Intraspecies Interaction of Fusarium graminearum Contributes to Reduced Toxin Production and Virulence

The landscape and predicted roles of structural variants in Fusarium graminearum genomes

Structural rearrangements, such as inversions, translocations, duplications, and large insertions and deletions, are large-scale genomic variants that can play an important role in shaping phenotypic variation and in genome adaptation and evolution. We used chromosomal-level assemblies from eight Fusarium graminearum isolates to study structural variants and their role in fungal evolution. We generated the assemblies of four of these genomes after Oxford Nanopore sequencing. A total of 87 inversions, 159 translocations, 245 duplications, 58,489 insertions, and 34,102 deletions were detected. Regions of high recombination rate are associated with structural rearrangements, and a significant proportion of inversions, translocations, and duplications overlap with the repeat content of the genome, suggesting recombination and repeat elements are major factors in the origin of structural rearrangements in F. graminearum. Large insertions and deletions introduce presence-absence polymorphisms for many genes, including secondary metabolite biosynthesis cluster genes and predicted effectors genes. Translocation events were found to be shuffling predicted effector-rich regions of the genomes and are likely contributing to the gain and loss of effectors facilitated by recombination. Breakpoints of some structural rearrangements fall within coding sequences and are likely altering the protein products. Structural rearrangements in F. graminearum thus have an important role to play in shaping pathogen-host interactions and broader evolution through genome reorganization, the introduction of presence-absence polymorphisms, and changing protein products and gene regulation.

The Role of Mycotoxins in Interactions between Fusarium graminearum and F. verticillioides Growing in Saprophytic Cultures and Co-Infecting Maize Plants

Fusarium graminearum (FG) and Fusarium verticillioides (FV) co-occur in infected plants and plant residues. In maize ears, the growth of FV is stimulated while FG is suppressed. To elucidate the role of mycotoxins in these effects, we used FG mutants with disrupted synthesis of nivalenol (NIV) and deoxynivalenol (DON) and a FV mutant with disrupted synthesis of fumonisins to monitor fungal growth in mixed cultures in vitro and in co-infected plants by real-time PCR. In autoclaved grains as well as in maize ears, the growth of FV was stimulated by FG regardless of the production of DON or NIV by the latter, whereas the growth of FG was suppressed. In autoclaved grains, fumonisin-producing FV suppressed FG more strongly than a fumonisin-nonproducing strain, indicating that fumonisins act as interference competition agents. In co-infected maize ears, FG suppression was independent of fumonisin production by FV, likely due to heterogeneous infection and a lower level of fumonisins in planta. We conclude that (i) fumonisins are agents of interference competition of FV, and (ii) trichothecenes play no role in the interaction between FG and FV. We hypothesize the following: (i) In vitro, FG stimulates the FV growth by secreting hydrolases that mobilize nutrients. In planta, suppression of plant defense by FG may additionally play a role. (ii) The biological function of fumonisin production in planta is to protect kernels shed on the ground by accumulating protective metabolites before competitors become established. Therefore, to decipher the biological function of mycotoxins, the entire life history of mycotoxin producers must be considered.

Divergent Outcomes of Direct Conspecific Pathogen Strain Interaction and Plant Co-Infection Suggest Consequences for Disease Dynamics

Plant diseases are often caused by co-infections of multiple pathogens with the potential to aggravate disease severity. In genetically diverse pathogen species, co-infections can also be caused by multiple strains of the same species. However, the outcome of such mixed infections by different conspecific genotypes is poorly understood. The interaction among pathogen strains with complex lifestyles outside and inside of the host are likely shaped by diverse traits, including metabolic capacity and the ability to overcome host immune responses. To disentangle competitive outcomes among pathogen strains, we investigated the fungal wheat pathogen Zymoseptoria tritici. The pathogen infects wheat leaves in complex strain assemblies, and highly diverse populations persist between growing seasons. We investigated a set of 14 genetically different strains collected from the same field to assess both competitive outcomes under culture conditions and on the host. Growth kinetics of cocultured strains (~100 pairs) significantly deviated from single strain expectations, indicating competitive exclusion depending on the strain genotype. We found similarly complex outcomes of lesion development on plant leaves following co-infections by the same pairs of strains. While some pairings suppressed overall damage to the host, other combinations exceeded expectations of lesion development based on single strain outcomes. Strain competition outcomes in the absence of the host were poor predictors of outcomes on the host, suggesting that the interaction with the plant immune system adds significant complexity. Intraspecific co-infection dynamics likely make important contributions to disease outcomes in the wild. IMPORTANCE Plants are often attacked by a multitude of pathogens simultaneously, and different species can facilitate or constrain the colonization by others. To what extent simultaneous colonization by different strains of the same species matters, remains unclear. We focused on intra-specific interactions between strains of the major fungal wheat pathogen Zymoseptoria tritici. The pathogen persists in the environment before infecting plant leaves early in the growing season. Leaves are typically colonized by a multitude of strains. Strains cultured in pairs without host were growing differently compared to strains cultured alone. Wheat leaves infected either with single or pairs of strains, we found also highly variable outcomes. Interactions between strains outside of the host were only poorly explaining how strains would interact when on the host, suggesting that pathogen strains engage in complex interactions dependent on the environment. Better understanding within-species interactions will improve our ability to manage crop infections.

Protocooperative Effect of Sphaerodes mycoparasitica Biocontrol and Crop Genotypes on FHB Mycotoxin Reduction in Bread and Durum Wheat Grains Intended for Human and Animal Consumption

The occurrence of Fusarium Head Blight (FHB) mycotoxins in wheat grains is a major threat to global food safety and security. Humans and animals are continuously being exposed to Fusarium mycotoxins such as deoxynivalenol (DON) and its acetylated derivatives 3ADON and 15ADON through the ingestion of contaminated food or grain-based diet. In this study, a host-specific mycoparasite biocontrol agent (BCA), Sphaerodes mycoparasitica, significantly reduced FHB mycotoxin occurrence in harvested wheat grains from Fusarium graminearum 3ADON chemotype infected plants in greenhouse. Four genotypes of wheat, two common wheat and two durum wheat cultivars with varying FHB resistance levels were used in this study. Principal Coordinate Analysis (PCoA) using Illumina ITS sequences depicted beta diversity changes in Fusarium species indicating that both plant cultivar and BCA treatments influenced the Fusarium species structure and mycotoxin occurrence in grains. Fusarium graminearum complex (cluster A), F. avenaceum and F. acuminatum (cluster B), and F. proliferatum (cluster C) variants were associated with different FHB mycotoxins based on LC-MS/MS analyses. The predominant FHB mycotoxins measured were DON and its acetylated derivatives 3ADON and 15ADON. The BCA reduced the occurrence of DON in grains of all four cultivars (common wheat: 1000-30,000 µg·kg^-1.; durum wheat: 600-1000 µg·kg^-1) to levels below the Limit of Quantification (LOQ) of 16 µg·kg^-1. A relatively higher concentration of DON was detected in the two common wheat genotypes when compared to the durum wheat genotype; however, the percentage reduction in the wheat genotypes was greater, reaching up to 99% with some S. mycoparasitica treatments. Similarly, a higher reduction in DON was measured in susceptible genotypes than in resistant genotypes. This study's findings underscore the potential of a Fusarium-specific S. mycoparasitica BCA as a safe and promising alternative that can be used in conjunction with other management practices to minimize FHB mycotoxins in cereal grain, food and feed intended for human and animal consumption.

Unraveling Plant-Pathogen Interactions in Cereals Using RNA-seq

Over the past two decades, there have been significant advancements in the realm of transcriptomics, or the study of genes and their expression. Modern RNA sequencing technologies and high-performance computing are creating a "big data" revolution that provides new opportunities to explore the interactions between cereals and pathogens that affect grain yield and food safety. These data are being used to annotate genes and gene variants, as well as identify differentially expressed genes and create global gene co-expression networks. Moreover, these data can unravel the complex interactions between pathogen and host and identify genes and pathways involved in these interactions. This information can then be used for disease mitigation and the development of crops with superior resistance.

Fusarium graminearum Ste3 G-Protein Coupled Receptor: A Mediator of Hyphal Chemotropism and Pathogenesis

Fungal hyphal chemotropism has been shown to be a major contributor to host-pathogen interactions. Previous studies on Fusarium species have highlighted the involvement of the Ste2 G-protein-coupled receptor (GPCR) in mediating polarized hyphal growth toward host-released peroxidase. Here, the role of the opposite mating type GPCR, Ste3, is characterized with respect to Fusarium graminearum chemotropism and pathogenicity. Fgste3Δ deletion strains were found to be compromised in the chemotropic response toward peroxidase, development of lesions on germinating wheat, and infection of Arabidopsis thaliana leaves. In the absence of FgSte3 or FgSte2, F. graminearum cells exposed to peroxidase showed no phosphorylation of the cell-wall integrity, mitogen-activated protein kinase pathway component Mgv1. In addition, transcriptomic gene expression profiling yielded a list of genes involved in cellular reorganization, cell wall remodeling, and infection-mediated responses that were differentially modulated by peroxidase when FgSte3 was present. Deletion of FgSte3 yielded the downregulation of genes associated with mycotoxin biosynthesis and appressorium development, compared to the wild-type strain, both in the presence of peroxidase. Together, these findings contribute to our understanding of the mechanism underlying fungal chemotropism and pathogenesis while raising the novel hypothesis that FgSte2 and FgSte3 are interdependent on each other for the mediation of the redirection of hyphal growth in response to host-derived peroxidase. IMPORTANCE Fusarium head blight of wheat, caused by the filamentous fungus Fusarium graminearum, leads to devastating global food shortages and economic losses. Fungal hyphal chemotropism has been shown to be a major contributor to host-pathogen interactions. Here, the role of the opposite mating type GPCR, Ste3, is characterized with respect to F. graminearum chemotropism and pathogenicity. These findings contribute to our understanding of the mechanisms underlying fungal chemotropism and pathogenesis.

A survey of Fusarium species and ADON genotype on Canadian wheat grain

Introduction

Wheat is a staple food that is important to global food security, but in epidemic years, fungal pathogens can threaten production, quality, and safety of wheat grain. Globally, one of the most important fungal diseases of wheat is Fusarium head blight (FHB). This disease can be caused by several different Fusarium species with known differences in aggressiveness and mycotoxin-production potential, with the trichothecene toxin deoxynivalenol (DON) and its derivatives being of particular concern. In North America, the most predominant species causing FHB is F. graminearum, which has two distinct sub-populations that are commonly classified into two main chemotypes/genotypes based on their propensity to form trichothecene derivatives, namely 15-acetyldeoxynivalenol (15-ADON) and 3-acetyldeoxynivalenol (3-ADON).

Materials and methods

We used a panel of 13 DNA markers to perform species and ADON genotype identification for 55, 444 wheat kernels from 7, 783 samples originating from across Canada from 2014 to 2020.

Results and discussion

Based on single-seed analyses, we demonstrate the relationships between Fusarium species and trichothecene chemotype with sample year, sample location, wheat species (hexaploid and durum wheat), severity of Fusarium damaged kernels (FDK), and accumulation of DON. Results indicate that various Fusarium species are present across wheat growing regions in Canada; however, F. graminearum is the most common species and 3-ADON the most common genotype. We observed an increase in the occurrence of the 3-ADON genotype, particularly in the western Prairie regions. Our data provides important information on special-temporal trends in Fusarium species and chemotypes that can aid with the implementation of integrated disease management strategies to control the detrimental effects of this devastating disease.

Diversity of Fusarium community assembly shapes mycotoxin accumulation of diseased wheat heads

Fusarium head blight (FHB) is a major disease worldwide on cultivated cereals, caused by several Fusarium species. FHB can cause not only yield reduction but also accumulation of mycotoxins in the grain contaminating the food supply. Much of the earlier research has focused on Fusarium pathogenesis, conditions required for disease development and toxin accumulation, and FHB management. However, the Fusarium community composition within the micro-habitat of a single diseased wheat head in the field has had limited investigation. Similarly, the relationship between the Fusarium community structure and mycotoxin accumulation within diseased heads remains unclear. In the present study, we investigated the Fusarium community in diseased heads sampled from different geographical sites in China. Several sites in Shandong province formed a transitional region which contained highly variable profiles of Fusarium OTUs, where a single diseased head could contain more than 10 Fusarium OTUs. Mycotoxin accumulation was independent of geographical properties, however, deoxynivalenol, 15-acetyldeoxynivalenol and zearalenone concentrations showed a significant negative correlation with Fusarium diversity on diseased heads while a significant positive correlation between nivalenol concentration and Fusarium diversity was observed. Taken together, the Fusarium OTU diversity within diseased heads in the field significantly influences mycotoxin accumulation, providing an important point to consider in FHB disease management and mycotoxin research.

Implications of Crop Rotation and Fungicide on Fusarium and Mycotoxin Spectra in Manitoba Barley, 2017–2019

Fusarium head blight (FHB) is one of the most important diseases of barley in Manitoba province (western Canada), and other major barley producing regions of the world. Little is known about the Fusarium species and mycotoxin spectra associated with FHB of barley in Manitoba. Hence, barley grain samples were collected from 149 commercial fields from 2017 to 2019, along with information on respective cropping history, and analyzed with respect to Fusarium species spectra, abundance, chemotype composition, and mycotoxin profiles. Fusarium poae was the predominant Fusarium species associated with FHB of barley in Manitoba, followed by F. graminearum, and F. sporotrichioides; F. equiseti and F. avenaceum were also detected but at low levels. F. poae strains with the nivalenol (NIV) chemotype and F. graminearum strains with 3-acetyl deoxynivalenol (3-ADON) and 15-acetyl deoxynivalenol (15-ADON) chemotypes were commonly detected in the barley grain samples. Nivalenol (597.7, 219.1, and 412.4 µg kg⁻¹) and deoxynivalenol (DON) (264.7, 56.7, and 65.3 µg kg⁻¹) were the two most prevalent mycotoxins contaminating Manitoba barley in 2017, 2018 and 2019, respectively. A substantially higher DON content was detected in grain samples from barley fields with cereals as a preceding crop compared to canola and flax. Furthermore, F. poae proved less sensitive to four triazole fungicides (metconazole, prothioconazole+tebuconazole, tebuconazole, and prothioconazole) than F. graminearum. Findings from this research will assist barley producers with improved understanding of FHB threat levels and optimizing practices for the best management of FHB in barley.

Fungal pathogens of cereal crops: Proteomic insights into fungal pathogenesis, host defense, and resistance

Fungal infections of cereal crops pose a significant risk to global food security through reduced grain production and quality, as well as contamination of animal feed and human products for consumption. To combat fungal disease, we need to understand how the pathogen adapts and survives within the hostile environment of the host and how the host's defense response can be modulated for protection from disease. Such investigations offer insight into fungal pathogenesis, host immunity, the development of resistance, and mechanisms of action for currently-used control strategies. Mass spectrometry-based proteomics provides a technologically-advanced platform to define differences among fungal pathogens and their hosts at the protein level, supporting the discovery of proteins critical for disease, and uncovering novel host responses driving susceptibly or resistance of the host. In this Review, we explore the role of mass spectrometry-based proteomics in defining the intricate relationship between a pathogen and host during fungal disease of cereal crops with a focus on recent discoveries derived from the globally-devastating diseases of Fusarium head blight, Rice blast, and Powdery mildew. We highlight advances made for each of these diseases and discuss opportunities to extrapolate findings to further our fight against fungal pathogens on a global scale.

The Dominance of Fusarium meridionale Over F. graminearum Causing Gibberella Ear Rot in Brazil May Be Due to Increased Aggressiveness and Competitiveness

In Brazil, Gibberella ear rot (GER) of maize is caused mainly by Fusarium meridionale, whereas F. graminearum is a minor contributor. To test the hypothesis that F. meridionale is more aggressive than F. graminearum on maize, six experiments were conducted in the south (summer) and one in the central-south (winter), totaling seven conditions (year × location × hybrid). Treatments consisted of F. graminearum or F. meridionale (two isolates of each) inoculated once 4 days after silk, inoculated sequentially and alternately (F. graminearum → F. meridionale or F. meridionale → F. graminearum) 6 days apart, or (in the central-south) inoculated sequentially without alternating species (F. meridionale → F. meridionale or F. graminearum → F. graminearum). Overall, severity was two times greater in the south (37.0%), where summer temperatures were warmer (20 to 25°C) than in central-south. In the south, severity was greatest in F. meridionale treatments (67.8%); followed by F. meridionale → F. graminearum (41.1%), then F. graminearum → F. meridionale (19.4%), and lowest in F. graminearum (2.1%), suggesting an antagonistic relationship. In the central-south (15 to 20°C), severity was generally higher in the sequential nonalternating inoculation treatments (F. meridionale → F. meridionale or F. graminearum → F. graminearum) than when either species was inoculated only once. Only nivalenol (NIV) or deoxynivalenol was detected when F. meridionale or F. graminearum, respectively, was inoculated singly, or sequentially with no alternation. Both toxins were found in grains harvested from the F. meridionale → F. graminearum treatment, whereas only NIV was found in kernels from the F. graminearum → F. meridionale treatment, suggesting that F. meridionale was more competitive than F. graminearum in coinoculations. The dominance of F. meridionale as a cause of GER in Brazil may be due in part to its higher aggressiveness and competitiveness compared with F. graminearum.

Transcriptome Alterations of an in vitro-Selected, Moderately Resistant, Two-Row Malting Barley in Response to 3ADON, 15ADON, and NIV Chemotypes of Fusarium graminearum

Fusarium head blight caused by Fusarium graminearum is a devastating disease of malting barley. Mycotoxins associated with contaminated grain can be transferred from malt to beer and pose a health risk to consumers. In western Canada, F. graminearum has undergone an adaptive shift from 15ADON constituency to dominance by virulent 3ADON-producers; likewise, NIV-producers have established in regions of southern United States. Lack of adapted resistance sources with adequate malting quality has promoted the use of alternative breeding methodologies, such as in vitro selection. We studied the low-deoxynivalenol characteristic of in vitro selected, two-row malting barley variety "Norman" by RNAseq in contrast to its parental line "CDC Kendall," when infected by 15ADON-, 3ADON-, and NIV-producing isolates of F. graminearum. The current study documents higher mycotoxin accumulation by 3ADON isolates, thereby representing increased threat to barley production. At 72-96-h post infection, significant alterations in transcription patterns were observed in both varieties with pronounced upregulation of the phenylpropanoid pathway and detoxification gene categories (UGT, GST, CyP450, and ABC), particularly in 3ADON treatment. Defense response was multitiered, where differential expression in "Norman" associated with antimicrobial peptides (thionin 2.1, defensing, non-specific lipid-transfer protein) and stress-related proteins, such as late embryogenesis abundant proteins, heat-shock, desiccation related, and a peroxidase (HvPrx5). Several gene targets identified in "Norman" would be useful for application of breeding varieties with reduced deoxynivalenol content.

Comparative Genomics of Eight Fusarium graminearum Strains with Contrasting Aggressiveness Reveals an Expanded Open Pangenome and Extended Effector Content Signatures

Fusarium graminearum, the primary cause of Fusarium head blight (FHB) in small-grain cereals, demonstrates remarkably variable levels of aggressiveness in its host, producing different infection dynamics and contrasted symptom severity. While the secreted proteins, including effectors, are thought to be one of the essential components of aggressiveness, our knowledge of the intra-species genomic diversity of F. graminearum is still limited. In this work, we sequenced eight European F. graminearum strains of contrasting aggressiveness to characterize their respective genome structure, their gene content and to delineate their specificities. By combining the available sequences of 12 other F. graminearum strains, we outlined a reference pangenome that expands the repertoire of the known genes in the reference PH-1 genome by 32%, including nearly 21,000 non-redundant sequences and gathering a common base of 9250 conserved core-genes. More than 1000 genes with high non-synonymous mutation rates may be under diverse selection, especially regarding the trichothecene biosynthesis gene cluster. About 900 secreted protein clusters (SPCs) have been described. Mostly localized in the fast sub-genome of F. graminearum supposed to evolve rapidly to promote adaptation and rapid responses to the host's infection, these SPCs gather a range of putative proteinaceous effectors systematically found in the core secretome, with the chloroplast and the plant nucleus as the main predicted targets in the host cell. This work describes new knowledge on the intra-species diversity in F. graminearum and emphasizes putative determinants of aggressiveness, providing a wealth of new candidate genes potentially involved in the Fusarium head blight disease.

QTL mapping in Fusarium graminearum identified an allele of FgVe1 involved in reduced aggressiveness

Fusarium graminearum is one of the most frequent causal agents of the Fusarium Head Blight, a cereal disease spread throughout the world, reducing grain production and quality. F. graminearum isolates are genetically and phenotypically highly diverse. Notably, remarkable variations of aggressiveness between isolates have been observed, which could reflect an adaptive potential of this pathogen. In this study, we aimed to characterize the genetic basis of aggressiveness variation observed in an F1 population (n = 94), for which genome sequences of both parental strains are available. Aggressiveness was assessed by a panel of in planta and in vitro proxies during two phenotyping trials including, among others, disease severity and mycotoxin accumulation in wheat spike. One major and single QTL was mapped for all the traits measured, on chromosome I, that explained up to 90% of the variance for disease severity. The confidence interval at the QTL spanned 1.2 Mb and contained 428 genes on the reference genome. Of these, four candidates were selected based on the postulate that a non-synonymous mutation affecting protein function may be responsible for phenotypic differences. Finally, a new mutation was identified and functionally validated in the gene FgVe1, coding for a velvet protein known to be involved in pathogenicity and secondary metabolism production in several fungi.

Fusarium Head Blight From a Microbiome Perspective

The fungal genus Fusarium causes several diseases in cereals, including Fusarium head blight (FHB). A number of Fusarium species are involved in disease development and mycotoxin contamination. Lately, the importance of interactions between plant pathogens and the plant microbiome has been increasingly recognized. In this review, we address the significance of the cereal microbiome for the development of Fusarium-related diseases. Fusarium fungi may interact with the host microbiome at multiple stages during their life cycles and in different plant organs including roots, stems, leaves, heads, and crop residues. There are interactions between Fusarium and other fungi and bacteria as well as among Fusarium species. Recent studies have provided a map of the cereal microbiome and revealed how different biotic and abiotic factors drive microbiome assembly. This review synthesizes the current understanding of the cereal microbiome and the implications for Fusarium infection, FHB development, disease control, and mycotoxin contamination. Although annual and regional variations in predominant species are significant, much research has focused on Fusarium graminearum. Surveying the total Fusarium community in environmental samples is now facilitated with novel metabarcoding methods. Further, infection with multiple Fusarium species has been shown to affect disease severity and mycotoxin contamination. A better mechanistic understanding of such multiple infections is necessary to be able to predict the outcome in terms of disease development and mycotoxin production. The knowledge on the composition of the cereal microbiome under different environmental and agricultural conditions is growing. Future studies are needed to clearly link microbiome structure to Fusarium suppression in order to develop novel disease management strategies for example based on conservation biological control approaches.

DNA Methylation Is Responsive to the Environment and Regulates the Expression of Biosynthetic Gene Clusters, Metabolite Production, and Virulence in Fusarium graminearum

Histone modifications play a significant role in the regulation of biosynthetic gene clusters (BGCs) in the phytopathogen Fusarium graminearum, by contrast, epigenetic regulation by DNA methyltransferases (DNMTs) is less documented. In this study, we characterized two DNMTs (FgDIM-2 and FgRID) in F. graminearum, with homologies to "Deficient in methylation" (DIM-2) and "Repeat-induced point (RIP) deficient" (RID) from Neurospora. The loss of DNMTs resulted in not only a decrease in average methylation density in the nutrient-poor, compared to nutrient-rich conditions, but also differences in the genes expressed between the WT and the DNMT mutant strains, implicating the external environment as an important trigger in altering DNA methylation patterns. Consequently, we observed significant changes in the regulation of multiple BGCs and alterations in the pathogenicity of the fungus.

Histology and RNA Sequencing Provide Insights Into Fusarium Head Blight Resistance in AAC Tenacious

Fusarium head blight (FHB) is a serious fungal disease affecting wheat and other cereals worldwide. This fungus causes severe yield and quality losses from a reduction in grain quality and contamination of grain with mycotoxins. Intensive breeding efforts led to the release of AAC Tenacious, which was the first spring wheat cultivar registered in Canada with a resistant (R) rating to FHB. To elucidate the physiological mechanisms of resistance, we performed histological and transcriptomic analyses of AAC Tenacious and a susceptible control Roblin after inoculation with Fusarium graminearum (Fg). The spikelet and rachis of infected wheat spikes were hand sectioned and monitored by confocal and fluorescent microscopy. Visible hyphae were observed within the inoculated spikelets for AAC Tenacious; however, the infection was largely restricted to the point of inoculation (POI), whereas the adjacent florets in Roblin were heavily infected. Significant cell wall thickening within the rachis node below the POI was evident in AAC Tenacious compared to Roblin in response to Fg inoculation. Rachis node and rachilla tissues from the POI and the rachis node below the POI were collected at 5 days post inoculation for RNAseq. Significant changes in gene expression were detected in both cultivars in response to infection. The rachis node below the POI in AAC Tenacious had fewer differentially expressed genes (DEGs) when compared to the uninoculated control, likely due to its increased disease resistance. Analysis of DEGs in Roblin and AAC Tenacious revealed the activation of genes and pathways in response to infection, including those putatively involved in cell wall modification and defense response.

Divergence and Gene Flow Between Fusarium subglutinans and F. temperatum Isolated from Maize in Argentina

Fusarium subglutinans and F. temperatum are two important fungal pathogens of maize whose distinctness as separate species has been difficult to assess. We isolated strains of these species from commercial and native maize varieties in Argentina and sequenced >28,000 loci to estimate genetic variation in the sample. Our objectives were to measure genetic divergence between the species, infer demographic parameters related to their split, and describe the population structure of the sample. When analyzed together, over 30% of each species' polymorphic sites (>2,500 sites) segregate as polymorphisms in the other. Demographic modeling confirmed the species split predated maize domestication, but subsequent between-species gene flow has occurred, with gene flow from F. subglutinans into F. temperatum greater than gene flow in the reverse direction. In F. subglutinans, little evidence exists for substructure or recent selective sweeps, but there is evidence for limited sexual reproduction. In F. temperatum, there is clear evidence for population substructure and signals of abundant recent selective sweeps, with sexual reproduction probably less common than in F. subglutinans. Both genetic variation and the relative number of polymorphisms shared between species increase near the telomeres of all 12 chromosomes, where genes related to plant-pathogen interactions often are located. Our results suggest that species boundaries between closely related Fusarium species can be semipermeable and merit further study. Such semipermeability could facilitate unanticipated genetic exchange between species and enable quicker permanent responses to changes in the agro-ecosystem, e.g., pathogen-resistant host varieties, new chemical and biological control agents, and agronomic practices.

Intrapopulation Antagonism Can Reduce the Growth and Aggressiveness of the Wheat Head Blight Pathogen Fusarium graminearum

Fusarium graminearum is a causal agent of Fusarium head blight (FHB), a disease that reduces yield and quality of cereal crops and contaminates grain with mycotoxins that pose health risks to humans and livestock. Interpopulation antagonistic interactions between isolates that produce different trichothecene mycotoxins can reduce FHB in wheat, but it is not known if interactions between isolates with a shared population identity that produce the same trichothecenes have a similar effect. Using isolates from the predominant F. graminearum populations in North America (NA1 and NA2), we examined intrapopulation interactions by comparing growth, disease progression, and toxin production of individual isolates with multi-isolate mixes. In vitro, mycelial growth was significantly greater when most NA1 and NA2 isolates were cultured individually versus when cultured as a mixture of isolates from the same population. In susceptible wheat Norm, FHB generally progressed faster in heads inoculated with an individual isolate versus a multi-isolate mixture, but the antagonistic effect of intrapopulation interactions was more pronounced for NA1 than NA2 isolates. By contrast, in moderately resistant wheat Alsen, mixtures of isolates from either population caused obvious reductions in FHB development. Mycotoxin contamination was not consistently affected by intrapopulation interactions and varied depending on the interacting isolates from either population. Our results indicate that antagonistic intrapopulation interactions can influence FHB in controlled environmental conditions. Understanding if the regional composition of pathogen populations similarly influences FHB in the field could improve disease forecasting and management practices.

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.

Trichothecenes in Cereal Grains - An Update

Trichothecenes are sesquiterpenoid mycotoxins produced by fungi from the order Hypocreales, including members of the Fusarium genus that infect cereal grain crops. Different trichothecene-producing Fusarium species and strains have different trichothecene chemotypes belonging to the Type A and B class. These fungi cause a disease of small grain cereals, called Fusarium head blight, and their toxins contaminate host tissues. As potent inhibitors of eukaryotic protein synthesis, trichothecenes pose a health risk to human and animal consumers of infected cereal grains. In 2009, Foroud and Eudes published a review of trichothecenes in cereal grains for human consumption. As an update to this review, the work herein provides a comprehensive and multi-disciplinary review of the Fusarium trichothecenes covering topics in chemistry and biochemistry, pathogen biology, trichothecene toxicity, molecular mechanisms of resistance or detoxification, genetics of resistance and breeding strategies to reduce their contamination of wheat and barley.

Fusarium Head Blight in Durum Wheat: Recent Status, Breeding Directions, and Future Research Prospects

Fusarium head blight (FHB) is a major fungal disease affecting wheat production worldwide. Since the early 1990s, FHB, caused primarily by Fusarium graminearum, has become one of the most significant diseases faced by wheat producers in Canada and the United States. The increasing FHB problem is likely due to the increased adoption of conservation tillage practices, expansion of maize production, use of susceptible wheat varieties in rotation, and climate variability. Durum wheat (Triticum turgidum sp. durum) is notorious for its extreme susceptibility to FHB and breeding for resistance is complicated because sources of FHB resistance are rare in the primary gene pool of tetraploid wheat. Losses due to this disease include yield, test weight, seed quality, food and feed quality, and when severe, market access. More importantly, it is the contamination with mycotoxins, such as deoxynivalenol, in Fusarium-infected durum kernels that causes the most serious economic as well as food and feed safety concerns. Several studies and thorough reviews have been published on germplasm development and breeding for FHB resistance and the genetics and genomics of FHB resistance in bread or common wheat (T. aestivum); however, similar reviews have not been conducted in durum wheat. Thus, the aim of this review is to summarize and discuss the recent research efforts to mitigate FHB in durum wheat, including quantitative trait locus mapping, genome-wide association studies, genomic prediction, mutagenesis and characterization of genes and pathways involved in FHB resistance. It also highlights future directions, FHB-resistant germplasm, and the potential role of morphological traits to enhance FHB resistance in durum wheat.

Redox signalling from NADPH oxidase targets metabolic enzymes and developmental proteins in Fusarium graminearum

NADPH oxidase (NOX) is one of the sources of reactive oxygen species (ROS) that modulates the activity of proteins through modifications of their cysteine residues. In a previous study, we demonstrated the importance of NOX in both the development and pathogenicity of the phytopathogen Fusarium graminearum. In this article, comparative proteomics between the wild-type and a Nox mutant of F. graminearum was used to identify active cysteine residues on candidate redox-sensing proteins. A two-dimensional gel approach based on labelling with monobromobimane (mBBR) identified 19 candidate proteins, and was complemented with a gel-free shotgun approach based on a biotin switch method, which yielded 99 candidates. The results indicated that, in addition to temporal regulation, a large number of primary metabolic enzymes are potentially targeted by NoxAB-generated ROS. Targeted disruption of these metabolic genes showed that, although some are dispensable, others are essential. In addition to metabolic enzymes, developmental proteins, such as the Woronin body major protein (FGSG_08737) and a glycosylphosphatidylinositol (GPI)-anchored protein (FGSG_10089), were also identified. Deletion of either of these genes reduced the virulence of F. graminearum. Furthermore, changing the redox-modified cysteine (Cys325 ) residue in FGSG_10089 to either serine or phenylalanine resulted in a similar phenotype to the FGSG_10089 knockout strain, which displayed reduced virulence and altered cell wall morphology; this underscores the importance of Cys325 to the function of the protein. Our results indicate that NOX-generated ROS act as intracellular signals in F. graminearum and modulate the activity of proteins affecting development and virulence in planta.

High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis

Arbuscular mycorrhizal fungi (AMF) are known to improve plant fitness through the establishment of mycorrhizal symbioses. Genetic and phenotypic variations among closely related AMF isolates can significantly affect plant growth, but the genomic changes underlying this variability are unclear. To address this issue, we improved the genome assembly and gene annotation of the model strain Rhizophagus irregularis DAOM197198, and compared its gene content with five isolates of R. irregularis sampled in the same field. All isolates harbor striking genome variations, with large numbers of isolate-specific genes, gene family expansions, and evidence of interisolate genetic exchange. The observed variability affects all gene ontology terms and PFAM protein domains, as well as putative mycorrhiza-induced small secreted effector-like proteins and other symbiosis differentially expressed genes. High variability is also found in active transposable elements. Overall, these findings indicate a substantial divergence in the functioning capacity of isolates harvested from the same field, and thus their genetic potential for adaptation to biotic and abiotic changes. Our data also provide a first glimpse into the genome diversity that resides within natural populations of these symbionts, and open avenues for future analyses of plant-AMF interactions that link AMF genome variation with plant phenotype and fitness.

Arbuscular mycorrhizal fungi: intraspecific diversity and pangenomes

Contents Summary 1129 I. Introduction 1129 II. Intraspecific phenotypic variation and the plant host 1130 III. High inter-isolate genetic diversity in model AMF 1130 IV. Genome diversity within the model AM fungus Rhizophagus irregularis 1131 V. Pangenomes and the future of AMF ecological genomics 1131 Acknowledgements 1133 References 1133 SUMMARY: Arbuscular mycorrhizal fungi (AMF) are ubiquitous plant symbionts with an intriguing population biology. Conspecific AMF strains can vary substantially at the genetic and phenotypic levels, leading to direct and quantifiable variation in plant growth. Recent studies have shown that high intraspecific diversity is very common in AMF, and not only found in model species. Studies have also revealed how the phenotype of conspecific isolates varies depending on the plant host, highlighting the functional relevance of intraspecific phenotypic plasticity for the AMF ecology and mycorrhizal symbiosis. Recent work has also demonstrated that conspecific isolates of the model AMF Rhizophagus irregularis harbor large and highly variable pangenomes, highlighting the potential role of intraspecific genome diversity for the ecological adaptation of these symbionts.

Population genomics of Fusarium graminearum reveals signatures of divergent evolution within a major cereal pathogen

The cereal pathogen Fusarium graminearum is the primary cause of Fusarium head blight (FHB) and a significant threat to food safety and crop production. To elucidate population structure and identify genomic targets of selection within major FHB pathogen populations in North America we sequenced the genomes of 60 diverse F. graminearum isolates. We also assembled the first pan-genome for F. graminearum to clarify population-level differences in gene content potentially contributing to pathogen diversity. Bayesian and phylogenomic analyses revealed genetic structure associated with isolates that produce the novel NX-2 mycotoxin, suggesting a North American population that has remained genetically distinct from other endemic and introduced cereal-infecting populations. Genome scans uncovered distinct signatures of selection within populations, focused in high diversity, frequently recombining regions. These patterns suggested selection for genomic divergence at the trichothecene toxin gene cluster and thirteen additional regions containing genes potentially involved in pathogen specialization. Gene content differences further distinguished populations, in that 121 genes showed population-specific patterns of conservation. Genes that differentiated populations had predicted functions related to pathogenesis, secondary metabolism and antagonistic interactions, though a subset had unique roles in temperature and light sensitivity. Our results indicated that F. graminearum populations are distinguished by dozens of genes with signatures of selection and an array of dispensable accessory genes, suggesting that FHB pathogen populations may be equipped with different traits to exploit the agroecosystem. These findings provide insights into the evolutionary processes and genomic features contributing to population divergence in plant pathogens, and highlight candidate genes for future functional studies of pathogen specialization across evolutionarily and ecologically diverse fungi.

Transcriptomics of cereal-Fusarium graminearum interactions: what we have learned so far

The ascomycete fungal pathogen Fusarium graminearum causes the globally important Fusarium head blight (FHB) disease on cereal hosts, such as wheat and barley. In addition to reducing grain yield, infection by this pathogen causes major quality losses. In particular, the contamination of food and feed with the F. graminearum trichothecene toxin deoxynivalenol (DON) can have many adverse short- and long-term effects on human and animal health. During the last decade, the interaction between F. graminearum and both cereal and model hosts has been extensively studied through transcriptomic analyses. In this review, we present an overview of how such analyses have advanced our understanding of this economically important plant-microbe interaction. From a host point of view, the transcriptomes of FHB-resistant and FHB-susceptible cereal genotypes, including near-isogenic lines (NILs) that differ by the presence or absence of quantitative trait loci (QTLs), have been studied to understand the mechanisms of disease resistance afforded by such QTLs. Transcriptomic analyses employed to dissect host responses to DON have facilitated the identification of the genes involved in toxin detoxification and disease resistance. From the pathogen point of view, the transcriptome of F. graminearum during pathogenic vs. saprophytic growth, or when infecting different cereal hosts or different tissues of the same host, have been studied. In addition, comparative transcriptomic analyses of F. graminearum knock-out mutants with altered virulence have provided new insights into pathogenicity-related processes. The F. graminearum transcriptomic data generated over the years are now being exploited to build a systems level understanding of the biology of this pathogen, with an ultimate aim of developing effective and sustainable disease prevention strategies.

Landscape of genomic diversity and host adaptation in Fusarium graminearum

BACKGROUND

Fusarium graminearum is one of the main causal agents of the Fusarium Head Blight, a worldwide disease affecting cereal cultures, whose presence can lead to contaminated grains with chemically stable and harmful mycotoxins. Resistant cultivars and fungicides are frequently used to control this pathogen, and several observations suggest an adaptation of F. graminearum that raises concerns regarding the future of current plant disease management strategies. To understand the genetic basis as well as the extent of its adaptive potential, we investigated the landscape of genomic diversity among six French isolates of F. graminearum, at single-nucleotide resolution using whole-genome re-sequencing.

RESULTS

A total of 242,756 high-confidence genetic variants were detected when compared to the reference genome, among which 96% are single nucleotides polymorphisms. One third of these variants were observed in all isolates. Seventy-seven percent of the total polymorphism is located in 32% of the total length of the genome, comprising telomeric/subtelomeric regions as well as discrete interstitial sections, delineating clear variant enriched genomic regions- 7.5 times in average. About 80% of all the F. graminearum protein-coding genes were found polymorphic. Biological functions are not equally affected: genes potentially involved in host adaptation are preferentially located within polymorphic islands and show greater diversification rate than genes fulfilling basal functions. We further identified 29 putative effector genes enriched with non-synonymous effect mutation.

CONCLUSIONS

Our results highlight a remarkable level of polymorphism in the genome of F. graminearum distributed in a specific pattern. Indeed, the landscape of genomic diversity follows a bi-partite organization of the genome according to polymorphism and biological functions. We measured, for the first time, the level of sequence diversity for the entire gene repertoire of F. graminearum and revealed that the majority are polymorphic. Those assumed to play a role in host-pathogen interaction are discussed, in the light of the subsequent consequences for host adaptation. The annotated genetic variants discovered for this major pathogen are valuable resources for further genetic and genomic studies.

Characterization of the Two-Speed Subgenomes of Fusarium graminearum Reveals the Fast-Speed Subgenome Specialized for Adaption and Infection

Fusarium head blight, caused by Fusarium graminearum, is one of the most severe diseases on wheat and barley worldwide. Although the genomic data of several strains were published, the intragenomic variation of F. graminearum was not well characterized. Here, we sequenced three Chinese strains and conducted genome-wide comparisons. Our data revealed that all the sequenced strains were distinct from each other and over 350 genes were functionally lost in each of them. Variants of each strain were unevenly distributed in a highly conserved pattern along the chromosomes, resulting in a conserved two-speed genome. The fast subgenome has a lower GC content, shorter gene length, and higher variation of exon numbers than the slow subgenome. Genes related to interaction and pathogenicity, under positive selection, and up-regulated in planta were all significantly enriched in the fast subgenome. Furthermore, we found that the fast subgenome coincided with facultative heterochromatin regions that were repressed in vegetative stage but activated during infection as measured by RNA-seq and ChIP-seq data, suggesting that the fast subgenome is epigenetically regulated. Taken together, our data demonstrated that F. graminearum has a highly conserved two-speed genome and the fast subgenome responsible for adaption and infection is under the control of heterochromatin.

Whole genome sequencing and comparative genomics of closely related Fusarium Head Blight fungi: Fusarium graminearum, F. meridionale and F. asiaticum

BACKGROUND

The Fusarium graminearum species complex is composed of many distinct fungal species that cause several diseases in economically important crops, including Fusarium Head Blight of wheat. Despite being closely related, these species and individuals within species have distinct phenotypic differences in toxin production and pathogenicity, with some isolates reported as non-pathogenic on certain hosts. In this report, we compare genomes and gene content of six new isolates from the species complex, including the first available genomes of F. asiaticum and F. meridionale, with four other genomes reported in previous studies.

RESULTS

A comparison of genome structure and gene content revealed a 93-99% overlap across all ten genomes. We identified more than 700 k base pairs (kb) of single nucleotide polymorphisms (SNPs), insertions, and deletions (indels) within common regions of the genome, which validated the species and genetic populations reported within species. We constructed a non-redundant pan gene list containing 15,297 genes from the ten genomes and among them 1827 genes or 12% were absent in at least one genome. These genes were co-localized in telomeric regions and select regions within chromosomes with a corresponding increase in SNPs and indels. Many are also predicted to encode for proteins involved in secondary metabolism and other functions associated with disease. Genes that were common between isolates contained high levels of nucleotide variation and may be pseudogenes, allelic, or under diversifying selection.

CONCLUSIONS

The genomic resources we have contributed will be useful for the identification of genes that contribute to the phenotypic variation and niche specialization that have been reported among members of the F. graminearum species complex.

RNA-Seq Revealed Differences in Transcriptomes between 3ADON and 15ADON Populations of Fusarium graminearum In Vitro and In Planta

Fusarium graminearum is the major causal agent of Fusarium head blight (FHB) in barley and wheat in North America. The fungus not only causes yield loss of the crops but also produces harmful trichothecene mycotoxins [Deoxynivalenol (DON) and its derivatives-3-acetyldeoxynivalenol (3ADON) and 15-acetyldeoxynivalenol (15ADON), and nivalenol (NIV)] that contaminate grains. Previous studies showed a dramatic increase of 3ADON-producing isolates with higher aggressiveness and DON production than the 15ADON-producing isolates in North America. However, the genetic and molecular basis of differences between the two types of isolates is unclear. In this study, we compared transcriptomes of the 3ADON and 15ADON isolates in vitro (in culture media) and in planta (during infection on the susceptible wheat cultivar 'Briggs') using RNA-sequencing. The in vitro gene expression comparison identified 479 up-regulated and 801 down-regulated genes in the 3ADON isolates; the up-regulated genes were mainly involved in C-compound and carbohydrate metabolism (18.6%), polysaccharide metabolism (7.7%) or were of unknown functions (57.6%). The in planta gene expression analysis revealed that 185, 89, and 62 genes were up-regulated in the 3ADON population at 48, 96, and 144 hours after inoculation (HAI), respectively. The up-regulated genes were significantly enriched in functions for cellular import, C-compound and carbohydrate metabolism, allantoin and allantoate transport at 48 HAI, for detoxification and virulence at 96 HAI, and for metabolism of acetic acid derivatives, detoxification, and cellular import at 144 HAI. Comparative analyses of in planta versus in vitro gene expression further revealed 2,159, 1,981 and 2,095 genes up-regulated in the 3ADON isolates, and 2,415, 2,059 and 1,777 genes up-regulated in the 15ADON isolates at the three time points after inoculation. Collectively, our data provides a foundation for further understanding of molecular mechanisms involved in aggressiveness and DON production of the two chemotype isolates of F. graminearum.

Fusarium Toxins in Cereals: Occurrence, Legislation, Factors Promoting the Appearance and Their Management

Fusarium diseases of small grain cereals and maize cause significant yield losses worldwide. Fusarium infections result in reduced grain yield and contamination with mycotoxins, some of which have a notable impact on human and animal health. Regulations on maximum limits have been established in various countries to protect consumers from the harmful effects of these mycotoxins. Several factors are involved in Fusarium disease and mycotoxin occurrence and among them environmental factors and the agronomic practices have been shown to deeply affect mycotoxin contamination in the field. In the present review particular emphasis will be placed on how environmental conditions and stress factors for the crops can affect Fusarium infection and mycotoxin production, with the aim to provide useful knowledge to develop strategies to prevent mycotoxin accumulation in cereals.