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Fungal tree of life. Cladogram of the kingdom Fungi based on published multi-gene and genome-scale phylogenies (11–14, 17, 18, 32, 33, 83, 98, 109, 112, 167, 168). Polytomies represent regions of the tree currently unresolved by molecular and genomic data.
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The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies, Page 1 of 2
Abstract
The kingdom Fungi is one of the more diverse clades of eukaryotes in terrestrial ecosystems, where they provide numerous ecological services ranging from decomposition of organic matter and nutrient cycling to beneficial and antagonistic associat...
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... coenocytic hyphae, and typically asexual reproduction by sporangia. The ascomycetes and ba- sidiomycetes were identified by the production of asci and basidia, respectively, possession of regularly sep- tate hyphae, and a dikaryotic nuclear phase in their life cycle. The classification of the kingdom Fungi used here recognizes eight phyla ( Fig. 1, Table 1), with the zoosporic fungi comprising the first three lineages of the kingdom-Cryptomycota/Microsporidia, Chytridio- mycota, and Blastocladiomycota-since the divergence from the last universal common ancestor (LUCA) of ...
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... remaining two phyla of zoosporic fungi are Blas- tocladiomycota and Chytridiomycota. The branching order of these two lineages is unresolved (Fig. 1), and both have been inferred as the sister lineage to the terrestrial, nonflagellated fungi in large multigene and genome-scale phylogenetic analyses (11,13,18). The failure to resolve this branching order appears to be at- tributed to low phylogenetic signal, rather than strong conflict among competing individual gene trees (18), ...
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... is the most recently described class of Taphrinomycotina. It is commonly detected in environmental sampling of soil and was ini- tially known informally as Soil Clone Group 1 (110, 111). One species was serendipitously described from a culture collection of root-associated fungi; it and a second recently described species are associated with the surfaces of tree roots (112,113). ...
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Citations
... Eukaryotic Mucoromycota is a division of mycorrhizal fungi that usually form mycorrhiza-like relationships with plants [79]. Little information is available for this fungal division in terms of its interaction with surrounding plant roots, except that its subdivision Macrophomina was proven to cause several plant diseases, e.g., stem and root rot, seedling blight, upon contact [80][81][82]. Pathogenicity is based on the fungus's ability to produce hydrolytic enzymes to degrade plant cell wall [83]. Less AB/RAB of Mucoromycota in rhizosphere of M. oleifera might raise the possibility that this wild plant might release root exudates that inhibit propagation of this fungus in plant rhizosphere region [66][67][68]. ...
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... Most of the anamorphic fungi are asexual stages of Ascomycota and rarely of Basidiomycota and comprise about 25 000 modern species (Kirk et al. 2008). Nowadays, fungi are classified not only on the basis of their morphology and life cycle, but also based on their phylogenies inferred using DNA sequence analysis (Spatafora et al. 2017;Voigt et al. 2021;Wijayawardene et al. 2022). In the fossil state, however, only morphological characters are available to researchers and their analysis is the key to assess their taxonomy and to reconstruct the evolutionary history of fungi (Le Renard et al. 2020). ...
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... Cryptococcus neoformans and C. gattii are responsible for cryptococcosis, often being isolated from soil and plant debris, respectively (Vélez & Escandón, 2020). The microfungi in the Ustilaginomycotina are smut fungi or more rarely yeasts (Spatafora et al., 2017), with the smut genera Ustilago and Sporisorium each having 12 species reported (see also Chapters 7 and 9). Yeasts are represented by the genus Malassezia, among others (Wang et al., 2015a). ...
... Although not yet known from Colombia, members of the Zoopagomycotina have bioprospective potential as biological controllers, as they can be found as nematode predators and mycoparasites (Spatafora et al., 2017). In the same way, species in the Kickxellomycotina are found in the gut of arthropods that have an aquatic stage (Spatafora et al., 2017). ...
... Although not yet known from Colombia, members of the Zoopagomycotina have bioprospective potential as biological controllers, as they can be found as nematode predators and mycoparasites (Spatafora et al., 2017). In the same way, species in the Kickxellomycotina are found in the gut of arthropods that have an aquatic stage (Spatafora et al., 2017). Owing to the high diversity of insects and other arthropods in Colombia, we expect that surveys of their associated fungal diversity will reveal species of these fungal lineages in the country. ...
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... Ascomycota account for about two-thirds of named fungal species. 1 Over 98% of known Ascomycota belong to the Pezizomycotina, including many economically important species as well as diverse pathogens, decomposers, and mutualistic symbionts. 2 Our understanding of Pezizomycotina evolution has until now been based on sampling traditionally well-defined taxonomic classes. 3-5 However, considerable diversity exists in undersampled and uncultured, putatively early-diverging lineages, and the effect of these on evolutionary models has seldom been tested. ...
Ascomycota account for about two-thirds of named fungal species.¹ Over 98% of known Ascomycota belong to the Pezizomycotina, including many economically important species as well as diverse pathogens, decomposers, and mutualistic symbionts.² Our understanding of Pezizomycotina evolution has until now been based on sampling traditionally well-defined taxonomic classes.³,⁴,⁵ However, considerable diversity exists in undersampled and uncultured, putatively early-diverging lineages, and the effect of these on evolutionary models has seldom been tested. We obtained genomes from 30 putative early-diverging lineages not included in recent phylogenomic analyses and analyzed these together with 451 genomes covering all available ascomycete genera. We show that 22 of these lineages, collectively representing over 600 species, trace back to a single origin that diverged from the common ancestor of Eurotiomycetes and Lecanoromycetes over 300 million years BP. The new clade, which we recognize as a more broadly defined Lichinomycetes, includes lichen and insect symbionts, endophytes, and putative mycorrhizae and encompasses a range of morphologies so disparate that they have recently been placed in six different taxonomic classes. To test for shared hidden features within this group, we analyzed genome content and compared gene repertoires to related groups in Ascomycota. Regardless of their lifestyle, Lichinomycetes have smaller genomes than most filamentous Ascomycota, with reduced arsenals of carbohydrate-degrading enzymes and secondary metabolite gene clusters. Our expanded genome sample resolves the relationships of numerous “orphan” ascomycetes and establishes the independent evolutionary origins of multiple mutualistic lifestyles within a single, morphologically hyperdiverse clade of fungi.
... wisc. edu/) should provide robust phylogenetic data on Saccharomycotina species [42][43][44][45][46][47][48][49][50][51][52][53] . A recent genomic analysis of fungi reported that Saccharomycotina species diverged earlier and evolved more quickly (~1.6 times faster) than Pezizomycotina 40) . ...
This review describes the changes in yeast species names in the previous decade. Several yeast species have been reclassified to accommodate the “One fungus=One name” (1F=1N) principle of the Code. As the names of medically important yeasts have also been reviewed and revised, details of the genera Candida, Cryptococcus, Malassezia, and Trichosporon are described in Section 3, along with the history of name changes. Since the phylogenetic positions of Candida species in several clades have not been clarified, revision of this species has not been completed. Among the species that remain unrevised despite their importance in the medical field, we propose the transfer of six Candida species to be reclassified in the Nakaseomyces clade, including Nakaseomyces glabratus and Nakaseomyces nivalensis.
... Fungi are closely related to human life; some fungi exist as edibles which are macrofungi with fruiting bodies [9], such as mushrooms, agaric, and tuckahoe. The fungi mainly involved in food fermentation are ascomycetes and zygomycetes [10,11]. Some fungi are used for treating different ailments in traditional Chinese medicine including Ganoderma lucidum, Poria cocos, and Cordyceps sinensis [12]. ...
Airborne fungi are one of the most ubiquitous kinds of inhalant allergens which can result in allergic diseases. Fungi tend to grow in warm and humid environments with regional and seasonal variations. Their nomenclature and taxonomy are related to the sensitization of immunoglobulin E (IgE). Allergic cross-reactivity among different fungal species appears to be widely existing. Fungus-related foods, such as edible mushrooms, mycoprotein, and fermented foods by fungi, can often induce to fungus food allergy syndrome (FFAS) by allergic cross-reactivity with airborne fungi. FFAS may involve one or more target organs, including the oral mucosa, the skin, the gastrointestinal and respiratory tracts, and the cardiovascular system, with various allergic symptoms ranging from oral allergy syndrome (OAS) to severe anaphylaxis. This article reviews the current knowledge on the field of allergic cross-reactivity between fungal allergens and related foods, as well as the diagnosis and treatment on FFAS.
... Mycoviruses have been reported in members of the three major fungal phyla: Chytridiomycota, Ascomycota, and Basidiomycota (Pearson et al., 2009). Note that the Zygomycota are no longer recognized as Fungi (Spatafora et al., 2017;Tedersoo et al., 2018). Fungi are extensively infected with mycoviruses (Ghabrial, 1998;Hong et al., 1999), which are hosted in their cytoplasm or limited to the mitochondria (Polashock et al., 1997;Varga et al., 2003). ...
Plants, fungi, and many other eukaryotes have evolved an RNA interference (RNAi) mechanism that is key for regulating gene expression and the control of pathogens. RNAi inhibits gene expression, in a sequence-specific manner, by recognizing and deploying cognate double-stranded RNA (dsRNA) either from endogenous sources (e.g. pre-micro RNAs) or exogenous origin (e.g. viruses, dsRNA, or small interfering RNAs, siRNAs). Recent studies have demonstrated that fungal pathogens can transfer siRNAs into plant cells to suppress host immunity and aid infection, in a mechanism termed cross-kingdom RNAi. New technologies, based on RNAi are being developed for crop protection against insect pests, viruses, and more recently against fungal pathogens. One example, is host-induced gene silencing (HIGS), which is a mechanism whereby transgenic plants are modified to produce siRNAs or dsRNAs targeting key transcripts of plants, or their pathogens or pests. An alternative gene regulation strategy that also co-opts the silencing machinery is spray-induced gene silencing (SIGS), in which dsRNAs or single-stranded RNAs (ssRNAs) are applied to target genes within a pathogen or pest. Fungi also use their RNA silencing machinery against mycoviruses (fungal viruses) and mycoviruses can deploy virus-encoded suppressors of RNAi (myco-VSRs) as a counter-defence. We propose that myco-VSRs may impact new dsRNA-based management methods, resulting in unintended outcomes, including suppression of management by HIGS or SIGS. Despite a large diversity of mycoviruses being discovered using high throughput sequencing, their biology is poorly understood. In particular, the prevalence of mycoviruses and the cellular effect of their encoded VSRs are under-appreciated when considering the deployment of HIGS and SIGS strategies. This review focuses on mycoviruses, their VSR activities in fungi, and the implications for control of pathogenic fungi using RNAi.
... This chapter reviews the status of mycology from the perspective of plant pathology and agriculture. This chapter will focus on true fungi (phyla Zygomycota, Ascomycota, Basidiomycota, Chytridiomycota, Blastocladiomycota, and Mucoromycota) (James, Kauff et al., 2006, James, Letcher et al., 2006Spatafora et al., 2017), associated with diseases of economically important crops (including mushroom) in the Philippines. The Oomycetes and Plasmodiophorids were previously regarded as part of the Kingdom Fungi. ...
Mycology in the Tropics: Updates on Philippine Fungi comprehensively discusses the current state of Philippine mycology, including historical developments in the field, listings of fungi with diverse utilizations or applications, and those that cause economic impact on crop production in the country. Specifically, the chapters in the book introduce tropical mycology, describe different fungal groups, their biodiversity and conservation, and give insights into the applications of mycology in agriculture, health, industry and the environment. The book also includes quarantine regulations on economically important diseases and describes the importance of developing local studies on fungi.
... Nevertheless, fungi [used hereafter in a broader sense, i.e., encompassing the true fungi (kingdom Fungi) and oomycetes (Pseudofungi; kingdom Straminipila)], are an important component of biological diversity, harboring an estimated minimum of 1.5 million species and their diversity remains largely unexplored (Hawksworth and Lücking 2017;Antonelli et al. 2020). They are vital for many ecosystem functions and consequently, ecosystem services (Spatafora et al. 2017;Willis 2018). Saprobic fungi are essential for nutrient cycling, as they can break down complex dead organic matter, while other fungi engage in mutualistic or antagonistic relationships (Antonelli et al. 2020). ...
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Fungal invasions can have far-reaching consequences, and despite increasing relevance, fungi are notoriously underrepresented in invasion science. Here, we present the second annotated checklist for alien and cryptogenic fungi and oomycetes in Austria. This list contains 375 taxa of which 278 are classified as established; compared to the first checklist from 2002, this amounts to an almost five-fold increase and the number of decade-wise first records is steadily rising since the mid-twentieth century. The introduction pathway is unclear for the vast majority of taxa, while the main means of spread within the country is unassisted secondary spread. Fungi were predominantly introduced from the Northern Hemisphere, especially North America and Temperate Asia. Rates of newly recorded alien fungi differ among phyla; the majority belongs to the Ascomycota, which experienced an 9.6-fold increase in numbers. Orders found most frequently are powdery mildews (Erysiphales, Ascomycota), downy mildews (Peronosporales, Oomycota), agarics (Agaricales, Basidiomycota), Mycosphaerellales (Ascomycota), rusts (Pucciniales, Basidiomycota) and Pleosporales (Ascomycota). The majority (about 80%) of the taxa are plant pathogens, while animal pathogens are few but severely affecting their native hosts. The dominance of pathogens in our checklist underlines the need of better tackling fungal invasions-especially in the light of emerging infectious diseases-and highlights potential knowledge gaps for ectomycorrhizal and saprobic alien fungi, whose invasion processes are often much more inconspicuous. Our results show that fungal invasions are a phenomenon of increasing importance, and collaborative efforts are needed for advancing the knowledge and management of this important group.
Supplementary information:
The online version contains supplementary material available at 10.1007/s10530-022-02896-2.
... (D) Cladogram of the subkingdom Dikarya, with its two divisions Basidiomycota and Ascomycota, listing for the latter division the three subdivisions Pezizomycotina, Saccharomycotina, and Taphrinomycotina, and some of their classes, plus representative species. This cladogram represents an excerpt of a formerly presented one (Spatafora et al, 2017). Note that while most fungi possess a ZC3HC1 homolog with a C-X(2)-C tetrapeptide as part of their BLD1 zinc finger, some classes of the Pezizomycotina instead feature a C-X(3)-C. ...
Proteins ZC3HC1 and TPR are construction elements of the nuclear pore complex (NPC)-attached nuclear basket (NB). NB-location of ZC3HC1 depends on TPR already occurring NPC-anchored, whereas additional TPR polypeptides are appended to the NB by ZC3HC1. The current study examined the molecular properties of ZC3HC1 that enable it to bind to the NB and TPR. We report the identification and definition of a nuclear basket-interaction domain (NuBaID) of Hs ZC3HC1 comprising two similarly built modules, both essential for the binding to the NB's NPC-anchored Hs TPR. Furthermore, we describe such a bimodular construction as evolutionarily conserved and exemplify the kinship of Hs ZC3HC1 by the NB- and Dd TPR-interacting homolog of Dictyostelium discoideum and by characterizing protein Pml39 as the ZC3HC1 homolog in Saccharomyces cerevisiae . Among several properties shared by the different species' homologs, we unveil the integrity of the bimodular NuBaID of Sc Pml39p as being essential for binding to the yeast's NBs and its TPR homologs Sc Mlp1p and Sc Mlp2p, and we further present Pml39p as enabling interlinkage of Mlp1p subpopulations. In addition to phyla-specific features, we delineate the three species' common NuBaID as the characterizing structural entity of a one-of-a-kind protein found not in all but likely most taxa of the eukaryotic realm.
