G3

The overall process of meiosis is conserved in many species, including some lineages that have lost various ancestrally present meiosis genes. The extent to which individual meiosis gene losses are independent from or dependent on one another is largely unknown. Various Eurotiomycete fungi were investigated as a case system of recent meiosis gene losses after BLAST and synteny comparisons found Msh4, Msh5, Pch2, and Zip3 to be either pseudogenized or undetected in Aspergillus nidulans yet intact in congeners such as A. fumigatus. Flanking gene-targeted degenerate PCR primers applied to 9 additional Aspergillus species found (i) Msh4, Msh5, and Zip3 pseudogenized in A. rugulosus (sister taxon to A. nidulans) but intact in all other amplified sequences; and (ii) Pch2 not present at the syntenic locus in most of the 9 species. Topology tests suggested two independent Pch2 losses in genus Aspergillus, neither directly coinciding with pseudogenization of the other three genes. The A. nidulans-A. conjunctus clade Pch2 loss was not associated with significant Ka/Ks changes for Msh4, Msh5, or Zip3; this suggests against prior Pch2 loss directly altering sequence evolution constraints on these three genes. By contrast, Zip3 Ka/Ks tended to be elevated in several other Eurotiomycete fungi with independently pseudogenized Msh4 and Msh5 (Talaromyces stipitatus, Eurotium herbariorum). The coinciding Ka/Ks elevation and/or clear pseudogenization of Zip3 in taxa with pseudogenized Msh4 and Msh5 is consistent with some degree of molecular coevolution. Possible molecular, environmental, and life history variables (e.g., homothallism) that may be associated with these numerous independent meiosis gene losses (Msh4: 3, Msh5: 3, Zip3: [≥] 1, Pch2: 4) are discussed.

BackgroundThe fungus gnat, Bradysia (Sciara) coprophila, has compelling chromosome biology. Paternal chromosomes are eliminated during spermatogenesis whereas both maternal X sister chromatids are retained. Embryos start with three copies of the X chromosome, but 1-2 copies are eliminated from somatic cells as part of sex determination, and one is eliminated in the germline to restore diploidy. These developmentally normal events present opportunities to study chromosome movements that are unusual in other systems. To support such studies, we previously generated a highly contiguous optical-map-scaffolded long-read assembly (Bcop_v1) of the male somatic genome. However, the scaffolds were not chromosome-scale, the majority of the assembly lacked chromosome assignments, and the order and orientation of the contigs along chromosomes remained unknown. FindingsMale pupae Hi-C data was used to correct, order, and orient the contigs from Bcop_v1 into chromosome-scale scaffolds, producing the updated assembly, Bcop_v2. Several orthogonal analyses allowed us to (i) identify the corresponding chromosome for each scaffold, (ii) orient them with respect to polytene maps, and (iii) determine that they were highly concordant with the chromosomes they represent. Gene annotations produced for Bcop_v1 were lifted over to Bcop_v2. Chromosomal repeat distributions highlight a potential telomeric sequence. Finally, the Hi-C data shed new light on three "fold-back regions" seen to physically interact in images of polytene X chromosomes. ConclusionsStudies of the unusual chromosome movements in Bradysia coprophila will benefit from the updated assembly (Bcop_v2) where each somatic chromosome is represented by a single scaffold.

BackgroundFusarium graminearum is a well characterized plant pathogenic fungus which is able to infect a broad range of economically relevant crop plants. Besides yield reduction this fungus is also responsible for mycotoxin contamination of food and feed. Upon propagation under laboratory conditions, mutations may occur which would be disadvantageous for fungal fitness in nature but not in the lab where the strains are usually grown on nutrient-rich media under optimal growth conditions. In this study we characterized four phenotypically different Fusarium graminearum strains for fitness traits and compared their genomes to trace down mutations responsible for the phenotypes. ResultsThe four tested F. graminearum PH1-derived strains revealed differences in their phenotypic appearance and also in their secondary metabolite profiles expressed on different growth media. Also, two of the investigated strains (94 and 96) showed significantly reduced virulence on wheat upon point inoculation of flowering wheat. We identified one high impact mutation in each of the two strains. In strain 96 a loss of function mutation occurred in FGSG_00355 which has a high similarity to Ras GTPase activating proteins and consequently may have an impact on the cell cycle. Even though strain 96 showed enhanced DON production in vitro, the strain was no longer able to spread within the wheat ear in infection assays. In strain 94 we identified an insertion of an A rather at the end of FGSG_00052 leading to a frameshift and consequently mutation of the last three amino acids and a shift of the stop codon by seven amino acids. Even though knock-out of this putative transcription factor has been described by Son et al (2011) to have no impact on virulence, changes at the C-terminal region may result in changes of the binding affinity. ConclusionsWe tracked down the mutations which might be responsible for the changes in phenotypic appearance, secondary metabolite profile as well as virulence. Yet, a closer biological characterization is necessary to determine the impact of these mutations on the fungus. Impact statementMutations under laboratory conditions can occur spontaneously. Due to the lack of selection pressure, also potentially deleterious mutations remain unnoticed as long as all nutrients are provided. In this study we analyzed four phenotypically different Fusarium graminearum PH-1 strains among which two showed significantly reduced virulence on wheat. In one strain we identified a loss of function mutation in a Ras-GTPase activating protein resulting in enhanced growth on complete media but at the same time strongly reduced virulence. The mutation in the second strain was an insertion in the C-terminal region of a transcription factor. The exact role of the Ras-GTPase activating protein during infection and the impact C-terminal elongation of a yet uncharacterized transcription factor is yet to be investigated. This study underscores the importance of regularly checking laboratory strains on their traits that such mutations which may have an impact on your research data, do not remain unnoticed. Data summaryThe code used for web scraping is available on github (https://github.com/cicci726/webscraping/tree/main). The sequencing files are deposited at NCBI in the sequence read archive (BioProject ID: PRJNA1293145).

BackgroundMost animals and plants have more than one set of chromosomes and package these haplotypes into a single nucleus within each cell. In contrast, many fungal species carry multiple haploid nuclei per cell. Rust fungi are such species with two nuclei (karyons) that contain a full set of haploid chromosomes each. The physical separation of haplotypes in dikaryons means that, unlike in diploids, Hi-C chromatin contacts between haplotypes are false positive signals. ResultsWe generate the first chromosome-scale, fully-phased assembly for the dikaryotic leaf rust fungus Puccinia triticina and compare Nanopore MinION and PacBio HiFi sequence-based assemblies. We show that false positive Hi-C contacts between haplotypes are predominantly caused by phase switches rather than by collapsed regions or Hi-C read mis-mappings. We introduce a method for phasing of dikaryotic genomes into the two haplotypes using Hi-C contact graphs, including a phase switch correction step. In the HiFi assembly, relatively few phase switches occur, and these are predominantly located at haplotig boundaries and can be readily corrected. In contrast, phase switches are widespread throughout the Nanopore assembly. We show that haploid genome read coverage of 30-40 times using HiFi sequencing is required for phasing of the leaf rust genome (~0.7% heterozygosity) and that HiFi sequencing resolves genomic regions with low heterozygosity that are otherwise collapsed in the Nanopore assembly. ConclusionsThis first Hi-C based phasing pipeline for dikaryons and comparison of long-read sequencing technologies will inform future genome assembly and haplotype phasing projects in other non-haploid organisms.

Under synchronized conidiation, over 2500 gene products show differential expression, including transcripts for both brlA and abaA, which increase steadily over time. In contrast, during wall-stress induced by the echinocandin micafungin, the brlA transcript is upregulated while the abaA transcript is not. In addition, when mpkA (last protein kinase in the cell wall integrity signaling pathway) is deleted, brlA expression is not upregulated in response to wall stress. Together, these data imply BrlA may play a role in a cellular stress-response which is independent of the canonical BrlA-mediated conidiation pathway. To test this hypothesis, we performed a genome-wide search and found 332 genes with a putative BrlA response element (BRE) in their promoter region. From this set, we identified 28 genes which were differentially expressed in response to wall-stress, but not during synchronized conidiation. This set included seven gene products whose homologues are involved in transmembrane transport and 14 likely to be involved in secondary metabolite biosynthesis. We selected six of these genes for further examination and find that they all show altered expression behavior in the brlA deletion strain. Together, these data support the idea that BrlA plays a role in various biological processes outside asexual development. ImportanceThe Aspergillus nidulans transcription factor BrlA is widely accepted as a master regulator of conidiation. Here, we show that in addition to this function BrlA appears to play a role in responding to cell-wall stress. We note that this has not been observed outside A. nidulans. Further, BrlA-mediated conidiation is highly conserved across Aspergillus species, so this new functionality is likely relevant in other Aspergilli. We identified several transmembrane transporters that have altered transcriptional responses to cell-wall stress in a brlA deletion mutant. Based on our observation, together with what is known about the brlA gene locus regulation, we identify brlA{beta} as the likely intermediary in function of brlA in the response to cell-wall stress.

BACKGROUNDFungicide resistance is a major concern both in agriculture and clinical disease control. Whilst several mechanisms of resistance have been elucidated, assigning phenotype to genotype is often difficult and reliant on correlations. Resistance to demethylase inhibitor (DMI) fungicides was recently reported in the economically important filamentous fungal barley (Hordeum vulgare) pathogen Pyrenophora teres f. teres (Ptt) in Australia. The target of DMI fungicides is encoded by the Cyp51 gene family; single allele of Cyp51B and two copies of the Cyp51A gene1. Five Cyp51A alleles (W1-A1, 9193-A1, KO103-A1, W1-A2 and 9193-A2) were identified in Ptt with KO103-A1 containing the mutation F489L (F495L) which correlates with resistance to various DMIs.1 RESULTSWe replaced the coding region of the native Cyp51B gene of the filamentous fungal Dothideomycete wheat pathogen Parastagonospora nodorum with each of the five Ptt Cyp51A alleles to compare the phenotypic effects of each allele in isolation. The native Cyp51B of P. nodorum could be functionally replaced by Cyp51-A1 but not Cyp51-A2. Transformants carrying KO103-A1 exhibited significantly higher gene expression than 9193-A1 and W1-A1, suggesting the mechanism of gene regulation lies within the coding sequence and is conserved between Ptt and P. nodorum. The EC50 values of the KO103-A1 transformants were significantly higher than any other transformants or wild type isolates for metconazole, prochloraz and tebuconazole but lower for epoxiconazole. CONCLUSIONThis system permits the functional characterisation of fungicide target genes in an isogenic background that mimics the physiological environment of plant pathogens. We suggest the system will prove useful in dissecting the impact of genetic mutations on a spectrum of fungicides and permit the design of fungal strains for screening active ingredients that may control strains resistant to existing fungicides.

Epimutations are changes in chromatin modifications, such as DNA methylation or histone modifications. Some of these epigenetic changes can be inherited for several generations, and they potentially contribute to evolutionary processes. Estimates of epimutation rates now exists in a few species, but the presence and function of epigenetic marks are not conserved across different species. To understand the properties of epimutations in fungi, we performed a mutation accumulation experiment with the filamentous fungus Neurospora crassa and investigated spontaneous changes in DNA methylation and trimethylation of lysine 9 on histone H3 (H3K9me3) in the mutation accumulation lines. We observed that centromeric regions are hotspots of spontaneous DNA methylation changes in N. crassa. In these hotspot regions, DNA methylation changes were transmitted across mitoses, but changes occurring in euchromatin were not maintained. The rate of DNA methylation changes was around 30 000 fold faster than the genetic mutation rate. We did not observe spontaneous changes in H3K9me3 that were transmitted across mitoses. Our results show that while spontaneous epimutations occur in this species, they occur predominantly in gene poor heterochromatic regions, so their impact for evolutionary adaptation may be limited.

Osmotic stress is a ubiquitous and potent stress for all living organisms, but few studies have investigated the genetic basis of salt tolerance in filamentous fungi. The main aim of this study was to identify regions of the genome associated with tolerance to potassium chloride in the wheat pathogen Zymoseptoria tritici. A secondary aim was to identify candidate genes affecting salt tolerance within the most promising chromosomal regions. We achieved these aims with a quantitative trait locus (QTL) mapping study using offspring from two crosses grown in vitro in the presence or absence of osmotic stress imposed by 0.75M KCl. We identified significant QTL for most of the traits in both crosses. Several QTL overlapped with QTL identified in earlier studies for other traits and some QTL explained trait variation in both the control and salt stress environments. A significant QTL on chromosome 3 explained variation in colony radius at 8 days post inoculation (dpi) in the KCl environment as well as colony radius KCl tolerance at 8 dpi. The QTL peak had a high LOD and encompassed an interval containing only 36 genes. Six of these genes present promising candidates for functional analyses. A GO enrichment analysis of QTL unique to the KCl environment found evidence for enrichment of functions involved in osmotic stress responses.

Fusarium head blight (FHB), a major disease of wheat, is primarily managed through applications of demethylation inhibitor (DMI) fungicides during anthesis. However, repeated use of DMIs has led to the emergence of Fusarium graminearum isolates with reduced sensitivity and, in some cases, resistance. In this study, we evaluated the sensitivity of 152 F. graminearum isolates to propiconazole and tebuconazole. While sensitivity varied among isolates, no resistant strains were detected. We also conducted a genome-wide association study (GWAS) to investigate the genetic basis of DMI sensitivity. GWAS identified 48 and 39 quantitative trait nucleotides (QTNs) associated with propiconazole and tebuconazole sensitivity, respectively, with 12 QTNs common to both fungicides--supporting their common mode of action. Candidate gene analysis highlighted genes encoding transporters, secondary metabolite synthesis enzymes, transcription factors, and a heat shock protein as potential candidates for DMI fungicide response. We propose that tolerance to DMIs in F. graminearum is linked to active fungicide efflux out of fungal cells, mediated by transporters, including those associated with secondary metabolite pathways. Data summaryInformation on all strains used in the experiments have been included in a supplemental file. All sequencing data used in this study are publicly available and were described in our previous publication, which has been cited. Additional supporting data (isolate genotype and phenotype files) and code written for the analyses described here are made available on GitHub: https://github.com/Toomajian-laboratory/files_fungicide_manuscript/ Impact statementIsolates from field populations of fungal plant pathogens vary in their sensitivity to DMI fungicides, though in most cases the genetic determinants of this variation are poorly understood. In this study, we measure the sensitivity of isolates from the main US population of Fusarium graminearum to two DMI fungicides. We used GWAS to identify genomic loci and candidate genes that might underlie variation in DMI sensitivity. Our work contributes to the broader effort to understand the evolution of fungicide tolerance and resistance in populations of plant pathogens. The candidate genes identified, most of which are novel, provide good targets for functional studies of the tools fungi use to survive fungicides. The identified variants can also be screened to monitor potential increases in fungicide tolerance. The high-throughput, rapid, and large-scale monitoring of fungicide sensitivity described here advances both fundamental research and resistance management efforts.

BackgroundFungi use the accessory segments of their pan-genomes to adapt to their environments. While gene presence-absence variation (PAV) contributes to shaping these accessory gene reservoirs, whether these events happen in specific genomic contexts remains unclear. Additionally, since pan-genome studies often group together all members of the same species, it is uncertain whether genomic or epigenomic features shaping pan-genome evolution are consistent across populations within the same species. Fungal plant pathogens are useful models for answering these questions because members of the same species often infect distinct hosts, and they frequently rely on gene PAV to adapt to these hosts. ResultsWe analyzed gene PAV in the rice and wheat blast fungus, Magnaporthe oryzae, and found that PAV of disease-causing effectors, antibiotic production, and non-self-recognition genes may drive the adaptation of the fungus to its environment. We then analyzed genomic and epigenomic features and data from available datasets for patterns that might help explain these PAV events. We observed that proximity to transposable elements (TEs), gene GC content, gene length, expression level in the host, and histone H3K27me3 marks were different between PAV genes and conserved genes, among other features. We used these features to construct a random forest classifier that was able to predict whether a gene is likely to experience PAV with high precision (86.06%) and recall (92.88%) in rice-infecting M. oryzae. Finally, we found that PAV in wheat- and rice-infecting pathotypes of M. oryzae differed in their number and their genomic context. ConclusionsOur results suggest that genomic and epigenomic features of gene PAV can be used to better understand and even predict fungal pan-genome evolution. We also show that substantial intra-species variation can exist in these features.

BackgroundThe Ustilaginales comprise hundreds of plant-parasitic fungi with a characteristic life cycle that directly links sexual reproduction and parasitism: One of the two mating-type loci codes for a transcription factor that not only facilitates mating, but also initiates the infection process. However, several species within the Ustilaginales have no described parasitic stage and were historically assigned to the genus Pseudozyma. Molecular studies have shown that the group is polyphyletic, with members being scattered in various lineages of the Ustilag-inales. Together with recent findings of conserved fungal effectors in these non-parasitic species, this raises the question if parasitism has been lost recently and in multiple independent events or if there are hitherto undescribed parasitic stages of these fungi. ResultsIn this study, we sequenced genomes of five Pseudozyma species together with parasitic species from the Ustilaginales to compare their genomic capability to perform two central functions in sexual reproduction: mating and meiosis. While the loss of sexual capability is assumed in certain lineages and asexual species are common in Asco- and Basidiomycota, we were able to successfully annotate functional mating and meiosis genes that are conserved throughout the whole group. ConclusionOur data suggest that at least the key functions of a sexual lifestyle are maintained in the analyzed genomes, challenging the current understanding of the so-called asexual species with respect to their evolution and ecological role.

An increase in the prevalence of fungal infections is coinciding with an increase of resistance to current clinical antifungals, placing pressure on the discovery of new antifungal candidates. One option is to investigate drugs that have been approved for use for other medical conditions that have secondary antifungal activity. Aprotinin, also known as Bovine Pancreatic Trypsin inhibitor (BPTI), is an antifibrinolytic that has been approved for systemic use in patients in some countries. Bleackley and coworkers (2014) revealed that BPTI also has antifungal activity against S. cerevisiae and C. albicans and does this by targeting the magnesium transporter ALR1. Here we have further investigated the potential for aprotinin to be used as an antifungal by assessing the development of resistance. We used an in vitro model to assess the evolution of BPTI resistance/tolerance whereby BPTI was serial passaged with the model organism S. cerevisiae. Resistance to BPTI developed more quickly than resistance to the plant defensin NaD1 and the clinical antifungal, caspofungin. Full genome sequencing of resistant lines revealed that resistance to BPTI developed as the result of a deleterious mutation in either the ptk2 or sky1 genes. This revealed that cation homeostasis and transport functions were particularly affected in S. cerevisiae after exposure to BPTI. Therefore, the mutations in these genes probably decreases release of magnesium and other cations from the cell, protecting the yeast from the limiting intracellular magnesium levels that arise when BPTI blocks the magnesium transporter Alr1p.

MotivationFusarium langsethiae is a T-2 and HT-2 mycotoxins producing Fusarium species firstly characterised in 2004. It is commonly isolated from oats in Northern Europe. T-2 and HT-2 mycotoxins exhibit immunological and haemotological effects in animal health mainly through inhibition of protein, RNA and DNA synthesis. The development of a high-quality and comprehensively annotated assembly for this species is therefore essential in providing the molecular understanding and the mechanism of T-2 and HT-2 biosynthesis in F. langsethiae to help develop effective control strategies. ResultsThe F. langsethiae assembly was produced using PacBio long reads, which were then assembled independently using Canu, SMARTdenovo and Flye; producing a genome assembly total length of 59Mb and N50 of 3.51Mb. A total of 19,336 coding genes were identified using RNA-Seq informed ab-initio gene prediction. Finally, predicting genes were annotated using the basic local alignment search tool (BLAST) against the NCBI non-redundant (NR) genome database and protein hits were annotated using InterProScan. Genes with blast hits were functionally annotated with Gene Ontology. Contactf.mohareb@cranfield.ac.uk Data availabilityRaw sequence reads and assembled genome can be downloaded from: GenBank under the accession JAFFKB000000000

Stereum is an exceedingly common but taxonomically confounding genus of basidiomycete fungus with a cosmopolitan distribution. Lack of consensus about morphological and geographic boundaries of many Stereum species has resulted in a lack of consistency in identification of physical specimens, a problem that cascades to their associated published DNA sequences. A critical initial step towards addressing these issues is determining the scope of the problem. Here, we first use integrative taxonomy to delimit species in the North American Stereum ostrea complex. We use morphological and ecological characters, alongside ITS rDNA sequences of specimens from midwestern and eastern North America to show that "Stereum ostrea" in this region is a complex of at least three reproductively isolated sister species: S. lobatum, S. fasciatum, and S. subtomentosum. We then extend lessons from this case study to a set of publicly available Stereum ITS sequences to assess the accuracy of species names represented by existing sequence data. ASAP species delimitation successfully discriminates among the three newly revealed species in the S. ostrea species complex, but also reveals considerable cryptic diversity across global Stereum and widespread inconsistency in application of species names. Though ITS alone should not be used to delimit species or describe evolutionary relationships, its application here helps direct new hypotheses and suggests several areas of Stereum taxonomy that require revision. The critical future work of disentangling Stereum taxonomy and evolution should combine a multilocus genetic approach with morphology, ecology, and a global sampling strategy.

Climate change can alter interactions between plants and their pathogens, which could adversely affect crop production. To better understand the molecular mechanisms underlying the responses of pathogenic fungal to temperature stress, we conducted a quantitative trait loci (QTL) mapping study in the wheat pathogen Zymoseptoria tritici to identify genomic regions associated with colony growth and melanisation at three temperatures (10{degrees}C, 18{degrees}C, 27{degrees}C). We then identified likely candidate genes for thermal adaptation within these intervals by combining information regarding gene function, GO annotation enrichment, transcriptional profile, and results from previous genome wide association studies (GWAS) investigating responses to climate, temperature and thermal adaptation. The QTL mapping, conducted for two separate crosses involving four Swiss parents, found significant QTL uniquely associated with traits measured in high and low temperatures. These intervals contained many genes known to regulate responses to temperature stress, including heat shock proteins (HSPs) and proteins involved in the mitogen-activated protein kinase (MAPK) pathways, and were enriched for genes with a zinc ion binding GO annotation. We highlight the most promising candidate genes for thermal adaptation, including an ammonium transporter gene, a stress response factor (Whi1) and two MAPK pathway genes - SSk2 and Opy2. Future validation work on these candidate genes could provide novel insight into the molecular mechanisms underlying temperature adaptation in this important wheat pathogen.

Long non-coding RNAs (lncRNAs) are regulatory molecules interacting in a wide array of biological processes. LncRNAs in fungal pathogens can be responsive to stress and play roles in regulating growth and nutrient acquisition. Recent evidence suggests that lncRNAs may also play roles in virulence, such as regulating pathogenicity-associated enzymes and on-host reproductive cycles. Despite the importance of lncRNAs, only few model fungi have well-documented inventories of lncRNA. In this study, we apply a machine-learning based pipeline to predict high-confidence lncRNA candidates in Zymoseptoria tritici, an important global pathogen of wheat impacting global food production. We analyzed genomic features of lncRNAs and the most likely associated processes through analyses of expression over a host infection cycle. We find that lncRNAs are frequently expressed during early infection, before the switch to necrotrophic growth. They are mostly located in facultative heterochromatic regions, which are known to contain many genes associated with pathogenicity. Furthermore, we find that lncRNAs are frequently co-expressed with genes that may be involved in responding to host signals, such as those responses to oxidative stress. Finally, we assess pangenome features of lncRNAs using four additional reference-quality genomes. We find evidence that the repertoire of expressed lncRNAs varies substantially between individuals, even though lncRNA loci tend to be shared at the genomic level. Overall, this study provides a repertoire and putative functions of lncRNAs in Z. tritici enabling molecular genetics and functional analyses in an important pathogen. Impact statementLong non-coding RNAs (lncRNAs) serve distinct roles from messenger RNA. Despite not encoding proteins, lncRNAs can control important cellular processes such as growth and response to stress. In fungal pathogens, lncRNAs are particularly interesting because they can influence how pathogens infect and harm their hosts. Yet, only very few fungal pathogens have high-quality repertoires of lncRNA established. Here, we used machine learning to identify lncRNA in the major wheat pathogen Zymoseptoria tritici. We found that lncRNAs are highly active during the early stages of infection, before the pathogen switches to necrotrophic growth. These lncRNAs are mainly located in regions of the genome associated with pathogenicity. The repertoire of expressed lncRNAs varies substantially among individuals highlighting the potential for pathogen adaptation based on variation in lncRNAs. By expanding our knowledge of lncRNAs in important pathogen models, we enable research to comprehensively investigating their roles across fungi.

Histone modifications and chromatin-binding proteins play crucial roles in regulating gene expression in eukaryotes, with significant implications for fungal pathogenicity and development. However, profiling these modifications or proteins across the genome in fungi remains challenging due to the technical limitations of the traditional, widely used ChIP-Seq method. Here, we present an optimized CUT&Tag-Seq protocol (fCUT&Tag-Seq) specifically designed for filamentous fungi and dimorphic fungi. Our approach involves the preparation of protoplasts and nuclear extraction to enhance antibody accessibility, along with formaldehyde crosslinking to improve protein-DNA binding efficiency. We then successfully applied fCUT&Tag-Seq to accurately profile multiple histone modifications like H3K9me3, H3K27me3, H3K4me3, and H3K18ac, across different plant pathogenic or model fungal species, including Verticillium dahliae, Neurospora crassa, Fusarium graminearum, and Sporisorium scitamineum, showing good signal-to-noise ratios, reproducibility, and detection sensitivity. Furthermore, we extended this method to profile chromatin-binding proteins, such as the histone acetyltransferase Gcn5. This study establishes fCUT&Tag-Seq as a robust and useful tool for fungal epigenetic research, enabling detailed exploration of chromatin dynamics and advancing our understanding of fungal gene regulation, development, and pathogenicity. Impact StatementWe developed a faster, lowLJinput method to study how genes are turned on and off in fungi, even in tough species that are difficult to analyze with standard methods. Our new approach, named fCUT&Tag-Seq, requires only 10,000 cells and can be completed in just two days. It delivers clearer, more reliable results and has already been successfully applied to multiple fungi, including crop pathogens. By revealing the molecular "control switches" that govern fungal development and virulence, we expect it will accelerate basic research and help identify new targets for controlling destructive plant diseases.

The genus Aspergillus includes industrially, medically and agriculturally important species. All of them, as do fungi in general, disperse to new niches principally by means of asexual spores. Regarding the genetic/molecular control of asexual development, Aspergillus nidulans is the main reference. In this species, two pathways control the production of conidiophores, the structures bearing asexual spores (conidia). The Upstream Developmental Activation (UDA) pathway transduces environmental signals, determining whether the Central Developmental Pathway (CDP) and the required morphological changes are induced. The transcriptional regulator BrlA links both pathways as loss-of-function mutations in flb (UDA) genes block brlA transcription and, consequently, conidiation. However, the aconidial phenotype of specific flb mutants is reverted under salt-stress conditions. Previously, we generated a collection of {Delta}flbB mutants unable to conidiate on culture medium supplemented with NaH2PO4 (0.65M). Here, we identified a Gly347Stop mutation within flpA as responsible for the FLIP57 phenotype. The putative cyclin FlpA and the remaining putative components of the C-terminal domain kinase-1 (CTDK-1) complex are necessary for proper germination, growth and developmental patterns in both A. nidulans and A. fumigatus. Cellular localization and functional interdependencies of the three proteins are also analyzed. Overall, this work links the putative CTDK-1 complex of aspergilli with growth and developmental control. One-sentence summaryIdentification of a mutation in flpA as inhibitor of conidiation in A. nidulans and functional characterization of FlpA, Stk47 and FlpB as putative members of the C-terminal domain kinase complex CTDK-1 in the genus Aspergillus.

Temperature poses a unique challenge to ectothermic species, as it affects all biochemical reactions in the cell and causes physiological stress. The effect of temperature on an organism can be described by a thermal performance curve (TPC), which displays organismal performance, such as growth rate, as a function of temperature. Previous studies on thermal performance have revealed different amounts of genetic variation and trade-offs in TPC shape and position within species and populations. However, very little is known about the genetic architecture of TPCs on the level of individual loci and alleles. We asked what is the identity of loci contributing to genetic variation in TPCs, and do the alleles exhibit trade-offs or thermodynamic scaling across the temperature range? We used genome-wide association mapping to find loci influencing growth rate at different temperatures and TPC traits in the filamentous fungus Neurospora crassa. We also evaluated the directions and magnitudes of allelic effects to investigate possible trade-offs. We observed both unique associations at specific temperatures, as some loci affected growth rate only at low, intermediate, or high temperatures, and associations that were shared across multiple temperatures. However, only weak evidence of trade-offs was detected, indicating that the evolution of TPCs in N. crassa is not constrained by allelic effects in opposite directions at hot and cold temperatures. Our findings indicate that trade-offs contribute little to variation in TPCs.

Balancing selection, an evolutionary force that retains genetic diversity, has been detected in multiple genes and organisms, such as the sexual mating loci in fungi. However, to quantify the strength of balancing selection and define the mating-related genes require a large number of specimens. In tetrapolar basidiomycete fungi, sexual type is determined by two unlinked loci, MATA and MATB. Genes in both loci defines mating type identity, control successful mating and completion of the life cycle. These loci are usually highly diverse. Previous studies have speculated, based on culture crosses, that species of the non-model genus Trichaptum (Hymenochaetales, Basidiomycota) possess a tetrapolar mating system, with multiple alleles. Here, we sequenced a hundred and eighty specimens of three Trichaptum species. We characterized the chromosomal location of MATA and MATB, the molecular structure of MAT regions and their allelic richness. Our sequencing effort was sufficient to molecularly characterize multiple MAT alleles segregating before the speciation event of Trichaptum species. Our analyses suggested that long-term balancing selection has generated trans-species polymorphisms. Mating sequences were classified in different allelic classes based on an amino acid identity (AAI) threshold supported by phylogenetics. The inferred allelic information mirrored the outcome of in vitro crosses, thus allowing us to support the degree of allelic divergence needed for successful mating. Even with the high amount of divergence, key amino acids in functional domains are conserved. The observed allelic classes could potentially generate 14,560 different mating types. We conclude that the genetic diversity of mating in Trichaptum loci is due to long-term balancing selection, with limited recombination and duplication activity. Our large number of sequenced specimens highlighted the importance of sequencing multiple individuals from different species to detect the mating-related genes, the mechanisms generating diversity and the evolutionary forces maintaining them. Author summaryFungi have complex mating systems, and basidiomycete fungi can encode thousands of mating types. Individuals with the same mating type cannot mate. This sexual system has evolved to facilitate sexual mating, increasing the chances to recombine into advantageous allelic combination and prune deleterious alleles. We explored the genomes of hundred and eighty specimens, combined with experimental mating studies of selected specimens, from a non-model organism (Trichaptum). We characterized the genomic regions controlling sex. The mating ability of the specimens confirmed the role of the mating alleles observed in the genomic data. The detailed analyses of many specimens allowed us to observe gene duplication and rearrangements within the mating loci, increasing the diversity within these loci. We supported previous suggestions of balancing selection in this region, an evolutionary force that maintains genomic diversity. These results supports that our fungal specimens are prone to outcross, which might facilitate the adaptation to new conditions.