Fungal Diversity最新文献

Basidiomycota is one of the major phyla in the fungal tree of life. The outline of Basidiomycota provides essential taxonomic information for researchers and workers in mycology. In this study, we present a time-framed phylogenomic tree with 487 species of Basidiomycota from 127 families, 47 orders, 14 classes and four subphyla; we update the outline of Basidiomycota based on the phylogenomic relationships and the taxonomic studies since 2019; and we provide notes for each order and discuss the history, defining characteristics, evolution, justification of orders, problems, significance, and plates. Our phylogenomic analysis suggests that the subphyla diverged in a time range of 443–490 Myr (million years), classes in a time range of 312–412 Myr, and orders in a time range of 102–361 Myr. Families diverged in a time range of 50–289 Myr, 76–224 Myr, and 62–156 Myr in Agaricomycotina, Pucciniomycotina, and Ustilaginomycotina, respectively. Based on the phylogenomic relationships and divergence times, we propose a new suborder Mycenineae in Agaricales to accommodate Mycenaceae. In the current outline of Basidiomycota, there are four subphyla, 20 classes, 77 orders, 297 families, and 2134 genera accepted. When building a robust taxonomy of Basidiomycota in the genomic era, the generation of molecular phylogenetic data has become relatively easier. Finding phenotypical characters, especially those that can be applied for identification and classification, however, has become increasingly challenging.

How the four major processes affecting community assembly—selection, dispersal, drift, and diversification—solely or jointly shape co-occurring assemblages of macro- and microorganisms at the same scales remains poorly understood. Here, we delved into the distance pattern of similarity (DPS) in tree and soil fungal communities in three c. 20-hectare forest plots spanning tropical to temperate climates in Yunnan province, Southwest China. Specifically, we decrypted the assembly contribution of individual-based random sampling, selection and/or dispersal using drift-inexplicit ordination and drift-explicit baseline models. Surprisingly, our findings demonstrated that most soil fungal realized distribution ranges (RDR) were shorter than most trees. Because of explicitly integrating drift and the range of DPS is broader than the RDR of most trees and fungi, selection baseline models overwhelmingly captured the DPS structures in trees and fungi across spatial scales in tropical, subtropical, and subalpine forest ecosystems and that for fungi across taxonomic levels and fungal guilds. Under the premise that modeling frameworks, ecosystems, spatial scales, sample intensities, selection variables, and dispersal variables are well unified, the ubiquitous dominance of selection elucidates no fundamental difference in the assembly mechanism between trees and soil fungi.

The field of mycology has grown from an underappreciated subset of botany, to a valuable, modern scientific discipline. As this field of study has grown, there have been significant contributions to science, technology, and industry, highlighting the value of fungi in the modern era. This paper looks at the current research, along with the existing limitations, and suggests future areas where scientists can focus their efforts, in the field mycology. We show how fungi have become important emerging diseases in medical mycology. We discuss current trends and the potential of fungi in drug and novel compound discovery. We explore the current trends in phylogenomics, its potential, and outcomes and address the question of how phylogenomics can be applied in fungal ecology. In addition, the trends in functional genomics studies of fungi are discussed with their importance in unravelling the intricate mechanisms underlying fungal behaviour, interactions, and adaptations, paving the way for a comprehensive understanding of fungal biology. We look at the current research in building materials, how they can be used as carbon sinks, and how fungi can be used in biocircular economies. The numbers of fungi have always been of great interest and have often been written about and estimates have varied greatly. Thus, we discuss current trends and future research needs in order to obtain more reliable estimates. We address the aspects of machine learning (AI) and how it can be used in mycological research. Plant pathogens are affecting food production systems on a global scale, and as such, we look at the current trends and future research needed in this area, particularly in disease detection. We look at the latest data from High Throughput Sequencing studies and question if we are still gaining new knowledge at the same rate as before. A review of current trends in nanotechnology is provided and its future potential is addressed. The importance of Arbuscular Mycorrhizal Fungi is addressed and future trends are acknowledged. Fungal databases are becoming more and more important, and we therefore provide a review of the current major databases. Edible and medicinal fungi have a huge potential as food and medicines, especially in Asia and their prospects are discussed. Lifestyle changes in fungi (e.g., from endophytes, to pathogens, and/or saprobes) are also extremely important and a current research trend and are therefore addressed in this special issue of Fungal Diversity.

The classes Dothideomycetes and Eurotiomycetes include constitutively melanized fungi adapted to extreme conditions and they are widely distributed in diverse hostile habitats worldwide. Yet, despite the growing interest in these fungi, there is a considerable gap of knowledge on their functionality. Their genomic analysis is still in its infancy and the possibility to understand their adaptive strategies and exploit their potentialities in bioremediation is very limited. Here, we supply a genome catalog of 118 black fungi, encompassing different ecologies, phylogenies and lifestyles, as a first example of a comparative genomic study at high level of diversity. Results indicate that, as a rule, Dothideomycetes show more variable genome size and that larger genomes are associated with harshest conditions; low temperature tolerance and DNA repair capacity are overrepresented in their genomes. In Eurotiomycetes high temperature tolerance and capacity to metabolize hydrocarbons are more frequently present and these abilities are positively correlated with the human presence. The genomic features are consistent with the prevalent ecologies in the two classes. Indeed, Dothideomycetes are more common in cold and dry environments with high capacity for DNA repair being consistent with the normally highly UV-impacted conditions in their habitats; in contrast, Eurotiomycetes spread mainly in hot human-impacted sites with industrial pollution. Mean annual temperature and isothermality are positively correlated with tolerance to high temperatures in Dothideomycetes, suggesting that, despite their preference for the cold, they are potentially equipped to survive even when temperatures rise due to the global warming.

Botryosphaeriaceae (Botryosphaeriales, Dothideomycetes, Ascomycota) encompasses commonly encountered opportunistic pathogens that cause stem cankers on woody plants. Lifestyles of Botryosphaeriaceae species could vary as endophytes, pathogens and saprobes and one species can have one or more lifestyles. Therefore, this family is an excellent candidate to study the relationships among lifestyles and lifestyle changes. It is postulated that this family has saprobic ancestors, and the mechanisms by which they evolved from nonpathogenic ancestors to woody pathogens remain unclear. Here, we present an analysis of 18 Botryosphaeriaceae genomes, including four newly generated high-quality genomes of Botryosphaeriaceae strains. We compared Botryosphaeriaceae genomes with phylogenetically closely related Dothideomycetes taxa including plant pathogens and saprobes which revealed significant net gene family expansion in Botryosphaeriaceae. This gene expansion is prominent in the early ancestors before the divergence of genera of Botryosphaeriaceae. This expansion affected the pathogenicity-related genes and detoxification genes. Furthermore, we analysed horizontal gene transfer, which is a mechanism of transfer to genetic material between organisms that are not in a parent–offspring relationship and identified widespread putative intra-kingdom horizontal gene transfer events in this family. Most were transferred during the evolution of ancient ancestors of Botryosphaeriaceae, before the divergence of the modern genera and were enriched in pathogenicity-related genes and detoxification genes. Furthermore, The RNA sequencing analysis of the Botryosphaeriaceae species Lasiodiplodia theobromae revealed that pathogenicity-related genes and detoxification genes, including those obtained through gene family expansion and horizontal gene transfers, were significantly induced after the infection of plant hosts rather than before infection. These insights reveal critical roles for gene family expansion and horizontal gene transfers in the evolutionary adaptation of Botryosphaeriaceae in the infection of woody plants. We postulate that the pathogenic lifestyle of Botryosphaeriaceae species evolved from saprobic or endophytic lifestyles in the early divergence of this family. However, there are few endophytic genomes available for closely related species of Botryosphaeriaceae, thus further studies are necessary to clarify the evolutionary relationships of the endophytes.

Most fungi display a mixed mating system with both asexual and sexual reproduction. The timing of the two modes of reproduction must be carefully coordinated through signal perception and coordination in the cell along with chromatin modification. Here, we investigated coordination of reproductive output by investigating the function of the histone chaperone anti-silencing factor 1 (ASF1) in a fungal species amenable to characterization of both asexual and sexual reproduction. We used knockout approach to show that SeASF1 influenced asexual and sexual reproduction in Stemphylium eturmiunum. SeASF1-deleted strains failed to produce pseudothecia, but produce abnormal conidia and showed an irregular distribution of nuclei in mycelium. Transcriptome sequencing was then used to identify genes with altered expression in the SeASF1-deleted strains. The transcriptional expression of the identified SeDJ-1 was strongly regulated by SeASF1. The interaction of SeDJ-1 and SeASF1 was confirmed using Y2H, Co-IP, and pull-down. Due to some components of phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT) signaling pathway were known to interact with DJ-1 in mammals, we verified SePI3K, an element of PI3K/AKT signaling pathway in S. eturmiunum, was directly linked to SeDJ-1 and then these two proteins were defined as a coordinator of reproduction. However, knockout of SeDJ-1 or SePI3K altered the asexual and sexual reproduction, but SePI3K recovered the asexual and sexual development of ∆Sedj-1. The SeDJ-1-M6 segment of SeDJ-1 was essential for its interaction with SePI3K and played a critical role in restoring sexual reproduction in the ∆Sepi3k, providing a deep understanding of the regulatory mechanism of SeDJ-1 in S. eturmiunum development. Summarily, SeASF1 is able to trigger SeDJ-1 and SeDJ-1can also activate SePI3K, which is orchestrally involved in asexual and sexual reproduction in S. eturmiunum. All these results reveal that SeASF1 manipulates asexual and sexual reproduction in S. eturmiunum by SeDJ-1 perception of PI3K/AKT signaling pathway. These data highlight the deep similarities in coordinating asexual and sexual processes in both fungi and eukaryotes in general.

The Clitocybaceae is a recently established family. Currently, the infrafamilial divisions and relationships within the family are vague due to limited sampling and genes employed for phylogenetic analysis. Some mushrooms of the family contain the neurotoxic muscarine, which has caused many severe and even deadly poisonings worldwide. However, the taxonomic distribution and evolution of the toxin within the family is largely unknown. In this study, phylogenetic analyses based on nucleotide sequences of ITS and of six molecular loci (ITS, LSU, TEF1, RPB1, RPB2 and ATP6), plus a phylogenomic analysis based on 485 single-copy orthologous genes, were performed to reconstruct the framework of Clitocybaceae. BEAST analysis was used to estimate the divergence times within the family. Additionally, biochemical analysis for muscarine was conducted of 32 representative species. Based on these analyses, an updated classification of Clitocybaceae into six genera (Clitocybe, Collybia, Dendrocollybia, Lepista, Pseudolyophyllum, and Singerocybe) is proposed. The genus Collybia is emended to accommodate four subgenera (Collybia, Crassicybe, Leucocalocybe, and Macrosporocybe). Seventeen new Chinese species and 15 new combinations are proposed. Keys to the genera of Clitocybaceae and the subgenera of Collybia, as well as to the known species of Clitocybe and Collybia subgen. Collybia in China, are presented. In addition, muscarine was detected in 18 species, and these muscarine-containing species formed a major monophyletic clade within Collybia subgen. Collybia. Finally, our phylogenetic, phylogenomic, chemotaxonomic and molecular dating results indicate that the Clitocybaceae is a natural group estimated to have arisen some 60 million years ago, and in this family, muscarine has evolved only once circa 20 million years ago without later losses.

Dermatophytes and other members of Onygenales are unique in their ability to degrade keratin, affecting hair and nails, and in the case of human hosts, causing skin infections. Subtillisins are essential proteases in keratin assimilation, and subtilisin-like protease 1 (SUB1) and SUB3–7 are specific for dermatophytes. eIF2α kinases are serine-threonine kinases that perform essential functions in response to infection, proteotoxicity, and nutrient scavenging. The relatively conserved nature of EIF2AK4 among fungi makes them potential evolutionary markers, which may contribute to a deeper understanding of dermatophyte taxonomy and evolution. This study aimed to assess the phylogeny of dermatophytes by examining the EIF2AK4 and SUB1 genes compared to the ITS gene marker. The phylogenetic trees generated from the EIF2AK4 and SUB1 genes exhibited a similar topology, which differed from that observed in the ITS tree. Our preliminary findings with a limited dataset suggest that the EIF2AK4 and SUB1 genes provide a reasonably correct reflection of the evolution of Arthrodermataceae. In addition, the study analyzed in vitro keratinolytic responses of 19 dermatophyte species using hairs of a broad range of mammals, including ancestral as well as derived species, as substrates. Trichophyton mentagrophytes and Nannizzia gypsea were the most active in degrading hair, while Trichophyton verrucosum, Trichophyton tonsurans and Epidermophyton floccosum showed low response. Hairs of Hyracoidea and Rodentia were most affected of all mammal hairs, while in contrast, bat hairs were difficult to degrade by nearly all tested dermatophyte species. Zoophilic species showed more activity than anthropophilic dermatophytes, but hair degradation profiles were not diagnostic for particular dermatophyte species.