in Relation to Climate and Cropping System

In the main wheat production area of China (the Huang Huai Plain [HHP]), both Fusarium graminearum and Fusarium asiaticum, the causal agents of Fusarium head blight (FHB), are present. We investigated whether the relative prevalence of F. graminearum and F. asiaticum is related to cropping systems and/or climate factors. A total of 1,844 Fusarium isolates were obtained from 103 fields of two cropping systems: maize-wheat and rice-wheat rotations. To maximize the differences in climatic conditions, isolates were sampled from the north and south HHP regions. Based on the phylogenetic analysis of EF-1α and Tri101 sequences, 1,207 of the 1,844 isolates belonged to F. graminearum, and the remaining 637 isolates belonged to F. asiaticum. The former was predominant in the northern region: 1,022 of the 1,078 Fusarium isolates in the north were F. graminearum. The latter was predominant in the southern region: 581 of the 766 Fusarium isolates belonged to F. asiaticum. Using an analysis based on generalized linear modeling, the relative prevalence of the two species was associated more with climatic conditions than with the cropping system. F. graminearum was associated with drier conditions and cooler conditions during the winter but also with warmer conditions in the infection and grain-colonization period as well as with maize-wheat rotation. The opposite was true for F. asiaticum. Except for the 15-acetyldeoxynvalenol genotype, the trichothecene chemotype composition of F. asiaticum differed between the two cropping systems. The 3-acetyldeoxynivalenol genotype was more prevalent in the maize-wheat rotation, whereas the nivalenol genotype was more prevalent in the rice-wheat rotation. The results also suggested that environmental conditions in the overwintering period appeared to be more important than those in the infection, grain-colonization, and preanthesis sporulation periods in affecting the relative prevalence of F. graminearum and F. asiaticum. More research is needed to study the effect of overwintering conditions on subsequent epidemic in the following spring.

Species Diversity and Toxigenic Potential of Fusarium incarnatum-equiseti Species Complex Isolates from Rice and Soybean in China

Fusarium incarnatum-equiseti species complex (FIESC) strains are generally considered moderately virulent to many agricultural crops and produce a variety of mycotoxins, which represent a serious threat to food safety and public health. The occurrence of the FIESC strain in agricultural crops has been reported in various climatic regions, but detailed information on the species composition and toxigenic ability is rare in China. In this study, phylogenetic analyses were performed with combined sequences of EF-1a and RPB2 of 186 Fusarium isolates obtained from rice (Oryza sativa) and soybean (Glycine max). Twelve species were identified and 156 of the isolates were resolved within the Incarnatum clade of the FIESC species. Host influenced the population composition: rice isolates belonged to 12 species, among which FIESC 16, 18, and 24 strains were predominant; whereas five species were found among soybean isolates and FIESC 1, 16, and 18 strains dominated. Forty-three isolates were arbitrarily selected and analyzed for their Tri gene sequences and mycotoxigenic potential. Phylogenetic results based on the combined Tri5, Tri7, and Tri13 sequences were coincident with those from housekeeping markers. Type-A and -B trichothecenes were the main metabolites. Diacetoxyscirpenol was detected in all strains at varying concentrations. Nivalenol, 4-acetyl nivalenol, 3-acetyl deoxynivalenol, and neosolaniol were produced in members of the FIESC 1, 3, 7, 8, 15, 16, 17, and 18 strains. Our findings contribute valuable phylogenetic and toxigenic information necessary for the risk evaluation of mycotoxins in agricultural products.

Mycotoxin Production in Fusarium According to Contemporary Species Concepts

Fusarium is one of the most important genera of plant-pathogenic fungi in the world and arguably the world's most important mycotoxin-producing genus. Fusarium species produce a staggering array of toxic metabolites that contribute to plant disease and mycotoxicoses in humans and other animals. A thorough understanding of the mycotoxin potential of individual species is crucial for assessing the toxicological risks associated with Fusarium diseases. There are thousands of reports of mycotoxin production by various species, and there have been numerous attempts to summarize them. These efforts have been complicated by competing classification systems based on morphology, sexual compatibility, and phylogenetic relationships. The current depth of knowledge of Fusarium genomes and mycotoxin biosynthetic pathways provides insights into how mycotoxin production is distributedamong species and multispecies lineages (species complexes) in the genus as well as opportunities to clarify and predict mycotoxin risks connected with known and newly described species. Here, we summarize mycotoxin production in the genus Fusarium and how mycotoxin risk aligns with current phylogenetic species concepts.

Phylogenomic Analysis of a 55.1-kb 19-Gene Dataset Resolves a Monophyletic Fusarium that Includes the Fusarium solani Species Complex

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option available.

Colocality to Cofunctionality: Eukaryotic Gene Neighborhoods as a Resource for Function Discovery

Diverging from the classic paradigm of random gene order in eukaryotes, gene proximity can be leveraged to systematically identify functionally related gene neighborhoods in eukaryotes, utilizing techniques pioneered in bacteria. Current methods of identifying gene neighborhoods typically rely on sequence similarity to characterized gene products. However, this approach is not robust for nonmodel organisms like algae, which are evolutionarily distant from well-characterized model organisms. Here, we utilize a comparative genomic approach to identify evolutionarily conserved proximal orthologous gene pairs conserved across at least two taxonomic classes of green algae. A total of 317 gene neighborhoods were identified. In some cases, gene proximity appears to have been conserved since before the streptophyte–chlorophyte split, 1,000 Ma. Using functional inferences derived from reconstructed evolutionary relationships, we identified several novel functional clusters. A putative mycosporine-like amino acid, “sunscreen,” neighborhood contains genes similar to either vertebrate or cyanobacterial pathways, suggesting a novel mosaic biosynthetic pathway in green algae. One of two putative arsenic-detoxification neighborhoods includes an organoarsenical transporter (ArsJ), a glyceraldehyde 3-phosphate dehydrogenase-like gene, homologs of which are involved in arsenic detoxification in bacteria, and a novel algal-specific phosphoglycerate kinase-like gene. Mutants of the ArsJ-like transporter and phosphoglycerate kinase-like genes in Chlamydomonas reinhardtii were found to be sensitive to arsenate, providing experimental support for the role of these identified neighbors in resistance to arsenate. Potential evolutionary origins of neighborhoods are discussed, and updated annotations for formerly poorly annotated genes are presented, highlighting the potential of this strategy for functional annotation.

Evaluation of Mycotoxin Production and Phytopathogenicity of the Entomopathogenic Fungi Fusarium caatingaense and F. pernambucanum from Brazil

Fusarium incarnatum-equiseti species complex (FIESC) is considered as one of the richest insecticolous species. Fusarium species synthesize toxic secondary metabolites that are not fully understood. Mycotoxin production and pathogenicity on germinating seeds, seedlings, and leaves must be carefully studied for the use of Fusarium species in the biological control of insect pests. In this study, we evaluated the mycotoxin production and phytopathogenic potential of entomopathogenic strains of Fusarium sulawesiensis (1), F. pernambucanum (3), and F. caatingaense (23). The phytopathogenicity tests of F. caatingaense (URM 6776, URM 6777, URM 6778, URM 6779, and URM 6782) were performed during the development of bean (Phaseolus vulgaris, Vigna unguiculata, and Phaseolus lunatus), and corn (Zea mays) seedlings, using four treatments (soil infestation with the inoculum, spraying on leaves, root dip, and negative control). The mycotoxins, monoacetyl-deoxynivalenols (AcDON), deoxynivalenol (DON), beauvericin (BEA), fusarenone-X (FUS), T-2 toxin (T2), diacetoxyscirpenol (DAS), and zearalenone (ZEA), were detected in the study; BEA (detected in 25 strains) and FUS (detected in 21 strains) were found to be predominant. None of the strains showed any ability to cause disease or virulence in beans and corn. The FIESC strains showed a highly variable production of mycotoxins without the potential to be used as phytopathogenic agents for the cultures tested.

Phylogenetic diversity, trichothecene potential, and pathogenicity within Fusarium sambucinum species complex

The Fusarium sambucinum species complex (FSAMSC) is one of the most taxonomically challenging groups of fusaria, comprising prominent mycotoxigenic plant pathogens and other species with various lifestyles. Among toxins produced by members of the FSAMSC, trichothecenes pose the most significant threat to public health. Herein a global collection of 171 strains, originating from diverse hosts or substrates, were selected to represent FSAMSC diversity. This strain collection was used to assess their species diversity, evaluate their potential to produce trichothecenes, and cause disease on wheat. Maximum likelihood and Bayesian analyses of a combined 3-gene dataset used to infer evolutionary relationships revealed that the 171 strains originally received as 48 species represent 74 genealogically exclusive phylogenetically distinct species distributed among six strongly supported clades: Brachygibbosum, Graminearum, Longipes, Novel, Sambucinum, and Sporotrichioides. Most of the strains produced trichothecenes in vitro but varied in type, indicating that the six clades correspond to type A, type B, or both types of trichothecene-producing lineages. Furthermore, five strains representing two putative novel species within the Sambucinum Clade produced two newly discovered type A trichothecenes, 15-keto NX-2 and 15-keto NX-3. Strains of the two putatively novel species together with members of the Graminearum Clade were aggressive toward wheat when tested for pathogenicity on heads of the susceptible cultivar Apogee. In planta, the Graminearum Clade strains produced nivalenol or deoxynivalenol and the aggressive Sambucinum Clade strains synthesized NX-3 and 15-keto NX-3. Other strains within the Brachygibbosum, Longipes, Novel, Sambucinum, and Sporotrichioides Clades were nonpathogenic or could infect the inoculated floret without spreading within the head. Moreover, most of these strains did not produce any toxin in the inoculated spikelets. These data highlight aggressiveness toward wheat appears to be influenced by the type of toxin produced and that it is not limited to members of the Graminearum Clade.

Antagonistic action of Streptomyces pratensis S10 on Fusarium graminearum and its complete genome sequence

Wheat scab, mainly caused by Fusarium graminearum, can decrease wheat yield and grain quality. Chemical pesticides are currently the main control method but have an inevitable negative consequence on the environment and in food safety. This research studies a promising substitute, Streptomyces pratensis S10, which was isolated from tomato leaf mould and shows a significant inhibition effect on F. graminearum based on antagonism assays. The biocontrol mechanism is studied by enhanced green fluorescent protein labelling, quantitative real-time PCR, the Doskochilova 8 solvents system test and complete genome sequencing. Strain S10 can colonize in the wheat root, control wheat scab and decrease deoxynivalenol (DON) content. The control effects in vitro, planta and the plot experiments were 92.86%, 68.67% and 40.87% to 86.62%, respectively. S10 decreased DON content by inhibiting the mycelium growth and DON synthesis gene expression. The active substances of the S10 secondary metabolites had a high-temperature resistance and 29 putative biosynthetic gene clusters in its genome. The S10 control mechanism is multivariate, which shows potential in controlling wheat scab.

The Fusarium graminearum t-SNARE Sso2 Is Involved in Growth, Defense, and DON Accumulation and Virulence

The plant-pathogenic fungus Fusarium graminearum, causal agent of Fusarium head blight (FHB) disease on small grain cereals, produces toxic trichothecenes that require facilitated export for full virulence. Two potential modes of mycotoxin transport are membrane-bound transporters, which move toxins across cellular membranes, and N-ethylmaleimide-sensitive factor attachment receptor (SNARE)-mediated vesicular transport, by which toxins may be packaged as cargo in vesicles bound for organelles or the plasma membrane. In this study, we show that deletion of a gene (Sso2) for a subapically localized t-SNARE protein results in growth alteration, increased sensitivity to xenobiotics, altered gene expression profiles, and reduced deoxynivalenol (DON) accumulation in vitro and in planta as well as reduced FHB symptoms on wheat. A double deletion mutant generated by crossing the ∆sso2 deletion mutant with an ATP-binding cassette transporter deletion mutant (∆abc1) resulted in an additive reduction in DON accumulation and almost complete loss of FHB symptoms in planta. These results suggest an important role of Sso2-mediated subapical exocytosis in FHB progression and xenobiotic defense and are the first report of an additive reduction in F. graminearum DON accumulation upon deletion of two distinct modes of cellular export. This research provides useful information which may aid in formulating novel management plans of FHB or other destructive plant diseases.

Biosynthetic gene clusters and the evolution of fungal chemodiversity

Covering: up to 2019Fungi produce a remarkable diversity of secondary metabolites: small, bioactive molecules not required for growth but which are essential to their ecological interactions with other organisms. Genes that participate in the same secondary metabolic pathway typically reside next to each other in fungal genomes and form biosynthetic gene clusters (BGCs). By synthesizing state-of-the-art knowledge on the evolution of BGCs in fungi, we propose that fungal chemodiversity stems from three molecular evolutionary processes involving BGCs: functional divergence, horizontal transfer, and de novo assembly. We provide examples of how these processes have contributed to the generation of fungal chemodiversity, discuss their relative importance, and outline major, outstanding questions in the field.

Signatures of TRI5, TRI8 and TRI11 Protein Sequences of Fusarium incarnatum-equiseti Species Complex (FIESC) Indicate Differential Trichothecene Analogue Production

The variability and phylogeny among TRI5, TRI8 and TRI11 nucleotide and translated protein sequences of isolates from Trinidad belonging to Fusarium incarnatum-equiseti species complex (FIESC) were compared with FIESC reference sequences. Taxa appeared to be more divergent when DNA sequences were analyzed compared to protein sequences. Neutral and non-neutral mutations in TRI protein sequences that may correspond to variability in the function and structure of the selected TRI proteins were identified. TRI5p had the lowest amino acid diversity with zero predicted non-neutral mutations. TRI5p had potentially three protein disorder regions compared to TRI8p with five protein disorder regions. The deduced TRI11p was more conserved than TRI8p of the same strains. Amino acid substitutions that may be non-neutral to protein function were only detected in diacetoxyscirpenol (DAS) and fusarenon-X (FUS-X) producers of the reference sequence subset for TRI8p and TRI11p. The deduced TRI5 and TRI8 amino acid sequences were mapped to known 3D-structure models and indicated that variations in specific protein order/disorder regions exist in these sequences which affect the overall structural conservation of TRI proteins. Assigning single or combination non-neutral mutations to a particular toxicogenic phenotype may be more representative of potential compared to using genotypic data alone, especially in the absence of wet-lab, experimental validation.

Genetic bases for variation in structure and biological activity of trichothecene toxins produced by diverse fungi

Trichothecenes are sesquiterpene toxins produced by diverse but relatively few fungal species in at least three classes of Ascomycetes: Dothideomycetes, Eurotiomycetes, and Sordariomycetes. Approximately 200 structurally distinct trichothecene analogs have been described, but a given fungal species typically produces only a small subset of analogs. All trichothecenes share a core structure consisting of a four-ring nucleus known as 12,13-epoxytrichothec-9-ene. This structure can be substituted at various positions with hydroxyl, acyl, or keto groups to give rise to the diversity of trichothecene structures that has been described. Over the last 30 years, the genetic and biochemical pathways required for trichothecene biosynthesis in several species of the fungi Fusarium and Trichoderma have been elucidated. In addition, phylogenetic and functional analyses of trichothecene biosynthetic (TRI) genes from fungi in multiple genera have provided insights into how acquisition, loss, and changes in functions of TRI genes have given rise to the diversity of trichothecene structures. These analyses also suggest both divergence and convergence of TRI gene function during the evolutionary history of trichothecene biosynthesis. What has driven trichothecene structural diversification remains an unanswered question. However, insight into the role of trichothecenes in plant pathogenesis of Fusarium species and into plant glucosyltransferases that detoxify the toxins by glycosylating them point to a possible driver. Because the glucosyltransferases can have substrate specificity, changes in trichothecene structures produced by a fungus could allow it to evade detoxification by the plant enzymes. Thus, it is possible that advantages conferred by evading detoxification have contributed to trichothecene structural diversification. KEY POINTS : • TRI genes have evolved by diverse processes: loss, acquisition and changes in function. • Some TRI genes have acquired the same function by convergent evolution. • Some other TRI genes have evolved divergently to have different functions. • Some TRI genes were acquired or resulted from diversification in function of other genes. • Substrate specificity of plant glucosyltransferases could drive trichothecene diversity.

Enlightening Gliotoxin Biological System in Agriculturally Relevant Trichoderma spp

Gliotoxin (GT) is a dual fungal secondary metabolite (SM). It displays pleiotropic activities and possesses medicinal properties and biocontrol abilities but, unfortunately, has toxic properties in humans. Various Trichoderma species are used as fungal biological control agents (BCAs), as a sustainable alternative for crop protection worldwide. Among them is Trichoderma virens, a GT-producing fungus. Since no information was available on the genetically coded prerequisites for the production of GT in other Trichoderma spp., genome analyses were carried out in 10 Trichoderma spp. genomes. Moreover, a real-time PCR assay setup ad hoc and high-performance liquid chromatography (HPLC) analyses were employed to understand the GT-producing biological systems in T. virens GV29-8 (TvGv29-8) and Trichoderma afroharzianum T6776 (TaT6776), two relevant biocontrol fungi. The structure of the GT biosynthesis genes (GT-BG) is polymorphic, with two distinct types associated with the ability to produce GT. GliH, a key protein for GT synthesis, is absent in most of the Trichoderma GT biosynthetic pathways, which may be the reason for their inability to produce GT. The GT-BG are expressed in TvGv29-8 as expected, while they are silent in TaT6776. Interestingly, in the GT-non-producing TaT6776, only gliA (putative GT transporter) and gtmA (putative GT S-methyltransferase) were induced by exogenous GT, underlining the ability of this strain to reduce the deleterious effect of the toxin. This ability is confirmed by growth assays and by the detection of the bis-thiomethylated form of GT catalyzed by GtmA in the culture medium supplemented with GT. To the best of our knowledge, this is the first general description of the GT biological system in different Trichoderma spp. as far as the GT-BG content and organization is concerned and a preliminary insight into their functionality.

Pathogenicity and Virulence Factors of Fusarium graminearum Including Factors Discovered Using Next Generation Sequencing Technologies and Proteomics

Fusarium graminearum is a devasting mycotoxin-producing pathogen of grain crops. F. graminearum has been extensively studied to understand its pathogenicity and virulence factors. These studies gained momentum with the advent of next-generation sequencing (NGS) technologies and proteomics. NGS and proteomics have enabled the discovery of a multitude of pathogenicity and virulence factors of F. graminearum. This current review aimed to trace progress made in discovering F. graminearum pathogenicity and virulence factors in general, as well as pathogenicity and virulence factors discovered using NGS, and to some extent, using proteomics. We present more than 100 discovered pathogenicity or virulence factors and conclude that although a multitude of pathogenicity and virulence factors have already been discovered, more work needs to be done to take advantage of NGS and its companion applications of proteomics.

Gain and loss of a transcription factor that regulates late trichothecene biosynthetic pathway genes in Fusarium

Trichothecenes are among the mycotoxins of most concern to food and feed safety and are produced by species in two lineages of Fusarium: the F. incarnatum-equiseti (FIESC) and F. sambucinum (FSAMSC) species complexes. Previous functional analyses of the trichothecene biosynthetic gene (TRI) cluster in members of FSAMSC indicate that the transcription factor gene TRI6 activates expression of other TRI cluster genes. In addition, previous sequence analyses indicate that the FIESC TRI cluster includes TRI6 and another uncharacterized transcription factor gene (hereafter TRI21) that was not reported in FSAMSC. Here, gene deletion analysisindicated that in FIESC TRI6 functions in a manner similar to FSAMSC, whereas TRI21 activated expression of some genes that function late in the trichothecene biosynthetic pathway but not early-pathway genes. Consistent with this finding, TRI21 was required for formation of diacetoxyscripenol, a late-trichothecene-pathway product, but not for isotrichodermin, an early-pathway product. Although intact homologs of TRI21 were not detected in FSAMSC or other trichothecene-producing fungal genera, TRI21 fragments were detected in some FSAMSC species. This suggests that the gene was acquired by Fusarium after divergence from other trichothecene-producing fungi, was subsequently lost in FSAMSC, but was retained in FIESC. Together, our results indicate fundamental differences in regulation of trichothecene biosynthesis in FIESC and FSAMSC.

Fusarium-Produced Mycotoxins in Plant-Pathogen Interactions

Pathogens belonging to the Fusarium genus are causal agents of the most significant crop diseases worldwide. Virtually all Fusarium species synthesize toxic secondary metabolites, known as mycotoxins; however, the roles of mycotoxins are not yet fully understood. To understand how a fungal partner alters its lifestyle to assimilate with the plant host remains a challenge. The review presented the mechanisms of mycotoxin biosynthesis in the Fusarium genus under various environmental conditions, such as pH, temperature, moisture content, and nitrogen source. It also concentrated on plant metabolic pathways and cytogenetic changes that are influenced as a consequence of mycotoxin confrontations. Moreover, we looked through special secondary metabolite production and mycotoxins specific for some significant fungal pathogens-plant host models. Plant strategies of avoiding the Fusarium mycotoxins were also discussed. Finally, we outlined the studies on the potential of plant secondary metabolites in defense reaction to Fusarium infection.

Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts

Background

Macrophomina phaseolina is a fungal plant pathogen with a broad host range, but one genotype was shown to exhibit host preference/specificity on strawberry. This pathogen lacked a high-quality genome assembly and annotation, and little was known about genomic differences among isolates from different hosts.

Results

We used PacBio sequencing and Hi-C scaffolding to provide nearly complete genome assemblies for M. phaseolina isolates representing the strawberry-specific genotype and another genotype recovered from alfalfa. The strawberry isolate had 59 contigs/scaffolds with an N50 of 4.3 Mb. The isolate from alfalfa had an N50 of 5.0 Mb and 14 nuclear contigs with half including telomeres. Both genomes were annotated with MAKER using transcript evidence generated in this study with over 13,000 protein-coding genes predicted. Unique groups of genes for each isolate were identified when compared to closely related fungal species. Structural comparisons between the isolates reveal large-scale rearrangements including chromosomal inversions and translocations. To include isolates representing a range of pathogen genotypes, an additional 30 isolates were sequenced with Illumina, assembled, and compared to the strawberry genotype assembly. Within the limits of comparing Illumina and PacBio assemblies, no conserved structural rearrangements were identified among the isolates from the strawberry genotype compared to those from other hosts, but some candidate genes were identified that were largely present in isolates of the strawberry genotype and absent in other genotypes.

Conclusions

High-quality reference genomes of M. phaseolina have allowed for the identification of structural changes associated with a genotype that has a host preference toward strawberry and will enable future comparative genomics studies. Having more complete assemblies allows for structural rearrangements to be more fully assessed and ensures a greater representation of all the genes. Work with Illumina data from additional isolates suggests that some genes are predominately present in isolates of the strawberry genotype, but additional work is needed to confirm the role of these genes in pathogenesis. Additional work is also needed to complete the scaffolding of smaller contigs identified in the strawberry genotype assembly and to determine if unique genes in the strawberry genotype play a role in pathogenicity.

Efflux pumps as an additional source of resistance to trichothecenes in Fusarium proliferatum and Fusarium oxysporum isolates

Role of efflux-mediated toxin resistance to trichothecenes is known in trichothecene-producing species. However, the role of trichothecene efflux pump homologues in non-producing fusaria such as F. oxysporum and F. proliferatum was not investigated in detail. Analysis of the homologues of trichothecene efflux pump from multiple fungal species allowed us to uncover and catalogue functional gene copies of conserved structure. Putative Tri12 candidates in Fusarium oxysporum and F. proliferatum were characterised via expression profiling in response to different trigger compounds, providing supporting evidence for role of Tri12 homologues in the resistance to trichothecenes. Our analysis of Tri12 phylogeny also suggests that efflux-mediated trichothecene resistance is likely to predate the divergence of Trichoderma and Fusarium species. On the regulatory level, we posit that the increased tolerance of trichothecenes by F. oxysporum is possibly related to the decoupling of Tri12 homologue expression from pH, due to the deletion of PACC/RIM101 transcription factor binding site in its promoter region.

The birth, evolution and death of metabolic gene clusters in fungi

Fungi contain a remarkable diversity of both primary and secondary metabolic pathways involved in ecologically specialized or accessory functions. Genes in these pathways are frequently physically linked on fungal chromosomes, forming metabolic gene clusters (MGCs). In this Review, we describe the diversity in the structure and content of fungal MGCs, their population-level and species-level variation, the evolutionary mechanisms that underlie their formation, maintenance and decay, and their ecological and evolutionary impact on fungal populations. We also discuss MGCs from other eukaryotes and the reasons for their preponderance in fungi. Improved knowledge of the evolutionary life cycle of MGCs will advance our understanding of the ecology of specialized metabolism and of the interplay between the lifestyle of an organism and genome architecture.

Neotypification of Fusarium chlamydosporum - a reappraisal of a clinically important species complex

Fusarium chlamydosporum represents a well-defined morpho-species of both phytopathological and clinical importance. Presently, five phylo-species lacking Latin binomials have been resolved in the F. chlamydosporum species complex (FCSC). Naming these phylo-species is complicated due to the lack of type material for F. chlamydosporum. Over the years a number of F. chlamydosporum isolates (which were formerly identified based on morphology only) have been accessioned in the culture collection of the Westerdijk Fungal Biodiversity Institute. The present study was undertaken to correctly identify these 'F. chlamydosporum' isolates based on multilocus phylogenetic inference supported by morphological characteristics. Closer scrutiny of the metadata associated with one of these isolates allowed us to propose a neotype for F. chlamydosporum. Phylogenetic inference revealed the presence of nine phylo-species within the FCSC in this study. Of these, eight could be provided with names supported by subtle morphological characters. In addition, a new species, as F. nodosum, is introduced in the F. sambucinum species complex and F. chlamydosporum var. fuscum is raised to species level, as F. coffeatum, in the F. incarnatum-equiseti species complex (FIESC).

Isolation, Molecular Identification and Mycotoxin Profile of Fusarium Species Isolated from Maize Kernels in Iran

Fusarium species are among the most important fungal pathogens of maize, where they cause severe reduction of yield and accumulation of a wide range of harmful mycotoxins in the kernels. In order to identify the Fusarium species and their mycotoxin profiles associated to maize ear rot and kernel contamination in Iran, a wide sampling was carried out from field in ten major maize-producing provinces in Iran, during 2015 and 2016. From 182 samples of maize kernels, 551 strains were isolated and identified as belonging to Fusarium genus. Among the 234 representative strains identified at species level by translation elongation factor (EF-1α) sequences, the main Fusarium species were F. verticillioides and F. proliferatum, together representing 90% of the Iranian Fusarium population, and, to a lesser extent, F. incarnatum equiseti species complex (FIESC), F. thapsinum and F. redolens. Fumonisin (FBs) production by F. verticillioides and F. proliferatum representative strains was analysed, showing that all strains produced FB₁. None of F. verticillioides strains produced FB₂ nor FB₃, while both FB₂ and FB₃ were produced only by F. proliferatum. Total mean of FBs production by F. verticillioides was higher than F. proliferatum. The occurrence of different Fusarium species on Iranian maize is reason of great concern because of the toxigenic risk associated to these species. Moreover, the diversity of the species identified increases the toxigenic risk associated to Fusarium contaminated maize kernels, because of the high possibility that a multi-toxin contamination can occur with harmful consequences on human and animal health.

Variation in secondary metabolite production potential in the Fusarium incarnatum-equiseti species complex revealed by comparative analysis of 13 genomes

Background

The Fusarium incarnatum-equiseti species complex (FIESC) comprises 33 phylogenetically distinct species that have been recovered from diverse biological sources, but have been most often isolated from agricultural plants and soils. Collectively, members of FIESC can produce diverse mycotoxins. However, because the species diversity of FIESC has been recognized only recently, the potential of species to cause mycotoxin contamination of crop plants is unclear. In this study, therefore, we used comparative genomics to investigate the distribution of and variation in genes and gene clusters responsible for the synthesis of mycotoxins and other secondary metabolites (SMs) in FIESC.

Results

We examined genomes of 13 members of FIESC that were selected based primarily on their phylogenetic diversity and/or occurrence on crops. The presence and absence of SM biosynthetic gene clusters varied markedly among the genomes. For example, the trichothecene mycotoxin as well as the carotenoid and fusarubin pigment clusters were present in all genomes examined, whereas the enniatin, fusarin, and zearalenone mycotoxin clusters were present in only some genomes. Some clusters exhibited discontinuous patterns of distribution in that their presence and absence was not correlated with the phylogenetic relationships of species. We also found evidence that cluster loss and horizontal gene transfer have contributed to such distribution patterns. For example, a combination of multiple phylogenetic analyses suggest that five NRPS and seven PKS genes were introduced into FIESC from other Fusarium lineages.

Conclusion

Our results suggest that although the portion of the genome devoted to SM biosynthesis has remained similar during the evolutionary diversification of FIESC, the ability to produce SMs could be affected by the different distribution of related functional and complete gene clusters.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5567-7) contains supplementary material, which is available to authorized users.

Complete biosynthetic pathways of ascofuranone and ascochlorin in Acremonium egyptiacum

Ascofuranone (AF) and ascochlorin (AC) are meroterpenoids produced by various filamentous fungi, including Acremonium egyptiacum (synonym: Acremonium sclerotigenum), and exhibit diverse physiological activities. In particular, AF is a promising drug candidate against African trypanosomiasis and a potential anticancer lead compound. These compounds are supposedly biosynthesized through farnesylation of orsellinic acid, but the details have not been established. In this study, we present all of the reactions and responsible genes for AF and AC biosyntheses in A. egyptiacum, identified by heterologous expression, in vitro reconstruction, and gene deletion experiments with the aid of a genome-wide differential expression analysis. Both pathways share the common precursor, ilicicolin A epoxide, which is processed by the membrane-bound terpene cyclase (TPC) AscF in AC biosynthesis. AF biosynthesis branches from the precursor by hydroxylation at C-16 by the P450 monooxygenase AscH, followed by cyclization by a membrane-bound TPC AscI. All genes required for AC biosynthesis (ascABCDEFG) and a transcriptional factor (ascR) form a functional gene cluster, whereas those involved in the late steps of AF biosynthesis (ascHIJ) are present in another distantly located cluster. AF is therefore a rare example of fungal secondary metabolites requiring multilocus biosynthetic clusters, which are likely to be controlled by the single regulator, AscR. Finally, we achieved the selective production of AF in A. egyptiacum by genetically blocking the AC biosynthetic pathway; further manipulation of the strain will lead to the cost-effective mass production required for the clinical use of AF.

Selection of Fusarium Trichothecene Toxin Genes for Molecular Detection Depends on TRI Gene Cluster Organization and Gene Function

Food security is a global concern. Fusarium are among the most economically important fungal pathogens because they are ubiquitous, disease management remains a challenge, they produce mycotoxins that affect food and feed safety, and trichothecene mycotoxin production can increase the pathogenicity of some Fusarium species depending on the host species. Although trichothecenes may differ in structure by their patterns of hydroxylation or acetylation, these small changes have a significant impact on toxicity and the biological activity of these compounds. Therefore, detecting and identifying which chemotype is present in a given population are important to predicting the specific toxins that may be produced and, therefore, to evaluating the risk of exposure. Due to the challenges of inducing trichothecene production by Fusarium isolates in vitro for subsequent chemical analysis, PCR assays using gene-specific primers, either singly or in combination, designed against specific genes of the trichothecene gene cluster of multiple species of Fusarium have been developed. The establishment of TRI genotypes that potentially correspond to a specific chemotype requires examination of an information and knowledge pipeline whose critical aspects in sequential order are: (i) understanding the TRI gene cluster organization which differs according to Fusarium species under study; (ii) knowledge of the re-arrangements to the core TRI gene cluster over evolutionary time, which also differs according to Fusarium species; (iii) the functions of the TRI genes in the biosynthesis of trichothecene analogs; and (iv) based on (i)⁻(iii), selection of appropriate target TRI gene(s) for primer design in PCR amplification for the Fusarium species under study. This review, therefore, explains this pipeline and its connection to utilizing TRI genotypes as a possible proxy to chemotype designation.