Search Results (28)

G protein-coupled receptors (GPCRs) are transmembrane proteins crucial for signal transduction in eukaryotes, responding to diverse extracellular signals. Researchers have found and systematically summarized 14 distinct types of GPCRs in fungi but their distribution among numerous fungal species remained largely unexamined. Additionally, three families of mammalian homologs (Rhodopsin, Glutamate, and Frizzled) have been found in previous studies, but they are not included in the systematic classification of fungal GPCRs. Our study establishes a unified classification of 17 GPCR classes in fungi, combining 14 fungal and 3 mammalian previously recognized groups, and classifies 28,294 GPCRs across 1357 fungal species, significantly expanding the scale of GPCRs in fungi and demonstrating their broader distribution. We found that mammalian homologs are notably more prevalent in Early Diverging Fungi (EDF), whereas the previous 14 classes are predominantly found in Ascomycota and Basidiomycota. The most abundant class detected in fungi was Pth11-like GPCRs, exclusively found in Pezizomycotina and involved in fungal pathogenicity. Our analysis suggested that Pezizomycotina ancestor possessed an extensive array of Pth11-like GPCRs, but over time, some species underwent considerable reductions in these GPCRs in conjunction with genome contractions. Utilizing a custom-built convolutional neural network (CNN) for the identification of fungal GPCRs, we identified several putative novel fungal GPCRs. Predicted interactions between these prospective new GPCRs and G-alpha proteins, as simulated by AlphaFold Multimer, provided additional support for their functional relevance. In conclusion, our work defines the first large-scale, unified classification of fungal GPCRs, reveals lineage-specific expansions and contractions, and uncovers previously unrecognized GPCR candidates with potential functional roles in fungal signaling. Full article

The genus Cunninghamella is widely distributed, primarily saprotrophic, occasionally endophytic and phytopathogenic. Analysis based on the internal transcribed spacer (ITS), the large subunit (LSU) of ribosomal DNA, and translation elongation factor 1 alpha (TEF1α), along with morphological comparisons, resulted in a discovery of eight new species. Molecular phylogenetic analyses placed each of these new species within well-supported clades. Cunninghamella crassior sp. nov., with short and thick spines, and C. fusca sp. nov. with brown sporangiola, are sister clades to each other. C. diffundens sp. nov., containing dispersed granules in sporangiola, is closely related to C. irregularis Zhao. C. tuberculata sp. nov., producing sporangiola with nodule-like protrusions. C. fulvicolor sp. nov., sister to C. irregularis, forms yellowish-brown pigmented colonies. C. guttulata sp. nov., with teardrop-shaped sporangiola, and C. inaequalis sp. nov., with uneven sporangiola, are both closely related to C. regularis Zhao. C. monosporangiola sp. nov., characterized by only one sporangiolum on some vesicles, is sister to C. verrucosa Zhao. This study represents the eleventh installment in a series investigating early-diverging fungal diversity in China and expands the number of accepted species in Cunninghamella to 39. Full article

Mucor species are fast-growing filamentous fungi, widespread in natural ecosystems. As opportunistic pathogens, some species can cause mucormycoses in humans and animals, while others hold significant economic value in food fermentation and bioengineering. In this study, four novel species were identified from soil samples collected in Xizang Autonomous Region and Yunnan Province, China, and their establishment as new species was supported by morphological characteristics and molecular data (ITS-LSU-RPB1), with phylogenetic analyses conducted using the Maximum Likelihood (ML) and Bayesian Inference (BI) methods. M. globosporus sp. nov. is characterized by producing globose chlamydospores. M. multimorphus sp. nov. is distinguished by swelling in the sporangiophores. M. polymorphus sp. nov. is differentiated by polymorphic chlamydospores. And M. xizangensis sp. nov. reflects its geographical origin in the Xizang Autonomous Region. Comprehensive descriptions of each novel taxon are presented herein. This study constitutes the ninth segment in an ongoing series elucidating early-diverging fungal diversity in China, expanding the understanding of the phylogeny of Mucor fungi and extending the worldwide number of known Mucor species to 137. Full article

The fungal family Mortierellaceae represents ubiquitous and ecologically significant components of soil ecosystems across terrestrial habitats. Through an integrative taxonomic approach combining multi-locus phylogenetic analyses (ITS, LSU, SSU rDNA, RPB1, and Act) with detailed morphological examinations of rhizosphere soil isolates, four novel species within this family were proposed. This study elucidates the morphological distinctions of novel species from allied species and the phylogenetic relationships among the novel and existing species within the family. Linnemannia rotunda sp. nov. (closely related to L. longigemmata) is distinguished by its globose sporangia and sporangiospores. Mortierella acuta sp. nov. (clustering with M. yunnanensis) is characterized by spiky collarettes. Mortierella oedema sp. nov. (a sister to M. macrocystis) exhibits distinctive ampulliform swellings. Mortierella tibetensis sp. nov. (clustering with M. parvispora) is named for its geographic origin in Tibet. As the eighth installment in a systematic investigation of early diverging fungal groups in China, this work expands the global taxonomic inventory of Mortierellaceae to 148 species, underscoring the ongoing discovery of cryptic biodiversity within this ecologically pivotal group. Full article

Absidia is the most species-rich genus within the family Cunninghamellaceae, with its members commonly isolated from diverse substrates, particularly rhizosphere soil. In this study, four novel Absidia species, A. irregularis sp. nov., A. multiformis sp. nov., A. ovoidospora sp. nov., and A. verticilliformis sp. nov., were discovered from soil samples collected in southern and southwestern China, using integrated morphological and molecular analyses. Phylogenetic analyses based on concatenated ITS, SSU, LSU, Act, and TEF1α sequence data reconstructed trees that strongly supported the monophyly of each of these four new taxa. Key diagnostic features include A. irregularis (closely related to A. oblongispora) exhibiting irregular colony morphology, A. multiformis (sister to A. heterospora) demonstrating polymorphic sporangiospores, A. ovoidospora (forming a clade with A. panacisoli and A. abundans) producing distinctive ovoid sporangiospores, and A. verticilliformis (next to A. edaphica) displaying verticillately branched sporangiophores. Each novel species is formally described with comprehensive documentation, including morphological descriptions, illustrations, Fungal Names registration identifiers, designated type specimens, etymological explanations, maximum growth temperatures, and taxonomic comparisons. This work constitutes the sixth instalment in a series investigating early-diverging fungal diversity in China aiming to enhance our understanding of the diversity of fungi in tropical and subtropical ecosystems in Asia. In this paper, the known species of Absidia are expanded to 71. Full article

The fungal genus Cunninghamella, ubiquitously distributed as saprotrophic organisms with occasional endophytic and phytopathogenic manifestations, holds significant biomedical and biochemical importance. During systematic investigations of fungal biodiversity in China, seven novel taxa (C. amphispora sp. nov., C. cinerea sp. nov., C. flava sp. nov., C. hainanensis sp. nov., C. rhizoidea sp. nov., C. simplex sp. nov., and C. yunnanensis sp. nov.) were delineated through integrated taxonomic approaches incorporating morphological characterization, multilocus phylogenetic analyses (ITS-LSU-TEF1α), and physiological assessments. Phylogenetic reconstructions positioned these novel species within a well-supported clade along with C. bainieri and C. verticillata. New species and their diagnostic features are C. amphispora, exhibiting dimorphic sporangiola production; C. cinerea, distinguished by gray pigmentation in the colony; C. flava, characterized by a yellow colony; C. hainanensis and C. yunnanensis, bearing eponymous designations reflecting their geographic origins; and C. simplex, displaying simplified sporangiophore branching. Comprehensive taxonomic descriptions accompanied by photomicrographic illustrations are provided herein. This study constitutes the seventh installment in an ongoing series elucidating early-diverging fungal diversity in China, expanding the global Cunninghamella taxonomic inventory to 63 species and advancing our understanding of mucoralean phylogeny. Full article

In eukaryotes, the mitogen-activated protein kinase (MAPK) cascade pathway is a highly conserved cell signaling mechanism that is essential for stress response, growth, and development. MAPK cascade genes have currently been identified and characterized in a wide range of fungi, although they have not been fully understood in early divergent fungal lineages like the Mucoromycota, which contains Mucoromycotina, Glomeromycotina, and Mortierellomycotina. In this study, a genome-wide investigation of Blakeslea trispora (Mucorales, Choanephoraceae) revealed a total of 19 MAPK cascade genes, including 9 BtMAPKKKs, 4 BtMAPKKs, and 6 BtMAPKs genes. Using phylogenetic analysis, it was found that the kinase domain sequences and motif composition of the three MAPK, MAPKK, and MAPKKK lineages are substantially conserved in fungi. Whole genome duplication analysis indicated that B. trispora has four and nine duplication pairs in the MAPK and MAPKKK genes, respectively, which are expanded by segmental replication events. BtHog2, the orthologous protein of Hog1, exhibits a substantial rise in transcription levels under blue light irradiation, indicating its function in light signal response and transduction. Several sets of interacting protein pairs were found using molecular docking analysis and yeast two-hybrid assay, providing a comprehensive MAPK cascade signaling network in B. trispore. Furthermore, MAPK cascade proteins show varying transcription levels in response to blue light and sex hormone stimulation, as well as variable treatment duration. BtMAPKKK9 and BtBck1 are strongly induced during sexual interaction, indicating their involvement in the response to trisporic acid and the subsequent alterations in hyphal cell wall structure. These findings shed light on the evolution of MAPK cascade genes and the functional mechanisms underlying MAPK cascade genes in response to light and sex hormone signaling pathways in B. trispore. Full article

Mucor lusitanicus has emerged as a model organism for studying RNAi in early-diverging fungi. This fungus exhibits intricate RNAi pathways that play crucial roles in regulating gene expression, destroying invasive exogenous genetic material, and controlling the movement of transposable elements (TEs) to ensure genome stability. One of the most fascinating RNAi pathways of this fungus is the non-canonical RNAi pathway (NCRIP), which is independent of Dicer and Argonaute proteins and uses the atypical RNase III R3B2 to degrade specific target messenger RNAs (mRNAs), playing an essential role in genome stability and virulence. Despite accumulating data suggesting that this pathway is a degradation mechanism, there has been no conclusive evidence. Here, we conducted a comparative transcriptomic analysis of mRNA and small RNAs regulated by r3b2, identifying 35 direct NCRIP targets. Most of these direct NCRIP targets correspond to TEs, highlighting the significant role of this RNAi pathway in TE control. Detailed functional analysis of the NCRIP targets confirmed the crucial role of r3b2 in regulating gene expression of protein-coding genes and controlling TEs other than centromeric GremLINE1 transposons, emphasizing the important role of r3b2 in genome stability. Interestingly, the RNAs of the NCRIP targets harbor a unique motif consisting of CAG repeats which are known to form hairpin structures which are targeted by RNA interference. Additionally, the generation of transformants expressing mRNAs containing the luciferase reporter gene along direct NCRIP targets reveals that this RNAi pathway is a true degradation mechanism for specific mRNAs. These results are expected to contribute to the understanding of the regulation of the NCRIP pathway through the analysis of its direct targets identified here. Full article

The family Bondarzewiaceae is an important and diverse group of macrofungi associated with wood as white rotting fungi, and some species are forest tree pathogens. Currently, there are nine genera and approximately 89 species in the family, distributed in tropical, subtropical, and temperate climates. To address the phylogenetic relationships among the genera, a combined ITS-28S dataset was subjected to maximum likelihood (ML), Bayesian inference (BI), and time divergence analyses using the BEAST package. Both ML and BI analyses revealed two major clades, where one major clade consisted of Amylosporus, Stecchericium, and Wrightoporia austrosinensisa. The second major clade is composed of Bondarzewia, Heterobasidion, Gloiodon, Laurilia, Lauriliella, and Wrightoporia, indicating that these genera are phylogenetically similar. Wrightoporia austrosinensisa recovered outside of Wrightoporia, indicating that this species is phylogenetically different from the rest of the species of the genus. Similarly, time divergence analyses suggest that Bondarzewiaceae diversified around 114 million years ago (mya), possibly during the Early Cretaceous Epoch. The genus Amylosporus is well resolved within the family, with an estimated stem age of divergent around 62 mya, possibly during the Eocene Epoch. Further, the species of the genus are recovered in two sister clades. One sister clade consists of species with pileate basidiomata and generative hyphae with clamp connections, corresponding to the proposed section Amylosporus sect. Amylosporus. The other consists of species having resupinate basidiomata and generative hyphae without clamps, which is treated here as Amylosporus sect. Resupinati. We provided the key taxonomic characters, known distribution, number of species, and stem age of diversification of each section. Furthermore, we also described a new species, Amylosporus wadinaheezicus, from Oman, based on morphological characters of basidiomata and multigene sequence data of ITS, 28S, and Tef1-α. With pileate basidiomata and phylogenetic placement, the new species is classified under the proposed A. sect. Amylosporus. An identification key to the known species of Amylosporus is presented. Ecology and distribution of species of the genera in the family are discussed. Full article

The current list of fungi from Colombia updated in the present review contains a total of 7619 species. The Ascomycota appears as the most diverse group, with 4818 species, followed by the Basidiomycota, with 2555 species. Despite this, we presume that the actual fungal diversity in Colombia could amount to between 105,600 and 300,000 species. Fungi represent an underestimated resource, indispensable for human well-being. Even though the current knowledge on potential applications of Colombian fungi is still limited, the number of studies on areas such as natural products discovery, biological control, and food and beverages, among other biotechnological applications, are increasing. With the current review, we aim to present a comprehensive update on the fungal diversity in Colombia and its potential applications. Colombia’s native fungal biodiversity holds much potential within the country’s current social-economical context, and the future must ensure efforts to preserve both the biodiversity and the untapped resources of the fungi in Colombia, which in alignment with the Sustainable Development Goals (SDGs) might result in new bioeconomy avenues for the country. Full article

Ten Candida species strains were isolated from the first known fatal case of rhinofacial and rhino–orbital–cerebral candidiasis. Among them, five strains of Candida parapsilosis complex were isolated during the early stage of hospitalization, while five strains of Candida tropicalis were isolated in the later stages of the disease. Using whole-genome sequencing, we distinguished the five strains of C. parapsilosis complex as four Candida metapsilosis strains and one Candida parapsilosis strain. Antifungal susceptibility testing showed that the five strains of C. parapsilosis complex were susceptible to all antifungal drugs, while five C. tropicalis strains had high minimum inhibitory concentrations to azoles, whereas antifungal-drug resistance gene analysis revealed the causes of azole resistance in such strains. For the first time, we analyzed the microevolutionary characteristics of pathogenic fungi in human hosts and inferred the infection time and parallel evolution of C. tropicalis strains. Molecular clock analysis revealed that azole-resistant C. tropicalis infection occurred during the first round of therapy, followed by divergence via parallel evolution in vivo. The presence/absence variations indicated a potential decrease in the virulence of genomes in strains isolated following antifungal drug treatment, despite the absence of observed clinical improvement in the conditions of the patient. These results suggest that genomic analysis could serve as an auxiliary tool in guiding clinical diagnosis and treatment. Full article

The first genome sequenced of a eukaryotic organism was for Saccharomyces cerevisiae, as reported in 1996, but it was more than 10 years before any of the zygomycete fungi, which are the early-diverging terrestrial fungi currently placed in the phyla Mucoromycota and Zoopagomycota, were sequenced. The genome for Rhizopus delemar was completed in 2008; currently, more than 1000 zygomycete genomes have been sequenced. Genomic data from these early-diverging terrestrial fungi revealed deep phylogenetic separation of the two major clades—primarily plant—associated saprotrophic and mycorrhizal Mucoromycota versus the primarily mycoparasitic or animal-associated parasites and commensals in the Zoopagomycota. Genomic studies provide many valuable insights into how these fungi evolved in response to the challenges of living on land, including adaptations to sensing light and gravity, development of hyphal growth, and co-existence with the first terrestrial plants. Genome sequence data have facilitated studies of genome architecture, including a history of genome duplications and horizontal gene transfer events, distribution and organization of mating type loci, rDNA genes and transposable elements, methylation processes, and genes useful for various industrial applications. Pathogenicity genes and specialized secondary metabolites have also been detected in soil saprobes and pathogenic fungi. Novel endosymbiotic bacteria and viruses have been discovered during several zygomycete genome projects. Overall, genomic information has helped to resolve a plethora of research questions, from the placement of zygomycetes on the evolutionary tree of life and in natural ecosystems, to the applied biotechnological and medical questions. Full article

Chytridiomycota (zoosporic true fungi) have a consistent presence in soils and have been frequently identified within many diverse terrestrial environments. However, Chytridiomycota and other early-diverging fungi have low representation in whole-genome sequencing databases compared to Dikarya. New molecular techniques have provided insights into the diversity and abundance of chytrids in soils and the changes in their populations both spatially and temporally. Chytrids complete their life cycle within rapidly changing soil environments where they may be more common within micropores due to protection from predation, desiccation, and extreme temperatures. Reproductive and morphological changes occur in response to environmental changes including pH, fluctuating nutrient concentrations, and metals at levels above toxic thresholds. Rhizoids share some features of hyphae, including the spatial regulation of branching and the ability to attach, adapt to, and proliferate in different substrates, albeit on a microscale. Soil chytrids provide a pool of novel enzymes and proteins which enable a range of lifestyles as saprotrophs or parasites, but also can be utilised as alternative tools with some biotechnological applications. Thus, 3D live-cell imaging and micromodels such as MicroCT may provide insight into zoospore functions and rhizoid plasticity, respectively, in response to various conditions. A combination of classical techniques of soil chytrid baiting with simultaneous molecular and ecological data will provide insights into temporal population changes in response to environmental change. The authors emphasise the need to review and improve DNA-based methodologies for identifying and quantifying chytrids within the soil microbiome to expand our knowledge of their taxonomy, abundance, diversity, and functionality within soil environments. Full article

The seven most early diverging lineages of the 18 phyla of fungi are the non-terrestrial fungi, which reproduce through motile flagellated zoospores. There are genes/proteins that are present only in organisms with flagellum or cilium. It was suggested that TPPP-like proteins (proteins containing at least one complete or partial p25alpha domain) are among them, and a correlation between the incidence of the p25alpha domain and the eukaryotic flagellum was hypothesized. Of the seven phyla of flagellated fungi, six have been known to contain TPPP-like proteins. Aphelidiomycota, one of the early-branching phyla, has some species (e.g., Paraphelidium tribonematis) that retain the flagellum, whereas the Amoeboaphelidium genus has lost the flagellum. The first two Aphelidiomycota genomes (Amoeboaphelidium protococcorum and Amoeboaphelidium occidentale) were sequenced and published last year. A BLASTP search revealed that A. occidentale does not have a TPPP, but A. protococcorum, which possesses pseudocilium, does have a TPPP. This TPPP is the ‘long-type’ which occurs mostly in animals as well as other Opisthokonta. P. tribonematis has a ‘fungal-type’ TPPP, which is found only in some flagellated fungi. These data on Aphelidiomycota TPPP proteins strengthen the correlation between the incidence of p25alpha domain-containing proteins and that of the eukaryotic flagellum/cilium. Full article

Mitoviruses are small vertically transmitted RNA viruses found in fungi, plants and animals. Taxonomically, a total of 105 species and 4 genera have been formally recognized by ICTV, and recently, 18 new putative species have been included in a new proposed genus. Transcriptomic and metatranscriptomic studies are a major source of countless new virus-like sequences that are continually being added to open databases and these may be good sources for identifying new putative mitoviruses. The search for mitovirus-like sequences in the NCBI databases resulted in the discovery of more than one hundred new putative mitoviruses, with important implications for taxonomy and also for the evolutionary scenario. Here, we propose the inclusion of four new putative members to the genus Kvaramitovirus, and the existence of a new large basally divergent lineage composed of 144 members that lack internal UGA codons (subfamily “Arkeomitovirinae”), a feature not shared by the vast majority of mitoviruses. Finally, a taxonomic categorization proposal and a detailed description of the evolutionary history of mitoviruses were carried out. This in silico study supports the hypothesis of the existence of a basally divergent lineage that could have had an impact on the early evolutionary history of mitoviruses. Full article