Candida albicans exhibits substantial phenotypic and ecological diversity; however, the exact relationship between its population structure, adaptation to specific niches, and antifungal resistance remains incompletely understood. To investigate these evolutionary dynamics, we analyzed the whole-genome sequences from 591 publicly available isolates, integrating nuclear and mitochondrial phylogenomics with ecological and resistance-associated genomic analyses. Phylogenomic analyses resolved 18 core nuclear clusters together with multiple admixed lineages. Strong cytonuclear concordance was noted in the majority of the central lineages, contrasting with a higher discordance among the admixed groups, consistent with recurrent genetic exchange. The analysis revealed that geographic origin explains a larger fraction of genetic variance than anatomical niche, supporting a predominantly generalist population structure. A notable exception was Cluster N16 (Candida africana), which presented a strict genital origin in our dataset (n = 34). Additionally, although the mitochondrial genome exhibits strong purifying selection, candidate residues under diversifying selection correlated with specific niches (e.g., bloodstream) have been identified. Analysis of five resistance-associated genes (ERG11, UPC2, FKS1, TAC1 and FUR1) revealed that resistance-associated variants were generally rare but exhibited distinct gene-specific patterns. In case of ERG11 and FUR1 they were concentrated in a specific clade (N11, N17, and their admixed Group A) and exhibit gene-dependent zygosity patterns. In summary, the evolution of C. albicans appears to be driven by a predominantly clonal model punctuated by episodic genetic exchange, where both ecological adaptation and antifungal resistance mutations exhibit genomic signatures marked by lineage specificity.
Fungal mitochondrial genomes exhibit exceptional variation in size and architecture, yet the genomic components and RNA-processing features associated with extreme expansion remain poorly understood. Here, we report the first complete mitochondrial genome for the genus Helvella, and characterize its architecture in H. bachu, an ectomycorrhizal ascomycete inhabiting hyper-arid desert ecosystems in western China. Using PacBio HiFi sequencing, Illumina polishing, and full-length Iso-Seq transcriptomics, we assembled a circular 587,425-bp mitogenome containing a canonical set of 15 protein-coding genes, 2 rRNAs, and 24 tRNAs. Its expanded size is associated with extensive non-coding sequence, including 103 introns within protein-coding and rRNA genes, totaling 372,582 bp and accounting for 63.4% of the mitogenome, as well as 121,658 bp of repetitive elements representing 20.7% of the genome. Most introns were classified as group I, and collectively harbored numerous open reading frames predicted to encode GIY-YIG or LAGLIDADG homing endonucleases. Full-length transcript data supported fully spliced major transcript models and revealed additional intron-retaining, alternative-splice, and polycistronic transcripts, highlighting substantial mitochondrial RNA-processing heterogeneity in H. bachu. Comparative analyses of 191 fungal mitogenomes showed that Pezizales encompasses multiple enlarged mitogenomes whose expansion is associated with varying contributions from intronic and intergenic sequences. Together, these findings define the structural basis of mitogenome expansion in H. bachu, reveal substantial heterogeneity in fungal mitochondrial RNA processing, and provide a comparative framework for investigating the evolution of giant mitogenomes in Pezizales.
Filamentous fungi rely on polarized hyphal growth, a process fundamentally driven by vesicular transport. Sec14, a conserved phosphatidylinositol/phosphatidylcholine transfer protein first identified in Saccharomyces cerevisiae, and its Sec14-like SFH proteins have been implicated in multiple trafficking- and/or lipid-linked processes in diverse yeasts and pathogenic fungi. Despite substantial progress in Sec14 research in yeasts and a limited number of other fungi, systematic functional studies of Sec14/SFH proteins in filamentous fungi remain scarce. Here, using Aspergillus nidulans as a model filamentous fungus, we investigated the physiological function of Sec14-family genes. We identified eight orthologs of S. cerevisiae SEC14 and SFH genes in A. nidulans: secN (SEC14 ortholog) and seven sfh genes (sfhA-sfhG). Phenotypic analysis of single-deletion strains revealed that the ΔsecN strain exhibited severe growth retardation, accompanied by increased hyphal branching, defective conidiophore development, and extremely low conidia germination rate. Scanning electron microscopy further revealed that secN deletion impairs conidiophore morphogenesis during conidiation. Lipidomic analysis revealed that loss of secN altered the mycelial phospholipid composition. Analysis of lipid species recovered with affinity-purified SecN-V5 identified various phosphatidylinositol species, along with selected phosphatidylcholine species, as candidate SecN-associated lipids. In contrast, most sfh deletion strains showed no major growth defects under normal growth conditions, although they exhibited reduced growth sensitivity to calcofluor white. These findings indicate that SecN is a major Sec14-family protein required for normal growth, asexual development, and phospholipid homeostasis in A. nidulans, while suggesting that other Sfh proteins may have redundant or condition-specific functions. (244 words).
The tangerine pathotype of Alternaria alternata infects multiple citrus cultivars, causing brown spot disease. The role of autophagy in toxin production and siderophore biosynthesis remains to be further confirmed. This study identifies autophagy-related protein 4 (AaAtg4) as a critical regulator of fungal growth, development, stress resistance, iron homeostasis, and virulence, as determined by genetic and biochemical analyses. Targeted deletion of the AaAtg4 gene using split-marker recombination generated two ΔAaAtg4 mutants, which displayed reduced growth on minimal medium, impaired conidiation, delayed germination, and diminished formation of appressorium-like structures compared with the wild-type strain. The mutants were hypersensitive to hydrogen peroxide and iron stress, highlighting the roles of AaAtg4 in oxidative stress tolerance and iron metabolism. ΔAaAtg4 mutant strains failed to produce detectable siderophores and exhibited downregulation of siderophore production-related genes (AaHapX, AaNps6, AaMirB) alongside upregulation of the AaSreA gene encoding a siderophore repressor. Toxin profiling further revealed altered host-selective toxin production, with distinct shifts in retention times in ΔAaAtg4 compared to the wild-type strain. However, AaAtg4, but not autophagy itself, was required for toxin production, as deletion of other autophagy-related genes had no effect. Reintroduction of functional AaAtg4 into a ΔAaAtg4 mutant rescues all defects, confirming that the loss of AaAtg4 function directly causes the observed phenotypes. These findings demonstrate that AaAtg4 is important for spore germination, siderophore biosynthesis, iron acquisition, oxidative stress resistance, and toxin production, thereby establishing its critical role in A. alternata virulence.
Phospholipid flippases (P4-ATPases) are central to the establishment of membrane lipid asymmetry, a property underlying membrane trafficking and polarized growth in eukaryotic cells. However, the specific contribution of individual flippases to hyphal morphogenesis in filamentous fungi remains poorly defined. Here, we characterize DNF-4, a putative P4-ATPase in Neurospora crassa with high sequence identity to the essential flippase Neo1 of Saccharomyces cerevisiae. Using endogenous tagging and live-cell imaging, we show that DNF-4 localizes to highly dynamic punctate structures associated with endoplasmic reticulum- and Golgi-related compartments, supported by quantitative co-localization analyses with the ER marker CSE-7-mChFP and the Golgi-associated Rab GTPase YPT-1-mChFP. FRAP experiments revealed partial fluorescence recovery, indicating dynamic exchange of DNF-4-associated compartments. These structures undergo bidirectional movement along the hypha, and their motility is strongly dependent on an intact microtubule cytoskeleton. Deletion of dnf-4 results in pronounced defects in hyphal growth and development, including reduced hyphal elongation, decreased biomass accumulation, smaller conidia, and a severe reduction in conidiation. These defects are accompanied by increased branching frequency, abnormal hyphal morphology, and altered Spitzenkörper positioning and dynamics, indicating impaired coordination of polarized growth. Our results demonstrate that DNF-4 contributes to membrane trafficking processes required for the maintenance of hyphal polarity and normal developmental progression in N. crassa. These findings provide new evidence that P4-ATPases play an important role in the spatial organization of membrane trafficking pathways underlying fungal morphogenesis.
In this research we localize the cytokinesis-inhibiting sepD5 mutation in Aspergillus nidulans to gene AN3659, previously named paxB, which is predicted to encode a LIM domain protein orthologous to the Pxl1 scaffold proteins of S. cerevisiae and S. pombe. The genetic lesion in sepD5 is predicted to result in a Q-to-R amino acid substitution at position 31 of the 776-residue PaxB protein within a region of intrinsic disorder. When grown at restrictive temperature, sepD5 strains are aseptate with impaired conidiogenesis. AN3659 null mutants replicate the sepD5 phenotype. Neither the sepD5 mutation nor deletion of paxB prevents assembly of the cortical contractile actomyosin rings (CARs) at putative septation sites, though the rings fail to constrict. Fluorescently tagged wild-type PaxB localizes to both the CAR and the Spitzenkörper (Spk) at the growing hyphal apex. Through structural truncation studies, we identify specific regions of PaxB whose presence is necessary for localization to the CAR and the Spk, as well as for proper formation of conidiophores. Deletion or downregulation of genes that prevent formation of actin rings at septation sites also blocks localization of PaxB to those same sites. Deletion or downregulation of genes that permit cortical actin ring formation while blocking constriction of those same rings does not prevent PaxB localization to CARs. When grown at restrictive temperature, sepD5 strains and paxB null strains permit normal targeting of several septation-associated proteins to cortical actin rings, while recruitment of the formin SepA, the serine-threonine protein kinase PkcA, and the chitin synthase ChsA is impaired.
Durum wheat is highly susceptible to Fusarium head blight (FHB) caused by the fungal pathogen Fusarium graminearum. Wheat can be protected with the use of environmentally-friendly and sustainable methods involving biological control agents (BCAs) such as yeasts. However, the mechanism underlying the antagonistic effects of yeasts on plant pathogens has not been fully elucidated. Therefore, the aim of this study was to expand the existing knowledge about the mechanisms of action of a Debaryomyces hansenii biopreparation through transcriptome profiling in F. graminearum cells using RNA sequencing (RNA-seq). The changes in the F. graminearum transcriptome resulting from biotic stress induced by the application of D. hansenii cells to durum wheat spikes, and abiotic stress induced by the application of a cell-free supernatant were compared and comprehensively analyzed. Each stressor elicited a completely different transcriptomic response, and differentially expressed genes (DEGs) encoding metabolic pathways essential for pathogen development associated with carbohydrate and amino acid metabolism, pathogenicity factors, effectors, and secondary metabolites. Numerous transporter genes were also identified, which indicates that fungi exhibit complex responses to biotic and abiotic stresses. The study demonstrated that F. graminearum uses various strategies to overcome the biotic stress associated with BCAs, including the upregulation of the brefeldin A resistance gene (FGSG_02870), which encodes an antifungal compound that inhibits the growth of BCA cells. The present findings provide novel insights into the interactions between pathogens and BCAs with specific mechanisms of action at the transcriptome level, thus helping to explain the relative ineffectiveness of BCAs under certain conditions.
Secretory phospholipases A2 (sPLA2) is a group of enzymes that cleave the sn-2 ester linkage of phospholipids, thereby releasing fatty acids and 1-acyl lysophospholipids. In this study we investigated the physiological roles two sPLA2s in the filamentous fungus Neurospora crassa. We found that the single and double gene deletion strains displayed higher sensitivity to oxidative and heat stresses compared to the wild-type strain. Complementation analysis demonstrated that the enzyme activity of sPLA2s is required for stress tolerance. The expression of both genes was upregulated by the stresses, and in the single gene deletion strain the expression of the other gene was attenuated. RNA-seq analysis of wild-type and double deletion strains revealed that the expression of genes involved in fatty acid biosynthesis was downregulated in the double deletion strain, which was further decreased by the stresses. Supplementation of fatty acids to the culture medium restored the tolerance of the double deletion strain to stresses, suggesting that sPLA2s are involved in stress tolerance through the regulation of fatty acid metabolism.
Cordyceps cicadae (C. cicadae), a species widely used in traditional Chinese medicine, belongs to the family Cordycepsaceae (order Hypocreales, class Ascomycota). Its potential as a novel food resource is limited by the high accumulation of beauvericin (BEA), a toxic secondary metabolite. The effects of gene deletion of two transcription factors and one global regulatory factor on beauvericin biosynthesis were investigated. The Δcc63tf mutant exhibited increased BEA accumulation (11.157 mg/kg), whereas Δcc12grf showed markedly reduced BEA accumulation (>90% reduction, 1.005 mg/kg), achieving food-safe thresholds (3 mg/kg). Notably, Δcc57ef impaired fruiting body development. Transcriptome profiling revealed key differentially expressed genes linked to BEA biosynthesis, with qPCR validation suggesting the regulatory roles of CC63TF as a negative and CC12GRF as a positive regulator. These findings provide evidence for regulatory mechanisms associated with BEA biosynthesis in C. cicadae and provide a genetic framework for strain improvement through precision metabolic engineering, enabling safe industrial application in the functional food and nutraceutical sectors.
The basidiomycetous yeast Pseudozyma antarctica secretes the biodegradable plastic-degrading enzyme PaE. The xylanase promoter pPaXyn1 in P. antarctica is strongly induced by xylose. A P. antarctica reporter strain carrying the pPaXyn1 promoter-fused PaE gene (a PaE high-production cassette) produced a large amount of PaE in the presence of xylose. Accordingly, to further improve PaE productivity, this study aimed to isolate the transcription activation factor pPaXyn1. In total, 109 genes with Zn2Cys6-type DNA-binding domains were selected from the whole genome sequence of P. antarctica as candidate transcription factor genes. A set of strains was generated from the reporter strain in which each candidate transcription factor gene on the chromosome was disrupted. Among the disruptants, only the strain lacking the locus_tag PAN1_003r02005 (gene id: g2005) suppressed PaE production and did not show biodegradable plastic degrading activity. Moreover, a reporter strain with multiple copies of g2005 exhibited a 1.6-fold increase in PaE secretion. In addition, the strain also increased xylanase secretion. Overall, these results indicate that g2005 is a transcriptional activator of xylanase; hence, g2005 was named P. antarctica xylanase regulator 1 (PaXyr1). The amino acid sequence of g2005 is conserved only in the basidiomycete subphylum Smut (Ustilaginomycotina).
Understanding the life cycle of fungal spores is essential for elucidating their roles in pathogenesis, dispersal, and survival. However, studying spore development under controlled, spatially defined conditions remains challenging. Here, we present the Spore Chamber, a custom-built microfluidic platform engineered for parallel trapping and long-term imaging of individual spores under defined media conditions, enabling real-time visualization of hyphal development. Using Aspergillus fumigatus as a model organism, we demonstrate that sparse trapping of individual spores within size-matched trap geometries enables long-term time-lapse imaging of key developmental stages, including germination, polarized hyphal elongation, branching, and conidiophore formation. To assess the device's capacity to resolve morphogenetic responses to exogenous signals, we introduced lipochitooligosaccharides (LCOs) and short-chain chitooligosaccharides (COs). Rhizobium-derived, non-sulfated LCO (nsLCO) mixtures induced enhanced secondary branching (hyperbranching), a response not previously reported in A. fumigatus under these signal conditions, to our knowledge, whereas sulfated LCOs and CO4 did not significantly alter branching patterns. In addition, long-term confinement and imaging revealed rare developmental morphologies previously described primarily in mutant strains, including split conidiophore formation, elongated phialides, and stress-associated phenomena such as microcyclic conidiation, and chlamydospore development. Together, these results establish the Spore Chamber as a targeted microfluidic platform for single-spore phenotyping and long-term developmental analysis, with applications in fungal biology, chemical signaling studies, and host-microbe interaction research.
Class III chitin synthases (CHSs) are specific to filamentous fungi and are associated with biosynthesis of chitin, a key structural component of fungal cell walls. While extensively studied in ascomycetes, their roles in basidiomycetes remain poorly understood. In this study, we present the first functional analysis of class III chss in the white-rot basidiomycete Pleurotus ostreatus. Through targeted single gene disruption of the class III chss, chs7 and chs9, as well as double disruption of chs7chs9, we demonstrate their distinct and sometimes overlapping roles in regulating hyphal growth, cell wall thickness, and stress resilience. Despite reduced cell wall thickness and decreased growth rates in disruption strains, compensatory upregulation of other chitin and glucan synthase genes maintains polysaccharide composition, revealing a robust regulatory network. Notably chs9 disruption strains had more severe impacts than those of chs7, suggesting that chs9 is the main class III chs and chs7 provides more of a supporting role. Double disruption strains also revealed straighter hyphae suggesting redundancy and highly specialized functions of clade III chss in hyphal straightness in P. ostreatus. Our findings highlight the evolutionary divergence and seemingly unique functions of class III CHSs in comparison to the previously analyzed basidiomycete-specific classes, providing foundational insights into filamentous basidiomycete cell wall dynamics.
A comprehensive understanding of a species' life cycle is crucial for advancing genetic breeding and cultivation strategies. Currently, the life cycle of species within the genus Morchella remains a topic of debate, and detailed analysis of the mating type gene structures is urgently needed. Here, we report the development of primers (Con_Mat1F/R and Con_Mat2F/R) targeting evolutionarily conserved domains of the Mat1-1-1 and Mat1-2-1 genes in Morchella. These primers were validated across 12 strains representing the Rufobrunnea, Elata, and Esculenta clades, enabling efficient genotyping and facilitating studies of the morel life cycle. Genotyping of single-spore populations of Mes-6, M. sextelata, and M. importuna revealed that each strain carries only one mating type gene, supporting heterothallism. Using these primers, genotyping of stipe and pileus tissues from ten cultivated populations (M. importuna, M. sextelata and M. eximia) revealed that all 189 pileus tissues carried both mating types, while some stipes harbored only one, reinforcing the heterothallic nature of these species and highlighting existing genotype imbalances. Additionally, amplification tests on large-scale, multi-batch tissue isolated strains revealed that 47.34% of the mating type genes were incomplete, a trend also observed in commercial strains. The incompleteness of mating type genes (genotype loss) may contribute significantly to the instability of cultivated heterothallic Morchella species, underscoring the importance of genotyping integrity screening prior to production. Collectively, our findings provide critical insights into the life cycle of Morchella and offer practical guidance for improving the stability of their cultivation.
The actin cytoskeleton is a complex, dynamic intracellular network that is involved in a multitude of cellular processes and essential for viability of eukaryotic cells. In hyphae of the oomycete plant pathogen Phytophthora infestans actin filaments (F-actin) are organized in higher order cables and plaques while the formation of an aster-like actin configuration is triggered in the tips of hyphae that face a barrier. Unlike the ubiquitous actin cables, actin plaques are unique for oomycetes and present in every life stage except zoospores, the wall-less, flagellated motile propagules. They are predominantly stationary clusters of F-actin that localize at the cell membrane with lifetimes that can exceed an hour. To unravel the potential role of actin plaques in oomycetes we visualized their dynamics in protoplasts of a P. infestans strain expressing the live cell actin probe Lifeact-GFP. In these wall-less cells, actin cables are present in the cortical cytoplasm and plaques have the same, membrane associated localization as in walled mycelium. In some protoplasts, we observed rotating rings of actin cables in the cortical cytoplasm. The F-actin plaques display a distinct behaviour when compared to those in walled hyphae; their lifetime is reduced and their motility, particularly of those that co-localize with the rotating actin rings, strongly increases. These findings suggest that actin plaques are immobilized by a connection with the cell wall and potentially function as an anchor for positioning the actin cables.
Fusarium fujikuroi, the causal agent of rice bakanae disease, comprises two pathotypes with distinct symptoms: the fumonisin-producing blight type (B14) and the gibberellin-producing elongation type (B20). Asexual spore production and secondary metabolism are essential for disease transmission and development in F. fujikuroi, and conidiation regulators frequently influence secondary metabolism and other phenotypes in filamentous fungi. To investigate the genetic basis underlying differences between the two pathotypes, we generated deletion mutants for 14 genes corresponding to well-characterized conidiation regulators (upstream activators, central regulators, and velvet complex components) in both B14 and B20. Phenotypic analyses revealed that several upstream regulators, including FfflbD, are essential for macroconidiation in both strains, whereas others, such as FfflbA, FfflbB, and FfflbE, showed pathotype-dependent roles. The central regulator FfabaA was indispensable for conidiation in both backgrounds, while FfwetA displayed divergent roles in conidial maturation. Velvet regulators (Ffvel1, Ffvel2, and Fflae1) promoted conidiation in both backgrounds, with Fflae1 additionally affecting macroconidiation in B20. In B14, deletion of Ffvel1, Ffvel2, FfabaA, or FfwetA abolished or significantly reduced virulence and was associated with decreased FUM1 expression, linking conidiation with fumonisin biosynthesis and pathogenicity. In B20, several mutants partially shifted toward blight-like symptoms and altered gibberellin gene expression. Notably, ΔFflae1 in B20 caused >500-fold FUM1 upregulation, increased fumonisin accumulation to near-B14 levels, and induced blight-like disease symptoms. Transcriptional profiling across mutants revealed distinct regulatory network architectures between B14 and B20. Together, these results show extensive divergence in developmental regulatory networks between F. fujikuroi pathotypes and implicate chromatin-associated control in pathotype differentiation.
Aspergillus species generate diverse secondary metabolites (SMs), including commercially valuable compounds and mycotoxins that affect food safety. The biosynthesis of these SMs is regulated through gene clusters controlled by epigenetic and transcriptional mechanisms. However, the function of the histone H3 lysine 4 (H3K4) methyltransferase CclA across different metabolic stages remains poorly understood during the metabolic switch from primary to secondary metabolism. We performed integrated transcriptomic, proteomic, and RT-qPCR analyses of a ΔcclA mutant and wild type Aspergillus nidulans during late exponential growth phase (20h) where primary metabolism (PM) is predominant and stationary phase (48 h) where secondary metabolism (SM) is predominant. At the PM stage, 2971 genes (∼25% of the genome) were upregulated in ΔcclA, including SM clusters for sterigmatocystin (ST), monodictyphenone, emodin, orsellinic acid, austinol, and emericellamides, as well as genes involved in xylan metabolism and oxidative stress response. Conversely, genes controlling cell wall biosynthesis, filamentation, and sexual development were downregulated. At the SM stage, 2798 genes (∼24% of the genome) were upregulated, but ST and terrequinone clusters were markedly downregulated, revealing CclA's dual role as a global repressor and selective activator of SMs. Proteomic assessment confirmed coherent expression patterns (Pearson r = 0.71-0.77) with transcriptomic data, and RT-qPCR validated important regulatory and SM genes (r = 0.9). Phenotypic tests demonstrated that ΔcclA exhibited improved resistance to oxidative, osmotic, and cell wall stress while maintaining conidiation and growth. Overall, these results identify CclA as a principal regulator of SM, development, and stress adaptation. Understanding its dual functions gives a foundation for reducing mycotoxin contamination and enhancing the production of valuable metabolites.
Aspergillus fumigatus is the primary causative agent of aspergillosis. Cryptic species may exhibit variable pathogenic potential and antifungal resistance and, particularly those within the section Fumigati, have significant clinical and environmental relevance. However, the genomic and proteomic bases underlying these differences remain poorly understood. This study presents a comparative analysis of 42 genomes (including five newly sequenced genomes), together with their corresponding predicted proteomes, from A. fumigatus, and from four cryptic species: A. lentulus, A. udagawae, A. felis and A. hiratsukae. Notably, these represent the only genomes currently available for these cryptic species, allowing us to integrate antifungal resistance mechanisms, and virulence factors across the full existing genomic landscape. We showed that A. fumigatus retains a highly conserved core proteome, whereas A. felis and A. lentulus exhibit greater genomic plasticity. Our preliminary findings suggest that azole resistance is primarily driven by species-specific point mutations, which are not shared across the section Fumigati. Secondary metabolism pathways are the main difference observed among section Fumigati, with variations in biosynthetic gene clusters and mycotoxin production. Our findings emphasize the evolutionary balance between genomic conservation and evolutionary divergence in A. fumigatus sensu lato, determining azole resistance and pathogenicity-associated fitness.
Endophytic fungi from Deschampsia antarctica, the southernmost flowering plant, provide insights into the cold adaptation mechanisms of plant-associated fungi in extreme environments. This study presents the genome sequences and comparative analysis of eight fungal isolates from D. antarctica leaves. These Antarctic fungal isolates were analyzed alongside 121 plant-associated fungal genomes to uncover signatures of adaptation and endophytic specialization. Antarctic endophytes show striking patterns, including reduced genome size (∼26.3 Mb on average), streamlined gene content (∼8844 genes), and notably small secretomes (∼288 proteins). Despite this reduced gene repertoire, they maintain a robust set of genes encoding carbohydrate-active enzymes (CAZymes) but lack those for lignin and bacterial cell wall degradation, indicating a symbiotic lifestyle that avoids host damage and predation. One isolate, Alternaria sp. UNIPAMPA017 stood out, with 26% of its genome occupied by transposable elements. Lifestyle, rather than phylogeny, was the main driver of CAZyme and secretome profiles, underscoring ecological convergence. Compared to endophytes from Arabidopsis and Populus, D. antarctica endophytes harbor fewer pectin-degrading enzymes, reflecting their adaptation to the cell wall structure of their monocot host. Together, these fungi reveal a pattern of genomic reduction and functional fine-tuning, hallmarks of life adapted to persist in cold, nutrient-scarce niches.
Fungal mitogenomes are significant for phylogenetic studies, however, constructing trees from full-length mitogenomes with varied sizes remains challenging. Recently, the dramatic increase of newly unannotated mitogenomes has created an urgent need for automated alignment tools. To address this, we developed WMAF, a novel Python-based tool that aligns full-length fungal mitogenomes by identifying and concatenating conserved genomic blocks. It overcomes recombination effects and prevents redundant locus detection. We further applied WMAF to five diverse genera, including Purpureocillium, Fusarium, Saccharomyces, Trichoderma, and Rhizoctonia, and generated mitochondrial trees that effectively identified intrageneric clades, as validated by nuclear trees. The method provides a foundation for advancing fungal phylogenetics and constructing the fungal tree of life.
Histoplasma is a genus of human fungal pathogens that frequently affects immunosuppressed patients. Previous genetic surveys have largely focused on nucleotide-level variation, but much less attention has been given to more complex forms of mutation. Among these, transposable elements (TEs) represent an important class of mobile genetic elements that can alter genome size and play key roles in adaptation and speciation. In this study, we address this gap by examining the content and evolutionary dynamics of TEs in the human pathogen Histoplasma. Using previously published Histoplasma genome assemblies, we quantified TE content across eight phylogenetic species within the genus. Our analyses reveal heterogeneity in the evolutionary patterns of different TE families. The majority of TE orders and superfamilies show strong phylogenetic signal suggesting that phylogenetic relatedness significantly constrains the content of mobile genetic elements. We find no correlation between RNA or DNA TEs and genome size. Together, our results highlight the diverse landscape of TEs in Histoplasma and suggest that future studies should investigate their impact on genome evolution, fitness, and virulence.
