Species in the Asteraceae, either cultivated or wild, are strongly affected by downy mildews. Despite its importance, the broad species concept used for decades and the lack of molecular data for the genera Plasmopara and Bremia have obscured the true diversity and distribution of downy mildew-causing species in Asteraceae. Given the great relevance of downy mildew-causing oomycetes in Asteraceae, the objective of this study was to investigate the phylogenetic relationships of downy mildew-causing oomycetes in lettuce and other Asteraceae in Brazil. Based on molecular and morphological data, we describe a new species, Plasmopara pernambucoensis sp. nov., and present the first record of Plasmopara sphagneticolae in Brazil and South America, as well as the first record of Bremia sonchicola in Brazil.
The integration of artificial intelligence (AI) into fungal classification and identification offers new opportunities to advance mycological research and accelerate fungal detection and diagnosis in healthcare, agriculture, and environmental monitoring. This review summarizes current single-modality AI approaches investigated in literature across DNA sequences, colony and microscopic imaging, spectral profiles, and metadata. It outlines their taxonomic interpretability and applicability, emphasizing the impact of reference coverage, model and benchmark design across modalities on performance and real-world generalization. Persistent challenges, including class imbalance, closed-set bias, and taxonomic concept drift, are also discussed. Building on these insights, we present a conceptual and forward-looking multimodal machine-learning framework based on a late-fusion strategy to exploit the complementarity between genotypic and phenotypic data for fungal identification. The framework treats DNA sequences and images as core modalities and incorporates collection data as informative priors. The development of large-scale, partially or completely paired datasets that integrate multiple data sources represents a necessary first step toward its future implementation and empirical validation.
Aspergillus fumigatus sensu lato comprises several cryptic species that are indistinguishable by morphology but differ in antifungal susceptibility and clinical relevance. Their frequent misidentification as A. fumigatus sensu stricto, has been associated with inappropriate therapy and poorer clinical outcomes. Reference identification relies on sequencing specific genes, which is costly and labor intensive. In this study, a multiplex RT-PCR assay combined with melting curve analysis was developed and validated for the rapid discrimination relevant cryptic species within Fumigati section. Primers targeting established sequencing loci were designed to specifically identify A. fumigatus, A. lentulus, A. felis complex and A. udagawae. Singleplex assays showed highly specific melting profiles with no cross-amplifications. In multiplex, specificity was maintained by supplementing the reaction with PCR enhancers, achieving excellent analytical performance (Area Under Curve 0.93 to 0.97), confirmed using 41 isolates. Method validation under a Portuguese surveillance program was performed for six months. The newly developed assay identifies Fumigati isolates to species level within 1 h and 40 min after DNA extraction, while sequencing required 1–2 days, with full concordance between methods. Additionally, manual and automated DNA extractions yield reliable results. This study reports, to the best of our knowledge, the first RT-PCR method enabling species-level identification within section Fumigati. The assay provides accurate and cost-effective identifications, while using a universal platform for surveillance settings, with potential for future expansion.
Four new species of Cruentomycena, C. clarophylla, C. gracilis, C. hymenidermatoides and C. pharica, are described from Vietnam based on morphology and nrITS phylogenetic evidence. Specimens were collected in the mountain evergreen mixed forests of Bidoup–Nui Ba National Park and Kon Chu Rang Nature Reserve, as well as in the bamboo forests of Bai Tu Long National Park. Illustrations, including photos of basidiomata in situ and microscopical structures, are provided. In addition to traditional squash preparations, fixed vibratome sections of basidiomata were examined, which proved particularly effective for the precise localization of hymenial cystidia and the visualization of the structure of the pileipellis. Phylogeny reconstructed from nrITS dataset revealed that the new species form four independent lineages, with C. gracilis and C. hymenidermatoides forming a group sister to C. uttarakhandina. Morphologically, the presence of pleurocystidia in these three species distinguishes them from all other known members of the genus. As a tentative hypothesis, C. clarophylla and C. pharica form sister clades to C. allochroa, and C. orientalis respectively, but these relationships require a more thorough investigation. Morphological features such as the structure of the pileipellis, variation in cheilocystidia shape and size, presence or absence of pleurocystidia among newly described and known species of the genus, are compared. The global distribution and substrate preferences of Cruentomycena specimens documented in scientific literature are summarized, noting their confinement to small woody debris and leaf litter.
Seven yeast strains, isolated from an alpine peatland, plants and insect frass in Europe (Italy, Russia and Germany), were accommodated in three new species belonging to the subphylum Pucciniomycotina. Phylogenetic analyses based on sequences of the D1/D2 domains of the 26S ribosomal RNA and the internal transcribed spacer (ITS) region placed two novel species closely related to Halobasidium xiangyangense and Halobasidium phyllopilum (Cystobasidiomycetes), while a third one was found to be closely related to Sterigmatospora layueensis (Agaricostilbomycetes). The tree topology positioned the Halobasidium isolates in two distinct subclades. Physiological characterization showed that the three novel species differed from their closest relatives. Sexual structures were not observed. These new species are primarily associated with the phyllosphere. The species described here are Halobasidium palustre sp. nov. (PYCC 10024T; MycoBank MB 862292), Halobasidium insectorum sp. nov. (PYCC 10357T; MycoBank MB 862293) and Sterigmatospora alpina sp. nov. (PYCC 10025T; MycoBank MB 862295).
The genus Diplocarpa is accepted with five lignicolous species: D. bloxamii (type of Diplocarpa), D. constans, D. fischeri comb. nov. (type of Poloniodiscus), D. iberica sp. nov., and D. irregularis (type of Ionomidotis). The North American D. irregularis and European D. fischeri have previously been considered synonyms. Australian records under the name D. bloxamii could belong to a sixth species. The genus is characterized by an ionomidotic reaction, inamyloid asci with thick-walled apex, paraphyses with lanceolate, septate, often thick-walled and pigmented protruding parts, and ellipsoid, biguttulate ascospores of uniform size and shape. Hairs on the receptacle similar to the paraphyses are typical, though absent in D. fischeri and D. irregularis. All five species are described in detail, predominantly from recent collections but also from type specimens. Anamorphs in Diplocarpa occur as pulveraceous mats or synnemata. They have been mostly overlooked in the past, although the D. bloxamii synnemata were seen in the present study in at least 25 of 42 specimens studied. Diplocarpa anamorphs exhibit the same ionomidotic reaction as the teleomorph. Their fertile part is composed of brownish, catenate conidiophores forming brownish, ellipsoid- to limoniform, non-septate blastoconidia in acropetal chains. Only in D. constans no anamorph was found. The connection between anamorph and teleomorph was confirmed for D. bloxamii and D. irregularis by rDNA comparison. Previously, members of Diplocarpa have been referred to five different families because of emphasis on single morphological traits: D. bloxamii to Hyaloscyphaceae and later Dermateaceae (Helotiales), D. irregularis to Helotiaceae, Dermateaceae, and Leotiaceae (Helotiales), and D. fischeri to Sarcoscyphaceae (Pezizales). Species of Diplocarpa grow on rotten hygric wood and bark of angiosperms. A possibly parasitic connection of D. bloxamii with black rhizomorphs of Armillaria was occasionally noted.
The present study is the first observation of mycoparasitic behavior in the predominantly plant-associated fungal genus Diaporthe. Several isolates of the Phomopsis dieback pathogen Diaporthe eres s.l. were obtained from grapevine and identified by sequencing the internal transcribed spacer, translation elongation factor 1-α, and β-tubulin loci. The interactions of the isolates with Botrytis cinerea strains were examined by detailed microscopic analysis. All the tested isolates showed necrotrophic mycoparasitism against the target organism. Additional experiments with a D. eres s.l. isolate showed that mycoparasitism was also expressed against a Botryosphaeria dothidea target organism, a causal agent of Botryosphaeria dieback, another grapevine trunk disease syndrome. In addition to the first description of the mycoparasitism of D. eres, the study points out the complexity of microbial interactions established by trunk disease pathogens.
This study summarizes data on the genus Micropsalliota obtained over 15 years. The specimens were collected in 18 locations in Vietnam, including protected areas. In sum, nine species are described as new to science, and additionally 17 species are reported as new to Vietnam. Among them eleven are nested within the clade /bifida, one belongs to /megaspora, seven to /globocystis, two to /furfuracea, one to /pleurocystidiata, three to /lateritia, and one species belongs to an unidentified clade. The study provides photographs of macrocharacters, drawings of microscopic structures, detailed descriptions of 26 identified species with comments and comparisons, as well as a phylogenetic analysis based on the nuclear ribosomal internal transcribed spacer (nrITS) region and the large subunit ribosomal RNA gene (nrLSU).
Fuscoporia (Hymenochaetaceae) is a genus of wood-decaying polypores widely distributed in tropical and temperate forests. Despite recent advances, its taxonomy remains challenging, especially for resupinate species. In this study, we describe three new resupinate species of Fuscoporia from Brazil combining morphological and phylogenetic analyses using ITS and nrLSU markers. The new taxa F. bahiana and F. serrana are placed within the F. ferrea group, whereas F. imperatrizensis is recovered as a sister lineage to the F. ferruginosa group. An identification key to Neotropical Fuscoporia species is also provided to support further taxonomic and ecological studies.
The mitochondrial transcriptome of fungi remains poorly characterized beyond protein-coding genes. Using long-read PacBio RNA sequencing, we report the first evidence for putative mitochondria-encoded long non-coding RNAs (lncRNAs) in a fungal organism, discovered in two isolates of the phytopathogenic ascomycete Monilinia laxa. A total of 15 and 12 putative lncRNAs were identified in isolates Ni-B3-A2 and MM-B4-A4, respectively, including sense-strand transcripts and natural antisense transcripts (NATs) positioned upstream of or overlapping core mitochondrial genes. Additionally, putative free-standing transcripts from intergenic homing endonuclease genes (HEGs) are reported for the first time in a fungal species. These findings provide evidence for previously undescribed transcriptional diversity in fungal mitochondria, establishing a framework for future functional investigation of mitochondrial non-coding transcriptomes across the fungal kingdom.
Systematic mycology relies on a large body of specimens for comparative analyses and taxonomic conclusions. However, many species, especially of plant-parasitic microfungi (Fungi and Oomycota) occur only sporadically and often cannot be cultured on artificial media, as they rely on living plant cells for their nutrition. This is further complicated by the difficulties inherent with old herbarium specimens, which cannot always be readily investigated using molecular phylogenetics. Thus, recent collections are of utmost importance. However, they are often lacking due to constraints of the current academic system, which is focused more on output than on broadening the basis for future studies by collections. Citizen scientists can play a vital role in filling this gap. We exemplify this in the current article, on the example of the late German amateur botanist and mycologist Horst Jage (1935–2024), who collected tens of thousands of specimens of plant parasitic fungi (Fungi and Oomycota) on various host plants throughout Central Europe and deposited them in public herbaria. These specimens were thus made accessible to the scientific community, particularly for DNA sequencing and subsequent phylogenetic analyses. The impact of Jage’s collections on taxonomy and new species concepts within the Peronosporales, Erysiphaceae (Helotiales), and other groups of plant-parasitic fungi is highlighted. His effective collecting methods are briefly described, and the publications and 33 type specimens based on his material have been compiled. This highlights the important role of such collections from citizen scientists, and emphasizes the need to support their endeavours, which are indispensable for the effort towards the complete inventory of extant species.
This study presents the results of fungal surveys conducted between 2023 and 2025 to investigate the biodiversity of the genus Pseudosperma across multiple sites in central Italy. Sampling encompassed a broad range of habitats, including thermophilous woodlands on mid-hill slopes dominated by Quercus spp., riparian zones dominated by willow and poplar, and urban parks characterized by varying altitudes and vegetation types. Based on integrated morphological and molecular evidence, we describe two new species: P. polymorphocystidiatum and P. olivaceoluteum. In addition, we report four species for the first time from Italy: P. aureocitrinum, P. permelliolens, P. ushae, and P. pollucis. Phylogenetic analyses were performed using Internal Transcribed Spacer (ITS) and nuclear large subunit (nc LSU rDNA) regions of ribosomal DNA, and part of the RNA Polymerase II second largest subunit gene (RPB2), complemented by detailed morphological comparisons with related taxa. These findings refine the phylogeny of the Pseudosperma clade and contribute to updating the checklist of basidiomycetes in central Italy.
Two morphologically similar fructicolous species are here assigned to the genus Hymenoscyphus. However, they exhibit a high level of genetic divergence. They form short- to long-stipitate apothecia on fallen pits of Cornus spp. One of them, H. corni-maris, was found exclusively on C. mas so far, while H. corni-sanguineae was recorded in Europe on C. sanguinea and in China on C. controversa. The two species share an ectal excipulum of textura prismatica(-porrecta), living paraphyses containing refractive vacuolar guttules, euamyloid ascus apical rings of the Hymenoscyphus-type, and ciborioid ascospores of similar size and low lipid content. Hymenoscyphus corni-maris differs from H. corni-sanguineae by a white vs. yellowish-ochraceous disc and asci arising from croziers vs. simple septa, respectively. No sporulation was observed in pure culture of both species. Two synonymous names exist in the literature. Sclerotinia corni from Czechia on C. mas is illegitimate (Art. 3.1) as it is a later homonym of a species now recognised as Monilinia corni. Lanzia glandicola var. cornicola from China on C. controversa was published at the varietal level only. Both synonymies were clarified by reexamination of the holotypes and by DNA sequence analysis in L. glandicola var. cornicola. Based on our phylogenetic analysis of ITS + LSU rDNA, H. corni-maris clustered in a strongly supported subclade comprising different anamorph- and teleomorph-based taxa, which were recently recognised as a new family, Tricladiaceae. Hymenoscyphus corni-sanguineae nested in another strongly supported clade that comprises species such as H. repandus and H. menthae, as well as two monotypic genera, the cleistocarpous Amylocarpus and the anamorphic Goniopila. Except for the latter two taxa, all these clades have morphologically similar apothecia and can hardly be separated into different groups based on their teleomorphs. For this reason, we prefer to adopt Hymenoscyphus in a broad, paraphyletic sense.
Species diversity of Penicillium and Talaromyces colonizing the leaf litter of Pinus luchuensis was evaluated on Chichijima and Hahajima in the Bonin Islands. In total, 318 isolates were obtained from leaf litter collected at one site on each island, and species were identified based on partial β-tubulin (BenA) sequences. Consequently, 26 Penicillium and six species of Talaromyces were identified, including three novel species. These novel species were described in this study: P. aurantium sp. nov. (NBRC 116976 T), T. pinistramentus sp. nov. (NBRC 116973 T), and T. sanguinolentus sp. nov. (NBRC 116975 T). Multi-locus phylogeny (BenA, calmodulin, and RNA polymerase II second largest subunit with or without rRNA internal transcribed spacer) and morphological observations were conducted on the novel species. Penicillium aurantium formed a well-supported independent clade in section Sclerotiorum series Herqueorum, which is a sister to Penicillium herquei. Penicillium aurantium can be morphologically distinguished from P. herquei by the color of the pigment on Czapek yeast extract agar, the colony color on dichloran 18
Fungi constitute a highly diverse and ecologically important kingdom with central roles in nutrient cycling, symbiosis, and pathogenesis. The regulation of these processes involves multiple layers of control, with transcription factors (TFs) playing key roles in shaping condition-specific gene expression within complex regulatory networks. In particular, fungal GATA TFs are a family of DNA-binding proteins characterized by a conserved GATA zinc finger motif that recognizes the consensus sequence WGATAR (W = A/T, R = A/G) in target gene promoters. They function as key regulators of light response, nitrogen and iron metabolism, secondary metabolism, and reproduction. Despite their functional importance, structural analyses of fungal GATA TFs across diverse species remain limited, hindering understanding of their structural diversity and evolutionary patterns. To address this gap, this study conducted a comprehensive genome-wide comparative analysis of the structural and molecular features of 7,846 fungal GATA TFs from 796 species across eleven divisions, sourced from EnsemblFungi and MycoCosm. Domain architecture, GATA motif diversity, and motif-domain associations of fungal GATA TFs were systematically characterized, and motif diversity was further compared with plant and animal GATA TFs to place fungal GATA evolution in a broader eukaryotic context. Phylogenetic relationships based on GATA domain sequences enabled the identification of putative orthologous groups and the inference of lineage-specific functional diversification. Structural predictions of representative fungal GATA TFs were performed to support functional interpretation. In addition, order-level analyses of Dikarya GATA TFs revealed lineage-specific architectural patterns. Taken together, this integrative analysis provides a comprehensive framework for understanding the evolutionary and functional diversification of fungal GATA TFs.
Parasitic oomycetes are ubiquitous in marine ecosystems, yet their phylogeny remains poorly characterized. While metabarcoding confirms their high diversity, the lack of formal descriptions leaves most of the sequences unclassified. In this study, we describe Miracula nipponica sp. nov., a parasitic oomycete from Sagami Bay, infecting the bloom-forming diatom Leptocylindrus sp. Phylogenetic analysis based on 18S rDNA sequences showed that all isolated strains were placed as a distinct lineage within the genus Miracula. Detailed microscopic observations revealed the formation of primary and secondary zoospores in the new species life cycle, with an occasional cyst cluster formation at the orifice of the discharge tube. Notably, the encysted stage demonstrated a long-term viability in the absence of hosts. Finally, laboratory experiments revealed a broad host range with low infection prevalence that includes other common diatoms from the study area. As the first parasitic oomycete infecting phytoplankton described in Japanese coastal waters, this study highlights their overlooked diversity and widespread presence of fungi-like organisms in marine ecosystems.
The genus Leotia (Leotiaceae) is globally distributed with approximately 45 named species and several subspecies, varieties and forms. Persoon first proposed Leotia in 1794. Most of the taxonomic work has been done in the last 100 years with the most recent species added in 1982 by Otani. Here we describe L. chiricana, a new species associated with tropical monodominant forests of Oreomunnea mexicana (Fagales, Juglandaceae) in Panama and Trigonobalanus excelsa (Fagales, Fagaceae) in Colombia. This new species is easily recognized by its distinctive vivid dark greenish blue color as compared to other species in the genus. The structure of the apothecia also differs in having only one gelatinous layer instead of two in the stipe. Phylogenetic analyses using ITS ribosomal DNA and a variable region of the RNA polymerase II (RPB2) gene strongly support a monophyletic L. chiricana clade that is sister to L. lubrica group I sensu Zhong and Pfister. Our field data showed that L. chiricana was more abundant in habitats with soils of high nitrogen availability. Illumina sequence data (ITS2) and stable isotope analysis suggest that this species forms mycorrhizal associations with O. mexicana. The discovery of this Leotia species from Panama and Colombia contributes to the knowledge of the understudied and diverse communities of ectomycorrhizal fungi within the Neotropics.
Damping-off disease caused by Rhizoctonia solani is a devastating soil-borne disease that severely impacts Pinus sylvestris var. mongolica seedlings in forest nurseries, often leading to significant economic losses. To develop an environmentally sustainable control strategy, this study evaluated the individual and combined effects of the biocontrol fungus Trichoderma virens T43 and the ectomycorrhizal fungus Suillus luteus N94 against R. solani. In vitro confrontation assays demonstrated that both fungi exhibited strong antagonistic activity, with T43 and N94 inhibiting R. solani growth by 58.8
Rhizopogon species are important ectomycorrhizal (ECM) symbionts of Pinaceae and play a vital role in seedling establishment. Although nearly three hundred Rhizopogon species have been recorded globally, Asian taxa remain poorly characterized. This study reported the first confirmed occurrence of Rhizopogon in Vietnam and the first evidence of its ECM association with Pinus kesiya. Field surveys in P. kesiya forests of Lam Dong Province (Vietnam) yielded three basidiomata and a cluster of ECM root tips. Both morphological features and ITS-based phylogenetic analysis identified the basidiomata and ECM fungal partner as Rhizopogon boninensis, which was previously considered endemic to the southern islands of Japan. Amplicon sequencing of bulk soil samples further confirmed the presence of R. boninensis propagules in the local forest ground. The in vitro co-culture of P. kesiya seedlings with R. boninensis successfully produced ECM root tips. The ECM seedlings exhibited significantly enhanced height, dried biomass, and root development, respectively 1.7, 2.9, and 3 times compared with non-inoculated controls. These results extend the known distribution of R. boninensis and highlight its potential as a native-compatible bioinoculant to support P. kesiya propagation and reforestation across Southeast Asia.
This study presents an updated molecular phylogeny of Allographa, including 5 new species and 5 known species from the Western Ghats of India. Utilizing mtSSU, nrLSU and RPB2 as molecular markers, we evaluated species boundaries and evolutionary relationships within the genus. The newly described species are: A. persistinspersa, differing from A. altamirensis in having a hymenium inspersion which persists in KOH (type A) and slightly broader, regularly muriform ascospores; A. semicarbonisata, differing from Graphis subintermedians in having an apically to laterally carbonized exciple, 1–2 ascospores per ascus, and larger ascospores; A. keralensis, differing from G. nigroglauca in having a complete thalline margin; A. nayakae, differing from A. macella in having elongate, irregularly branched, erumpent lirellae; and A. paraconsanguinea, differing from A. calcea in having an entire, laterally carbonized exciple and (1) 2–8 spored asci. New data on the phylogenetic placement of A. calcea and A. macella are also given. We further include a list of Allographa species reported from the Western Ghats, along with the availability of molecular sequence data.
