Histone demethylases regulate epigenetic modifications and DNA damage repair in fungal pathogens, yet their specific functions in Magnaporthe oryzae remain poorly understood. This study identifies MoRph1, a JmjC domain-containing histone demethylase that interacts with the COMPASS complex. Targeted deletion of MoRph1 resulted in significantly reduced vegetative growth, impaired conidiation, and defective appressorium formation. The mutant displayed compromised appressorial turgor pressure due to delayed degradation of glycogen and lipid reserves, leading to inefficient host penetration and attenuated virulence on rice and barley. MoRph1 localized to the nucleus, and its absence caused increased nuclear abnormalities under DNA damage stress, suggesting impaired genome stability maintenance. Biochemical analysis confirmed that MoRph1 specifically demethylates histone H3 lysine 36 trimethylation. Transcriptome analysis revealed altered expression of genes associated with DNA replication, mismatch repair, and oxidative stress response. These results establish MoRph1 as a crucial epigenetic regulator coordinating fungal development, infection structure function, energy mobilization, and DNA damage repair. This study underscores the importance of chromatin-level regulation in fungal pathogenicity and provides a foundation for future evaluation of MoRph1 as a potential antifungal target.

Indole-3-acetic acid (IAA) is a central auxin regulating plant growth and developmental plasticity, including cell division, elongation, vascular differentiation, and root architecture. Beyond plants, many fungi—including endophytic fungi that reside within plant tissues without visible disease symptoms—can synthesize IAA and thereby modulate plant performance and plant–fungus interactions. However, fungal IAA biosynthesis remains less resolved than bacterial or plant pathways, and mechanistic evidence is uneven across taxa. This review summarizes recent (2020–2025) advances in IAA-producing endophytic fungi, the main proposed biosynthetic routes and intermediates, and methodological considerations for attributing IAA production to the fungal partner. The reported associations of fungal IAA with beneficial interactions are then discussed, including growth promotion, stress tolerance, and interaction-mediated changes in the root system’s architecture, with emphasis on the concentration- and context-dependent nature of plant responses. Overall, fungal IAA is associated with diverse plant–fungus interactions, as discussed in this review.

High-quality genomic DNA extraction remains a major bottleneck for fungal genomics, particularly for worldwide aerobic and non-photosynthetic mushroom species that rely on their rigid cell walls, interference between metabolites, polysaccharides, etc., and complex genomes. This study systematically compares five DNA extraction protocols involving four distinct sample preparation procedures (fresh (A), filtered (B), frozen (C) and cryogenic mycelium (D)) across mycelial cultures of eight Tunisian fungal strains representing Ascomycota and Basidiomycota to identify the optimal combination for genomic DNA extraction from mycelium. The eight phylogenetically diverse fungal species were analyzed using short-read (MiSeq and NextSeq550) and/or long-read (MinION Mk1C) sequencing technologies, giving a depth coverage between 3.7× and 83×. The generation and quality of the assemblies were assessed within the Galaxy platform, which revealed a gap percentage of 0–0.509%. Taxonomic characterization and phylogenetic inference were performed with SANGER technology using the Internal Transcribed Spacer (ITS) and D1/D2 region of the 26S rRNA gene, assigning the species to our eight different strains: Clitopilus baronii (BS6), Porostereum spadiceum (BS200), Trametes versicolor (BS22-9), Schizophyllum commune (BS23-13), Gloeophyllum abietinum (BS23-14), Irpex laceratus (BS100), Trichoderma asperellum (GC9) and Trichoderma harzianum (S3). The optimized DNeasy Plant Pro Kit protocol with cryogenic biomass treatment presents a safe and cost-effective method for fungal genome sequencing and taxonomic resolution. This integrated comparative evaluation of extraction for sequencing identifies an optimal Qiagen-based extraction strategy combined with cryogenic treatment for eight diverse Tunisian fungal species, guiding method selection based on specific cell wall characteristics rather than proposing a universal protocol limited by unequal replication and strain numbers.

Coccidioidomycosis (CM) is a fungal infection caused by the inhalation of airborne arthroconidia released by Coccidioides spp. Endemic areas include the southwestern United States, Mexico, and parts of South America. The estimated CM cases exceed 300,000 per year. Current treatment for CM is limited and primarily relies on antifungals such as azoles and Amphotericin B. Moreover, concerns about drug cytotoxicity and rising of azole-resistance underscore the need for alternative or adjunctive immune-based prevention and therapies. This review presents recent advances in immune CM intervention and discusses the potential application of emerging antifungal immunotherapy to treat invasive CM. For preventive vaccination, we reviewed the recent development of subunit protein vaccines and mRNA-based vaccines. Prospects for formulating vaccines with potent adjuvants and delivery systems to enhance protective immunity against CM are also provided. For immunotherapy, we reviewed recent reports of antifungal treatment with immunomodulators, CAR-cells and checkpoint inhibitors. Finally, we discuss the application of experimental animal and in vitro models for advancing vaccine and immunotherapeutic development for CM.

(1) Background: Improving nitrogen use efficiency in peanuts is essential for achieving a high yield with reduced nitrogen fertilizer input. This study investigates the role of the fungal endophyte Phomopsis liquidambaris in regulating nitrogen utilization throughout the entire growth cycle of peanuts. (2) Methods: Field pot experiments and a two-year plot trial were conducted. The effects of Ph. liquidambaris colonization on the rhizosphere microbial community, soil nitrogen forms, and peanut physiology were analyzed. (3) Results: Colonization by Ph. liquidambaris significantly suppressed the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the rhizosphere at the seedling stage. This led to a transient decrease in nitrate and an increase in ammonium availability, which enhanced nodulation-related physiological responses. Concurrently, the peanut-specific rhizobium Bradyrhizobium sp. was enriched in the rhizosphere, and the root exudates induced by the fungus further stimulated nodulation activity. These early-stage effects promoted the establishment of peanut–Bradyrhizobium symbiosis. During the mid-to-late growth stages, the fungus positively reshaped the composition of key functional microbial groups (including diazotrophs, AOA, and AOB), thereby increasing rhizosphere nitrogen availability. (4) Conclusions: Under low nitrogen fertilization, inoculation with Ph. liquidambaris maintained yield stability in long-term monocropped peanuts by enhancing early nodulation and late-stage rhizosphere nitrogen availability. This study provides a promising microbe-based strategy to support sustainable legume production with reduced nitrogen fertilizer application.

Cyclocybe chaxingu is a well-known edible fungus in China, in which pileus size and color are key traits determining its commercial value. However, the molecular genetic mechanisms underlying the morphological development of its pileus remains limited at present. To address this, our study first completed the high-quality genome assembly of the monokaryotic strain Ag.c0002-1 of albino C. chaxingu, anchoring it to 13 chromosomes via Hi-C technology. The final genome size was 51.7 Mb with a GC content of 51.06%, and 11,332 protein-coding genes were annotated. Phenotypic observations and comparative transcriptome analyses were then conducted on the pilei of the brown cultivar Ag.c0067 and the white cultivar Ag.c0002 at the primordium, elongation, and mature stages. Phenotypic analysis revealed continuous pileus expansion accompanied by progressive color lightening in both cultivars during development. Comparative transcriptomic analyses revealed significant differences in gene expression patterns between the two cultivars across developmental stages. KEGG enrichment analysis indicated that pileus expansion is closely associated with pathways related to DNA replication, cell cycle of yeast, carbon metabolism, and carbohydrate digestion and absorption. Among these, differentially expressed genes involved in cell division tended to be downregulated, whereas genes associated with energy metabolism and substance transport were upregulated, providing the necessary energy and material support for pileus growth. Changes in pileus pigmentation were primarily associated with tyrosine metabolism, betalain biosynthesis, tryptophan metabolism, and melanogenesis pathways. Notably, the downregulation of tyrosinase genes and the upregulation of glutathione S-transferase genes during development may represent major molecular mechanisms underlying pileus color lightening. Overall, this study provides important insights into the molecular mechanisms regulating pileus development and pigmentation in C. chaxingu, while also offering valuable theoretical support for genetic analysis of basidiomycete morphogenesis and the molecular breeding of edible mushrooms.

The assembly of telomere-to-telomere (T2T) genomes is essential for understanding genomic architecture, especially in fungal pathogens with complex karyotypes, such as Colletotrichum lini, causing flax anthracnose disease. This study provides optimized guidelines for the T2T genome assembly using Oxford Nanopore Technologies (ONT) R9.4.1 and R10.4.1 sequencing data processed with the Hifiasm 0.25.0 assembler (with --ont module). We analyzed ONT sequencing data for four C. lini strains and compared basecalling tools (Guppy and Dorado), read filtration strategies (quality thresholds Q10/Q15 and length cut-offs 5 kb/10 kb), and genome coverage levels from 5× to 160×. Our results demonstrated that Dorado-basecalled reads consistently had higher average quality, especially the R10.4.1 data, leading to improved telomere resolution and complete mitochondrial genome assembly. Moderate genome coverage (40–65×) combined with Q15 quality and 5 kb length filtration for R10.4.1 data, or Q10 and 5 kb for R9.4.1 data, produced the most contiguous and complete assemblies. Overfiltration of reads by length and quality or conversely excessive coverage (>90×) reduced assembly quality, causing fragmentation or erroneous chromosome merging. With optimized parameters of ONT R9.4.1 and R10.4.1 sequencing data preprocessing, Hifiasm efficiently generated T2T and near-T2T assemblies of C. lini genomes: 53.7–56.1 Mb length, 13–30 contigs, 12–13 chromosomes (including 3–12 T2T chromosomes), complete mitochondrial genome, and >98.5% BUSCO completeness. These findings provide a solid framework for ONT-based fungal genome assembly, facilitating future research on genomic variation and pathogenicity in Colletotrichum and related genera.

This study investigated the fungal species associated with symptomatic cultivated Brassica crops in Apulia, Southern Italy, during the 2022–2023 growing seasons. Twenty-two samples from Brassica oleracea var. botrytis, B. oleracea var. italica, and B. rapa var. cymosa showing stunting, wilting, necrotic spots, and lesions were analyzed using morphological and molecular analyses. A total of 259 fungal isolates were obtained, mainly belonging to the genera Alternaria, Plectosphaerella, Fusarium, and Sclerotinia, with Alternaria and Plectosphaerella being the most frequent. Microsatellite PCR (MSP-PCR) profiling revealed considerable genetic diversity within the Alternaria and Plectosphaerella genera, whereas Fusarium and Sclerotinia showed uniform profiles. Multilocus analyses (ITS, tef-1α, rpb2, Alt-a1, and gapdh) identified nine species as Alternaria alternata, A. brassicicola, A. japonica, Fusarium solani species complex, Plectosphaerella cucumerina, P. pauciseptata, P. plurivora, Sclerotinia sclerotiorum, and Stemphylium vesicarium. While Alternaria, Fusarium, and Sclerotinia species are well-known Brassicaceae pathogens, P. pauciseptata, P. plurivora, and S. vesicarium have been detected here for the first time on cultivated Brassica crops worldwide. These findings highlight significant intraspecific diversity among the detected fungi and expand the current knowledge of fungal diversity associated with symptomatic cultivated Brassica plants.

The Poaceae family, commonly known as grasses, is one of the most strategically important plant groups on earth. They are globally distributed, found in virtually every terrestrial habitat on earth, from deserts and grasslands to forests and wetlands. An investigation was conducted on the fungi associated with grasses in Sichuan and Guizhou Provinces, China. Based on morphological characteristics and multi-locus phylogenetic analyses (from Maximum Likelihood (ML) and Bayesian Inference (BI)) of combined LSU, SSU, ITS, and tef1-α sequence data, a new genus, Neokeissleriella, and three novel species—Keissleriella guttata, K. sichuanensis, and Neokeissleriella fusispora—were introduced. Two new host records of Keissleriella caraganae, K. yunnanensis and a new geographical record of K. gloeospora in Sichuan Province, China, are reported. To substantiate the newly established taxa, detailed morphological descriptions and illustrations are provided and supported with molecular phylogenetic analysis. This study broadens the understanding of fungal diversity on Poaceae hosts in Sichuan and Guizhou provinces, China, revealing the high potential for identifying novel taxa.

Background: Nosocomial infections represent a significant clinical burden due to high morbidity, mortality and healthcare costs. Invasive fungal infections, particularly those caused by Candida species, are of growing concern due to increasing antifungal resistance, which limits therapeutic options and worsens patient outcomes. This study aimed to characterize the prevalence, species distribution, antifungal susceptibility profiles, and molecular mechanisms of resistance in clinical Candida isolates from hospitalized patients. Methods: A cross-sectional study was conducted involving 55 hospitalized patients, yielding 60 isolates from blood, secretions, fluids, and catheter tips. Species identification was performed using chromogenic media and confirmed by MALDI-TOF MS. Antifungal susceptibility testing followed CLSI M27-A4 broth microdilution guidelines for amphotericin B, fluconazole and 5-flucytosine. Gene expression of ERG2, ERG11 and MDR1 was evaluated by RT-qPCR after exposure to subinhibitory antifungal concentrations using the 2−∆∆Ct method. Results:Candida albicans was the most frequent species, followed by Nakaseomyces glabratus, C. tropicalis and C. parapsilosis. Resistance varied among species, with elevated rates for fluconazole. ERG2 was notably overexpressed in amphotericin B-resistant isolates, while ERG11 and MDR1 showed species-dependent variation. Conclusions: Resistance mechanisms in Candida are species-specific and drug-dependent. Accurate species identification and understanding their molecular profiles are essential to guide targeted antifungal therapy and improve clinical outcomes.