JournalTOCs

Fungal Diversity
Journal Prestige (SJR): 6.432

Citation Impact (citeScore): 11
Number of Followers: 2

Hybrid journal (It can contain Open Access articles)
ISSN (Print) 1560-2745 - ISSN (Online) 1878-9129
Published by Springer-Verlag

[2469 journals]

The numbers of fungi
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  PubDate: 2022-05-30
Phylogenetic and ecological reevaluation of the order Onygenales
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  Abstract: Abstract The order Onygenales is classified in the class Eurotiomycetes of the subphylum Pezizomycotina. Families in this order have classically been isolated from soil and dung, and two lineages contain causative agents of superficial, cutaneous and systemic infections in mammals. The ecology and habitat choices of the species are driven mainly by the keratin and cellulose degradation abilities. The present study aimed to investigate whether the ecological trends of the members of Onygenales can be interpreted in an evolutionary sense, linking phylogenetic parameters with habitat preferences, to achieve polyphasic definitions of the main taxonomic groups. Evolutionary processes were estimated by multiple gene genealogies and divergence time analysis. Previously described families, namely, Arthrodermataceae, Ajellomycetaceae, Ascosphaeraceae, Eremascaceae, Gymnoascaceae, Onygenaceae and Spiromastigoidaceae, were accepted in Onygenales, and two new families, Malbrancheaceae and Neogymnomycetaceae, were introduced. A number of species could not be assigned to any of the defined families. Our study provides a revised overview of the main lines of taxonomy of Onygenales, supported by multilocus analyses of ITS, LSU, TUB, TEF1, TEF3, RPB1, RPB2, and ribosomal protein 60S L10 (L1) (RP60S) sequences, combined with available data on ecology, physiology, morphology, and genomics.
  PubDate: 2022-05-23
Freshwater fungal numbers
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  Abstract: Abstract A comprehensive account of fungal classification from freshwater habitats is outlined and discussed in the present review based on literature of biodiversity studies and recent morpho-phylogenetic analyses. A total of 3,870 freshwater fungal species are listed with additional details on the isolation source, habitat, geographical distribution, and molecular data. The Ascomycota (2,968 species, 1,018 genera) dominated the freshwater fungal taxa wherein Sordariomycetes (823 species, 298 genera) had the largest number, followed by Dothideomycetes (677 species, 229 genera), Eurotiomycetes (276 species, 49 genera), and Leotiomycetes (260 species, 83 genera). Other phyla included in the updated classification of freshwater fungi are: Chytridiomycota (333 species, 97 genera), Rozellomycota (221 species, 105 genera), Basidiomycota (218 species, 100 genera), Blastocladiomycota (47 species, 10 genera), Monoblepharomycota (29 species, 6 genera), Mucoromycota (19 species, 10 genera), Aphelidiomycota (15 species, 3 genera), Entomophthoromycota (6 species, 4 genera), Mortierellomycota (5 species, 3 genera), Olpidiomycota (4 species, 1 genus), Zoopagomycota (3 species, 2 genera), and Sanchytriomycota (2 species, 2 genera). The freshwater fungi belong to 1,361 genera, 386 families and 145 orders. The Pleosporales and Laboulbeniaceae are the largest freshwater fungal order and family comprised of 391 and 185 species, respectively. The most speciose genera are Chitonomyces (87, Laboulbeniomycetes), Verrucaria (50, Eurotiomycetes), Rhizophydium (52, Rhizophydiomycetes), Penicillium (47, Eurotiomycetes), and Candida (42, Saccharomycetes).
  PubDate: 2022-05-04
High-throughput sequencing view on the magnitude of global fungal
diversity
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  Abstract: Abstract High-throughput DNA sequencing has dramatically transformed several areas of biodiversity research including mycology. Despite limitations, high-throughput sequencing is nowadays a predominant method to characterize the alpha and beta diversity of fungal communities. Across the papers utilizing high-throughput sequencing approaches to study natural habitats in terrestrial ecosystems worldwide, > 200 studies published until 2019 have generated over 250 million sequences of the primary mycological metabarcoding marker, the nuclear ribosomal internal transcribed spacer 2 (ITS2). Here we show that at a 97% sequence similarity threshold, the total richness of non-singleton fungal taxa across the studies published so far is 1.08 million, mostly Ascomycota (56.8% of the taxa) and Basidiomycota (36.7% of the taxa). The Chao-1 estimate of the total extant fungal diversity based on this dataset is 6.28 million taxa, representing a conservative estimate of global fungal species richness. Soil and litter represent the habitats with the highest alpha diversity of fungi followed by air, plant shoots, plant roots and deadwood with Chao-1 predictions, for samples containing 5000 sequences, of 1219, 569, 392, 228, 215 and 140 molecular species, respectively. Based on the high-throughput sequencing data, the highest proportion of unknown fungal species is associated with samples of lichen and plant tissues. When considering the use of high-throughput sequencing for the estimation of global fungal diversity, the limitations of the method have to be taken into account, some of which are sequencing platform-specific while others are inherent to the metabarcoding approaches of species representation. In this respect, high-throughput sequencing data can complement fungal diversity predictions based on methods of traditional mycology and increase our understanding of fungal biodiversity.
  PubDate: 2022-05-01
The numbers of fungi: contributions from traditional taxonomic studies and
challenges of metabarcoding
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  Abstract: Abstract The global diversity of fungi has been estimated using several different approaches. There is somewhere between 2–11 million estimated species, but the number of formally described taxa is around 150,000, a tiny fraction of the total. In this paper, we examine 12 ascomycete genera as case studies to establish trends in fungal species descriptions, and introduce new species in each genus. To highlight the importance of traditional morpho-molecular methods in publishing new species, we introduce novel taxa in 12 genera that are considered to have low species discovery. We discuss whether the species are likely to be rare or due to a lack of extensive sampling and classification. The genera are Apiospora, Bambusicola, Beltrania, Capronia, Distoseptispora, Endocalyx, Neocatenulostroma, Neodeightonia, Paraconiothyrium, Peroneutypa, Phaeoacremonium and Vanakripa. We discuss host-specificity in selected genera and compare the number of species epithets in each genus with the number of ITS (barcode) sequences deposited in GenBank and UNITE. We furthermore discuss the relationship between the divergence times of these genera with those of their hosts. We hypothesize whether there might be more species in these genera and discuss hosts and habitats that should be investigated for novel species discovery.
  PubDate: 2022-04-28
The numbers of fungi: are the most speciose genera truly diverse'
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  Abstract: Abstract Fungi play vital roles in ecosystems as endophytes, pathogens and saprobes. The current estimate of fungal diversity is highly uncertain, ranging from 1.5 to 12 million, but only around 150,000 species have been named and classified to date. Since the introduction of DNA based methods for species identification, the number of newly described taxa has increased from approximately 1000 to around 2000 yearly. This demonstrates the importance of DNA based methods to identify and distinguish species, especially cryptic species. Many novel species from recent studies have been found in historically understudied regions and habitats, but these still represent only a small percentage of the estimated species. In this paper, we examine 16 genera from the top 40 most speciose genera as listed in Species Fungorum as case studies to examine the diversity of taxa in each genus. The genera treated herein are Cercospora, Diaporthe, Meliola, Passalora, Phyllachora, Phyllosticta, Pseudocercospora, Ramularia (ascomycetes) and Cortinarius, Entoloma, Inocybe, Marasmius, Psathyrella, Puccinia, Russula, Uromyces (basidiomycetes). We critically evaluate the number of species in these genera and correlate these numbers with the number of entries in GenBank. We introduce 18 new species Apiospora multiloculata, Candolleomyces thailandensis, Cortinarius acutoproximus, Cortinarius melleoalbus, Cortinarius pacificus, Cortinarius parvoacetosus, Diaporthe guizhouensis, Entoloma pseudosubcorvinum, Inocybe meirensongia, Marasmius albulus, Marasmius obscuroaurantiacus, Meliola camporesii, Phyllachora siamensis, Phyllosticta doitungensis, Picipes yuxiensis, Pseudocercospora vignae, Puccinia maureanui and Russula inornata. We also introduce a new record of Candolleomyces cladii-marisci and Inocybe iringolkavensis. We discuss the genera Colletotrichum and Pleurotus that are speciose, but do not occur in the top 40. We hypothesize whether there might be more species in these genera and discuss why these genera have some of the largest number of species.
  PubDate: 2022-03-27
  DOI: 10.1007/s13225-022-00501-4
Global diversity and systematics of Hymenochaetaceae with poroid
hymenophore
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  Abstract: Abstract Taxonomy and phylogeny of poroid Hymenochaetaceae based on the most comprehensive phylogenetic analyses are presented. A phylogeny based on a combined dataset of ITS and nLSU sequences for accepted genera of Hymenochaetaceae was analyzed and two or multigene phylogenies for most species of ten large genera including Coltricia, Fomitiporella, Fomitiporia, Fulvifomes, Fuscoporia, Inonotus, Phylloporia, Porodaedalea, Sanghuangporus and Tropicoporus, were carried out. Based on samples from 37 countries of five continents, seven new genera, Meganotus, Neophellinus, Nothonotus, Pachynotus, Perenninotus, Pseudophylloporia and Rigidonotus, are introduced, 37 new species, Coltricia tibetica, Fomitiporella crassa, F. queenslandica, Fomitiporia eucalypti, F. gatesii, F. ovoidospora, Fulvifomes azonatus, F. caligoporus, F. costaricense, F. floridanus, F. jouzaii, F. nakasoneae, F. subindicus, Fuscoporia sinuosa, F. submurina, Inonotus subradiatus, I. vietnamensis, Neomensularia castanopsidis, Pachynotus punctatus, Phellinus cuspidatus, P. subellipsoideus, Phylloporia minutissima, P. tabernaemontanae, Porodaedalea occidentiamericana, P. orientoamericana, P. qilianensis, P. schrenkianae, Pseudophylloporia australiana, Sanghuangporus australianus, S. lagerstroemiae, Tropicoporus angustisulcatus, T. hainanicus, T. lineatus, T. minus, T. ravidus, T. substratificans and T. tenuis, are described, and 108 new combinations are proposed. In addition, one illegitimate name and two invalid names are renamed, and Coltricia and Coltriciella were synonymized. The taxonomic relevance and limits of the new taxa are discussed. Photos and illustrations for 37 new species are presented, and a full description for each new species is given. Eventually, this study recognizes 672 species in 34 genera and provides a modern treatment of the poroid Hymenochaetaceae in the world. A key to the accepted poroid genera of Hymenochaetaceae is provided, and identification keys to the accepted species of 32 poroid genera worldwide are given. A synopsis description of each species is included in these keys.
  PubDate: 2022-03-17
  DOI: 10.1007/s13225-021-00496-4
Forecasting the number of species of asexually reproducing fungi
(Ascomycota and Basidiomycota)
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  Abstract: Abstract Asexually reproducing fungi play a significant role in essential processes in managed and wild ecosystems such as nutrients cycling and multitrophic interactions. A large number of such taxa are among the most notorious plant and animal pathogens. In addition, they have a key role in food production, biotechnology and medicine. Taxa without or rare sexual reproduction are distinguished based on their sporulating structures and conidiomata in traditional morphology-based taxonomy. The number, variation and diversity of asexually reproducing taxa are insufficiently known, even though fungi capable of asexual reproduction may provide an untapped, rich biological resource for future exploitation. Currently, ca. 30,000 asexual species belonging to ca. 3800 genera have been reported (including 1388 coelomycetous and 2265 hyphomycetous genera). Recent reports (2017–2020) reiterate that the number of asexually producing fungi is higher than the number of frequently sexually-reproducing fungi. With the advent of molecular tools and the abandonment of the dual nomenclature system for pleomorphic fungi, priority criteria were established and revisited in the latest outline of fungi and fungus-like taxa. However, species numbers and taxonomic boundaries of pleomorphic taxa and their synanamorphs or synasexual morphs have yet to be addressed. The number of species of speciose genera (e.g. Alternaria, Aspergillus, Cercospora, Fusarium, Phoma and Pseudocercospora), cryptic species, species of pleomorphic genera, less studied life modes (such as lichenicolous taxa, taxa from extreme environments) and species from biodiversity-rich areas still need evaluation to achieve more reliable estimates of their diversity. This paper discusses the current knowledge on the matter, with diversity estimates, and potential obstacles in several chapters on (1) speciose genera; (2) pleomorphic genera; (3) cryptic species; (4) well-studied but insufficiently resolved taxa, e.g. leaf inhabiting species, marine fungi, (5) less studied life modes, e.g. lichenicolous, rock-inhabiting fungi, insect-associated and yeast-forming taxa and (6) species from biodiversity-rich areas.
  PubDate: 2022-03-13
  DOI: 10.1007/s13225-022-00500-5
Correction to: Proposed nomenclature for Pseudallescheria, Scedosporium
and related genera
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  PubDate: 2022-03-10
  DOI: 10.1007/s13225-022-00505-0
Correction to: Predicting global numbers of teleomorphic ascomycetes
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  PubDate: 2022-03-01
  DOI: 10.1007/s13225-022-00504-1
Taming the beast: a revised classification of Cortinariaceae based on
genomic data
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  Abstract: Abstract Family Cortinariaceae currently includes only one genus, Cortinarius, which is the largest Agaricales genus, with thousands of species worldwide. The species are important ectomycorrhizal fungi and form associations with many vascular plant genera from tropicals to arctic regions. Genus Cortinarius contains a lot of morphological variation, and its complexity has led many taxonomists to specialize in particular on infrageneric groups. The previous attempts to divide Cortinarius have been shown to be unnatural and the phylogenetic studies done to date have not been able to resolve the higher-level classification of the group above section level. Genomic approaches have revolutionized our view on fungal relationships and provide a way to tackle difficult groups. We used both targeted capture sequencing and shallow whole genome sequencing to produce data and to perform phylogenomic analyses of 75 single-copy genes from 19 species. In addition, a wider 5-locus analysis of 245 species, from the Northern and Southern Hemispheres, was also done. Based on our results, a classification of the family Cortinariaceae into ten genera—Cortinarius, Phlegmacium, Thaxterogaster, Calonarius, Aureonarius, Cystinarius, Volvanarius, Hygronarius, Mystinarius, and Austrocortinarius—is proposed. Seven genera, 10 subgenera, and four sections are described as new to science and five subgenera are introduced as new combinations in a new rank. In addition, 41 section names and 514 species names are combined in new genera and four lecto- and epitypes designated. The position of Stephanopus in suborder Agaricineae remains to be studied. Targeted capture sequencing is used for the first time in fungal taxonomy in Basidiomycetes. It provides a cost-efficient way to produce -omics data in species-rich groups. The -omics data was produced from fungarium specimens up to 21 years old, demonstrating the value of museum specimens in the study of the fungal tree of life. This study is the first family revision in Agaricales based on genomics data and hopefully many others will soon follow.
  PubDate: 2022-02-23
  DOI: 10.1007/s13225-022-00499-9
Predicting global numbers of teleomorphic ascomycetes
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  Abstract: Abstract Sexual reproduction is the basic way to form high genetic diversity and it is beneficial in evolution and speciation of fungi. The global diversity of teleomorphic species in Ascomycota has not been estimated. This paper estimates the species number for sexual ascomycetes based on five different estimation approaches, viz. by numbers of described fungi, by fungus:substrate ratio, by ecological distribution, by meta-DNA barcoding or culture-independent studies and by previous estimates of species in Ascomycota. The assumptions were made with the currently most accepted, “2.2–3.8 million” species estimate and results of previous studies concluding that 90% of the described ascomycetes reproduce sexually. The Catalogue of Life, Species Fungorum and published research were used for data procurement. The average value of teleomorphic species in Ascomycota from all methods is 1.86 million, ranging from 1.37 to 2.56 million. However, only around 83,000 teleomorphic species have been described in Ascomycota and deposited in data repositories. The ratio between described teleomorphic ascomycetes to predicted teleomorphic ascomycetes is 1:22. Therefore, where are the undiscovered teleomorphic ascomycetes' The undescribed species are no doubt to be found in biodiversity hot spots, poorly-studied areas and species complexes. Other poorly studied niches include extremophiles, lichenicolous fungi, human pathogens, marine fungi, and fungicolous fungi. Undescribed species are present in unexamined collections in specimen repositories or incompletely described earlier species. Nomenclatural issues, such as the use of separate names for teleomorph and anamorphs, synonyms, conspecific names, illegitimate and invalid names also affect the number of described species. Interspecies introgression results in new species, while species numbers are reduced by extinctions.
  PubDate: 2022-02-17
  DOI: 10.1007/s13225-022-00498-w
Taxonomy, phylogeny, molecular dating and ancestral state reconstruction
of Xylariomycetidae (Sordariomycetes)
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  Abstract: Abstract Xylariomycetidae (Ascomycota) is a highly diversified group with variable stromatic characters. Our research focused on inconspicuous stromatic xylarialean taxa from China, Italy, Russia, Thailand and the United Kingdom. Detailed morphological descriptions, illustrations and combined ITS-LSU-rpb2-tub2-tef1 phylogenies revealed 39 taxa from our collections belonging to Amphisphaeriales and Xylariales. A new family (Appendicosporaceae), five new genera (Magnostiolata, Melanostictus, Neoamphisphaeria, Nigropunctata and Paravamsapriya), 27 new species (Acrocordiella photiniicola, Allocryptovalsa sichuanensis, Amphisphaeria parvispora, Anthostomella lamiacearum, Apiospora guiyangensis, A. sichuanensis, Biscogniauxia magna, Eutypa camelliae, Helicogermslita clypeata, Hypocopra zeae, Magnostiolata mucida, Melanostictus longiostiolatus, M. thailandicus, Nemania longipedicellata, N. delonicis, N. paraphysata, N. thailandensis, Neoamphisphaeria hyalinospora, Neoanthostomella bambusicola, Nigropunctata bambusicola, N. nigrocircularis, N. thailandica, Occultitheca rosae, Paravamsapriya ostiolata, Peroneutypa leucaenae, Seiridium italicum and Vamsapriya mucosa) and seven new host/geographical records are introduced and reported. Divergence time estimates indicate that Delonicicolales diverged from Amphisphaeriales + Xylariales at 161 (123–197) MYA. Amphisphaeriales and Xylariales diverged 154 (117–190) MYA with a crown age of 127 (92–165) MYA and 147 (111–184) MYA, respectively. Appendicosporaceae (Amphisphaeriales) has a stem age of 89 (65–117) MYA. Ancestral character state reconstruction indicates that astromatic, clypeate ascomata with aseptate, hyaline ascospores that lack germ slits may probably be ancestral Xylariomycetidae having plant-fungal endophytic associations. The Amphisphaeriales remained mostly astromatic with common septate, hyaline ascospores. Stromatic variations may have developed mostly during the Cretaceous period. Brown ascospores are common in Xylariales, but they first appeared in Amphisphaeriaceae, Melogrammataceae and Sporocadaceae during the early Cretaceous. The ascospore germ slits appeared only in Xylariales during the Cretaceous after the divergence of Lopadostomataceae. Hyaline, filiform and apiospores may have appeared as separate lineages, providing the basis for Xylariaceae, which may have diverged independently. The future classification of polyphyletic xylarialean taxa will not be based on stromatic variations, but the type of ring, the colour of the ascospores, and the presence or absence or the type of germ slit.
  PubDate: 2022-01-16
  DOI: 10.1007/s13225-021-00495-5
Species diversity of basidiomycota
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  Abstract: Abstract Fungi are eukaryotes that play essential roles in ecosystems. Among fungi, Basidiomycota is one of the major phyla with more than 40,000 described species. We review species diversity of Basidiomycota from five groups with different lifestyles or habitats: saprobic in grass/forest litter, wood-decaying, yeast-like, ectomycorrhizal, and plant parasitic. Case studies of Agaricus, Cantharellus, Ganoderma, Gyroporus, Russula, Tricholoma, and groups of lichenicolous yeast-like fungi, rust fungi, and smut fungi are used to determine trends in discovery of biodiversity. In each case study, the number of new species published during 2009–2020 is analysed to determine the rate of discovery. Publication rates differ between taxa and reflect different states of progress for species discovery in different genera. The results showed that lichenicolous yeast-like taxa had the highest publication rate for new species in the past two decades, and it is likely this trend will continue in the next decade. The species discovery rate of plant parasitic basidiomycetes was low in the past ten years, and remained constant in the past 50 years. We also found that the establishment of comprehensive and robust taxonomic systems based on a joint global initiative by mycologists could promote and standardize the recognition of taxa. We estimated that more than 54,000 species of Basidiomycota will be discovered by 2030, and estimate a total of 1.4–4.2 million species of Basidiomycota globally. These numbers illustrate a huge gap between the described and yet unknown diversity in Basidiomycota.
  PubDate: 2022-01-14
  DOI: 10.1007/s13225-021-00497-3
Fungal diversity notes 1387–1511: taxonomic and phylogenetic
contributions on genera and species of fungal taxa
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  Abstract: Abstract This article is the 13th contribution in the Fungal Diversity Notes series, wherein 125 taxa from four phyla, ten classes, 31 orders, 69 families, 92 genera and three genera incertae sedis are treated, demonstrating worldwide and geographic distribution. Fungal taxa described and illustrated in the present study include three new genera, 69 new species, one new combination, one reference specimen and 51 new records on new hosts and new geographical distributions. Three new genera, Cylindrotorula (Torulaceae), Scolecoleotia (Leotiales genus incertae sedis) and Xenovaginatispora (Lindomycetaceae) are introduced based on distinct phylogenetic lineages and unique morphologies. Newly described species are Aspergillus lannaensis, Cercophora dulciaquae, Cladophialophora aquatica, Coprinellus punjabensis, Cortinarius alutarius, C. mammillatus, C. quercoflocculosus, Coryneum fagi, Cruentomycena uttarakhandina, Cryptocoryneum rosae, Cyathus uniperidiolus, Cylindrotorula indica, Diaporthe chamaeropicola, Didymella azollae, Diplodia alanphillipsii, Dothiora coronicola, Efibula rodriguezarmasiae, Erysiphe salicicola, Fusarium queenslandicum, Geastrum gorgonicum, G. hansagiense, Helicosporium sexualis, Helminthosporium chiangraiensis, Hongkongmyces kokensis, Hydrophilomyces hydraenae, Hygrocybe boertmannii, Hyphoderma australosetigerum, Hyphodontia yunnanensis, Khaleijomyces umikazeana, Laboulbenia divisa, Laboulbenia triarthronis, Laccaria populina, Lactarius pallidozonarius, Lepidosphaeria strobelii, Longipedicellata megafusiformis, Lophiotrema lincangensis, Marasmius benghalensis, M. jinfoshanensis, M. subtropicus, Mariannaea camelliae, Melanographium smilaxii, Microbotryum polycnemoides, Mimeomyces digitatus, Minutisphaera thailandensis, Mortierella solitaria, Mucor harpali, Nigrograna jinghongensis, Odontia huanrenensis, O. parvispina, Paraconiothyrium ajrekarii, Parafuscosporella niloticus, Phaeocytostroma yomensis, Phaeoisaria synnematicus, Phanerochaete hainanensis, Pleopunctum thailandicum, Pleurotheciella dimorphospora, Pseudochaetosphaeronema chiangraiense, Pseudodactylaria albicolonia, Rhexoacrodictys nigrospora, Russula paravioleipes, Scolecoleotia eriocamporesi, Seriascoma honghense, Synandromyces makranczyi, Thyridaria aureobrunnea, Torula lancangjiangensis, Tubeufia longihelicospora, Wicklowia fusiformispora, Xenovaginatispora phichaiensis and Xylaria apiospora. One new combination, Pseudobactrodesmium stilboideus is proposed. A reference specimen of Comoclathris permunda is designated. New host or distribution records are provided for Acrocalymma fici, Aliquandostipite khaoyaiensis, Camarosporidiella laburni, Canalisporium caribense, Chaetoscutula juniperi, Chlorophyllum demangei, C. globosum, C. hortense, Cladophialophora abundans, Dendryphion hydei, Diaporthe foeniculina, D. pseudophoenicicola, D. pyracanthae, Dictyosporium pandanicola, Dyfrolomyces distoseptatus, Ernakulamia tanakae, Eutypa flavovirens, E. lata, Favolus septatus, Fusarium atrovinosum, F. clavum,
  PubDate: 2021-12-07
  DOI: 10.1007/s13225-021-00489-3
Trends in yeast diversity discovery
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  Abstract: Abstract Yeasts, usually defined as unicellular fungi, occur in various fungal lineages. Hence, they are not a taxonomic unit, but rather represent a fungal lifestyle shared by several unrelated lineages. Although the discovery of new yeast species occurs at an increasing speed, at the current rate it will likely take hundreds of years, if ever, before they will all be documented. Many parts of the earth, including many threatened habitats, remain unsampled for yeasts and many others are only superficially studied. Cold habitats, such as glaciers, are home to a specific community of cold-adapted yeasts, and, hence, there is some urgency to study such environments at locations where they might disappear soon due to anthropogenic climate change. The same is true for yeast communities in various natural forests that are impacted by deforestation and forest conversion. Many countries of the so-called Global South have not been sampled for yeasts, despite their economic promise. However, extensive research activity in Asia, especially China, has yielded many taxonomic novelties. Comparative genomics studies have demonstrated the presence of yeast species with a hybrid origin, many of them isolated from clinical or industrial environments. DNA-metabarcoding studies have demonstrated the prevalence, and in some cases dominance, of yeast species in soils and marine waters worldwide, including some surprising distributions, such as the unexpected and likely common presence of Malassezia yeasts in marine habitats.
  PubDate: 2021-12-03
  DOI: 10.1007/s13225-021-00494-6
The Global Soil Mycobiome consortium dataset for boosting fungal diversity
research
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  Abstract: Abstract Fungi are highly important biotic components of terrestrial ecosystems, but we still have a very limited understanding about their diversity and distribution. This data article releases a global soil fungal dataset of the Global Soil Mycobiome consortium (GSMc) to boost further research in fungal diversity, biogeography and macroecology. The dataset comprises 722,682 fungal operational taxonomic units (OTUs) derived from PacBio sequencing of full-length ITS and 18S-V9 variable regions from 3200 plots in 108 countries on all continents. The plots are supplied with geographical and edaphic metadata. The OTUs are taxonomically and functionally assigned to guilds and other functional groups. The entire dataset has been corrected by excluding chimeras, index-switch artefacts and potential contamination. The dataset is more inclusive in terms of geographical breadth and phylogenetic diversity of fungi than previously published data. The GSMc dataset is available over the PlutoF repository.
  PubDate: 2021-11-30
  DOI: 10.1007/s13225-021-00493-7
Species diversity, taxonomy and multi-gene phylogeny of phlebioid clade
(Phanerochaetaceae, Irpicaceae, Meruliaceae) of Polyporales
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  Abstract: Abstract The phlebioid clade (Polyporales, Basidiomycota) accommodates numerous species of corticioid and polyporoid fungi of the Phanerochaetaceae, Irpicaceae, and Meruliaceae. The present study used morphological and phylogenetic approaches to revise the generic classification of the phlebioid clade and survey species diversity. The phylogenetic analyses were performed using sequences of multiple genes, including the nuc rDNA ITS1-5.8S-ITS2 (ITS), the D1-D2 domains of 28S rDNA (28S), the RNA polymerase II largest subunit (rpb1), the RNA polymerase II second largest subunit (rpb2), and the translation elongation factor 1-α (tef1). We overall recognize 57 genera including six new ones (Alboefibula, Cremeoderma, Gelatinofungus, Luteochaete, Phanerochaetella and Quasiphlebia). We describe 26 new species belonging to 15 genera (Alboefibula bambusicola, A. gracilis, Crustodontia taiwanensis, Cytidiella albomarginata, Efibula matsuensis, E. turgida, E. subglobispora, Gelatinofungus brunneus, Hydnophlebia aurantia, H. crocata, Irpex lenis, Mycoaciella efibulata, Phanerochaete alpina, P. crystallina, P. guangdongensis, P. rhizomorpha, P. spadicea, P. subcarnosa, Phanerochaetella formosana, Phlebiopsis odontoidea, P. yushaniae, Quasiphlebia densa, Rhizochaete chinensis, Roseograndinia jilinensis, R. minispora, and Scopuloides allantoidea), and present 18 new combinations belonging to 12 genera (Cremeoderma unicum, Crustodontia nigrodontea, C. tongxiniana, Cytidiella albida, Efibula intertexta, Hydnophlebia alachuana, Irpex laceratus, I. latemarginatus, I. rosettiformis, Luteochaete subglobosa, Luteoporia lutea, Phanerochaetella angustocystidiata, P. exilis, P. leptoderma, P. xerophila, Phlebiopsis alba, Rhizochaete lutea, Scopuloides dimorpha). Descriptions, illustrations and notes of new species and some new records are provided, as well as identification keys to genera of each family.
  PubDate: 2021-11-15
  DOI: 10.1007/s13225-021-00490-w
Taxonomic studies of some often over-looked Diaporthomycetidae and
Sordariomycetidae
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  Abstract: Abstract Sordariomycetes is an earlier-introduced and one of the widely distributed class of Ascomycota. The class was initially classified based on morphology in having inoperculate and unitunicate asci. With the development of DNA based phylogenetic analysis, several undetermined or polyphyletic members of Sordariomycetes were reclassified. However, not all species belonging to this class have been sequenced and analyzed. There are a number of species, especially those old and poorly studied ones which have never been sequenced before and not even recollected again for further taxonomic verification. One of the main objective in this study is to revise and update the taxonomy of several well-known early and poorly studied species whose classification are still obscure. Herein, we re-examined the type materials and/or authentic specimens together to explore 74 relatively poorly-studied genera, which mainly belong to Boliniales, Calosphaeriales, Chaetosphaeriales, Jobellisiales, and Sordariales classified under Diaporthomycetidae and Sordariomycetidae. We provide descriptions, notes, figures and/or drawings and discussed their phylogenetic relationships. As a result, the monotypic Jobellisiales is transferred from Hypocreomycetidae to Diaporthomycetidae. Based on phylogenetic analysis, the polyphyletic Lasiosphaeriaceae is divided into five families, Bombardiaceae (Apodospora, Bombardia, Bombardioidea, Fimetariella and Ramophialophora), Lasiosphaeriaceae (Anopodium, Bellojisia, Corylomyces, Lasiosphaeria, Mammaria and Zopfiella), Lasiosphaeridaceae (Lasiosphaeris), Strattoniaceae (Strattonia) and Zygospermellaceae (Episternus and Zygospermella). In addition, a new family Neoschizotheciaceae is established based on Neoschizothecium. Analysis of the type species of Boothiella, Stellatospora, Sulcatistroma and Tengiomyces placed them in Sordariaceae, Chaetomiaceae, Hypocreales and Coronophorales, respectively. We classify the genera lacking molecular data based on their morphology and expect them to be recollected; that is, Kacosphaeria in Calosphaeriales; Arnium, Biconiosporella, Camptosphaeria, Diffractella, Emblemospora, Eosphaeria, Periamphispora, Synaptospora and Tripterosporella in Sordariales; Conidiotheca in Sordariomycetes; Copromyces, Effetia, Endophragmiella and Tulipispora are accommodated in Ascomycota. Besides, we establish a new genus Neoschizothecium based on phylogenetic analysis. New combinations proposed: Camaropella amorpha, Cam. microspora, Cam. plana, Cladorrhinum grandiusculum, Cla. leucotrichum, Cla. terricola, Cla. olerum, Helminthosphaeria plumbea, Immersiella hirta, Jugulospora minor, Lasiosphaeris arenicola, Neoschizothecium aloides, Neo. carpinicola, Neo. conicum, Neo. curvisporum, Neo. fimbriatum, Neo. glutinans, Neo. inaequale, Neo. minicaudum, Neo. selenosporum, Neo. tetrasporum, Neurospora autosteira, Podospora brunnescens, P. flexuosa, P. jamaicensis, P. hamata, P. macrospora, P. spinosa, Strattonia petrogale and Triangularia microsclerotigena, T. nannopodalis, T. praecox, T. samala, T. tarvisina, T. unicaudata, T. yaeyamensis. New epithets a...
  PubDate: 2021-11-10
  DOI: 10.1007/s13225-021-00488-4
Phylogenomic reconstruction addressing the Peltigeralean backbone
(Lecanoromycetes, Ascomycota)
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  Abstract: Abstract Rapid radiations in Fungi are only beginning to be studied with phylogenomic data. The evolutionary history of the lichenized fungal order Peltigerales has not been well resolved, particularly for the Collematineae. Here, we used concatenation and coalescent-based species tree methods to reconstruct the phylogeny of the Peltigerales based on sequences of 125 nuclear single-copy exon sequences among 60 samples, representing 58 species. Despite uneven, lineage-specific missing data and significant topological incongruence of individual exon trees, the resulting phylogenies were concordant and successfully resolved the phylogenetic relationships of the Peltigerales. Relationships in the Collematineae were defined by short branches and lower nodal support than in other parts of the tree, due in part to conflicting signal in exon trees, suggesting rapid diversification events in the early evolution of the suborder. Using tree distance measures, we were able to identify a minimum subset of exons that could reconstruct phylogenetic relationships in Peltigerales with higher support than the 125-exon dataset. Comparisons between the minimum and complete datasets in species tree inferences, bipartition analyses, and divergence time estimations displayed similar results, although the minimum dataset was characterized by higher levels of error in estimations of divergence times. Contrasting our inferences from the complete and minimum datasets to those derived from few nuclear and mitochondrial loci reveal that our topology is concordant with topologies reconstructed using the nuclear large subunit and mitochondrial small subunit ribosomal DNA markers, but the target capture datasets had much higher support values. We demonstrated how target capture approaches can effectively decipher ancient rapid radiations in cases where well resolved individual exon trees are sufficiently sampled and how to identify subsets of loci that are appropriate for fungal order-level phylogenetics.
  PubDate: 2021-06-24
  DOI: 10.1007/s13225-021-00476-8