Macrophomina phaseolina, a soilborne necrotrophic pathogen causing charcoal rot across more than 500 host plant species, poses a significant and escalating threat to global food security under climate change-driven abiotic stresses. Despite its destructive importance, the molecular architecture underlying its broad host range and virulence versatility remains poorly characterized. De novo whole-genome sequencing, assembly, and multi-platform functional annotation were performed using BUSCO v6.0.0, eggNOG-mapper, Gene Ontology, KEGG, COG, PHI-base, SignalP 6.0, DeepTMHMM, EffectorP 3.0, CAZy, and antiSMASH. The draft genome assembly of M. phaseolina comprised 50.2 Mb across 1551 contigs (N50 = 125.1 kb, L50 = 118; GC = 51.9%) and showed 99.3% BUSCO completeness and 14,633 predicted protein-coding genes. Functional annotation revealed 10,954 genes classified across COG, GO, and KEGG databases, GO and KEGG over-representation analyses identified significant enrichment of extracellular, carbohydrate- and cell-wall-associated functions in the predicted secretome, including polysaccharide metabolism and degradation, together with selected metabolic and host-interaction pathways. PHI-base comparative screening identified 2000 pathogenicity-associated homologs showing strong conservation with virulence determinants from Fusarium graminearum and Magnaporthe oryzae. Secretome analysis yielded 1070 extracellular proteins, including 254 apoplastic effectors, 124 cytoplasmic effectors, and 135 cysteine-rich apoplastic effectors. CAZyme annotation identified 639 enzymes spanning six classes, with glycoside hydrolases (301) constituting the largest category. AntiSMASH analysis detected 73 secondary metabolite biosynthetic gene clusters enriched in terpene, NRPS, and polyketide synthase pathways. These findings reveal a highly diversified, multifactorial virulence arsenal in M. phaseolina, providing a comprehensive genomic framework for advancing host–pathogen interaction research and developing targeted disease management strategies.
The architecture of filamentous fungi is essential for foraging and the transport of resources, yet little is known about how these structures emerge during early development. We present a comparative, quantitative analysis of early mycelial formation in the model systems Trichoderma atroviride and Neurospora crassa. Using label-free microscopy and automated image processing to extract networks from colonies, we characterized the temporal evolution of two-dimensional (2D) hyphal networks beginning shortly after single-cell germination. We applied the framework of graph theory to evaluate metrics that describe growth dynamics, structure and connectivity for the two species. Both fungi exhibited exponential increase in hyphal tips and branching points (node number), hyphae (edge number), and total mycelium length, consistent with properties of filamentous growth. However, N. crassa displayed faster expansion, greater spatial anisotropy, and a more hierarchical organization dominated by hyphae with high connectivity, whereas T. atroviride formed more isotropic and decentralized networks. Notably, both species developed essentially tree-like architectures and converged to similar fractal dimensions, indicating comparable properties to fill 2D space. These results suggest that early networks in T. atroviride are decentralized, robust and resilient to localized damage, whereas in N. crassa they are hierarchical, favoring rapid and efficient spatial expansion.
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.
Candida glabrata is an important opportunistic fungal pathogen affecting immunocompromised individuals. Yeast cells exist in logarithmic-phase (LP) and stationary-phase (SP) states, with SP cells exhibiting high resistance to oxidative stress. Here, we show that LP cells become resistant to oxidative stress when exposed to nutritional stress and to conditioned medium from SP cells (CM, SP cell-free conditioned/spent medium). This adaptation requires the induction of CTA1 (catalase I) and the transcription factors (TFs) Yap1, Skn7, Msn2, and Msn4. In addition, CM reduces reactive oxygen species (ROS) production. Key secreted metabolites identified in the C. glabrata secretome include 1-dodecene (C12) and the aromatic alcohols (AAs) tyrosol and tryptophol. These metabolites increase H₂O₂ resistance in LP cells, but C12 induces the expression of CTA1, indicating that these are signaling molecules that confer resistance to ROS but through different pathways. C12-dependent induction of CTA1 depends on Yap1 and Skn7, while induction of CTA1 by nutrient starvation requires Msn2 and Msn4 suggesting different signal transduction pathways. RNA-seq analysis reveals that CM, C12, and AA up-regulate oxidative stress response genes, with C12 and CM inducing transcriptional profiles that resemble SP cells. This transcriptional reprogramming enhances OSR in LP cells, highlighting the role of quorum sensing molecules (QSM) in adaptive defense mechanisms of C. glabrata.
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.
