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Molecular systematics of Barbatosphaeria (Sordariomycetes): Multigene phylogeny and secondary ITS structure
Abstract and Figures
Thirteen morphologically similar strains of barbatosphaeria- and tectonidula-like fungi were studied based on the comparison of cultural and morphological features of sexual and asexual morphs and phylogenetic analyses of five nuclear loci, i.e. internal transcribed spacer rDNA operon (ITS), large and small subunit nuclear ribosomal DNA, β-tubulin, and second largest subunit of RNA polymerase II. Phylogenetic results were supported by in-depth comparative analyses of common core secondary structure of ITS1 and ITS2 in all strains and the identification of non-conserved, co-evolving nucleotides that maintain base pairing in the RNA transcript. Barbatosphaeria is defined as a well-supported monophyletic clade comprising several lineages and is placed in the Sordariomycetes incertae sedis. The genus is expanded to encompass nine species with both septate and non-septate ascospores in clavate, stipitate asci with a non-amyloid apical annulus and non-stromatic ascomata with a long decumbent neck and carbonized wall often covered by pubescence. The asexual morphs are dematiaceous hyphomycetes with holoblastic conidiogenesis belonging to Ramichloridium and Sporothrix types. The morphologically similar Tectonidula, represented by the type species T. hippocrepida, grouped with members of Barbatosphaeria and is transferred to that genus. Four new species are introduced and three new combinations in Barbatosphaeria are proposed. A dichotomous key to species accepted in the genus is provided.
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Supplementary resource (1)
Nucleotide Sequence
January 2009
... Synanamorph is the term of use for fungal taxa producing two or more different asexual morphs which were often linked by the sporulation in culture (Wijayawardene et al. 2021a(Wijayawardene et al. , 2022c. Many fungal taxa have been reported for their synanamorphism, such as Botryosphaeria with dichomera-like in vitro and Neofusicoccum (as Fusicoccum) (Barber et al. 2005), Barbatosphaeria fagi (≡ Calosphaeria fagi) with ramichloridium-like and sporothrix-like asexual morphs (Réblová et al. 2015) and Synnemasporella with sporodochial and pycnidial asexual morphs on natural hosts (Fan et al. 2018). The formation of two or more different morphs in a single species has led to misidentification and the distinct morphs have been somehow counted as different species (Wijayawardene et al. 2021a(Wijayawardene et al. , 2022c. ...
This article presents the results of an ongoing inventory of Ascomycota in Yunnan, China, carried out as part of the research project series “Exploring ascomycete diversity in Yunnan”. From over 100 samples collected from diverse host substrates, microfungi have been isolated, identified and are currently being documented. The primary objective of this research is to promote the discovery of novel taxa and explore the ascomycete diversity in the region, utilising a morphology-phylogeny approach. This article represents the second series of species descriptions for the project and introduces three undocumented species found in the families Bambusicolaceae, Dictyosporiaceae and Periconiaceae, belonging to the suborder Massarineae (Pleosporales, Dothideomycetes). These novel taxa exhibit typical morphological characteristics of Bambusicola, Periconia and Trichobotrys, leading to their designation as Bambusicola hongheensis, Periconia kunmingensis and Trichobotrys sinensis. Comprehensive multigene phylogenetic analyses were conducted to validate the novelty of these species. The results revealed well-defined clades that are clearly distinct from other related species, providing robust support for their placement within their respective families. Notably, this study unveils the phylogenetic affinity of Trichobotrys within Dictyosporiaceae for the first time. Additionally, the synanamorphism for the genus Trichobotrys is also reported for the first time. Detailed descriptions, illustrations and updated phylogenies of the novel species are provided, and thus presenting a valuable resource for researchers and mycologists interested in the diversity of ascomycetes in Yunnan. By enhancing our understanding of the Ascomycota diversity in this region, this research contributes to the broader field of fungal taxonomy and their phylogenetic understanding.
... Hence, to corroborate the species delimitation revealed by the phylogeny and consensus model (Type I-IV with a total of four to six domains), a minimum of nine CBCs among individual structural helices and a total of 645 CBCs were identified between the internal and external subclasses of different species, as an additional molecular marker. It has been experimentally demonstrated that taxa separated by one CBC are totally incapable of intercrossing [24,25,60], and that it could be said that they represent separate species. ...
Background:
The delimitation of species of Tulasnella has been extensively studied, mainly at the morphological (sexual and asexual states) and molecular levels-showing ambiguity between them. An integrative species concept that includes characteristics such as molecular, ecology, morphology, and other information is crucial for species delimitation in complex groups such as Tulasnella.
Objectives:
The aim of this study is to test evolutionary relationships using a combination of alignment-based and alignment-free distance matrices as an alternative molecular tool to traditional methods, and to consider the secondary structures and CBCs from ITS2 (internal transcribed spacer) sequences for species delimitation in Tulasnella.
Methodology:
Three phylogenetic approaches were plotted: (i) alignment-based, (ii) alignment-free, and (iii) a combination of both distance matrices using the DISTATIS and pvclust libraries from an R package. Finally, the secondary structure consensus was modeled by Mfold, and a CBC analysis was obtained to complement the species delimitation using 4Sale.
Results and conclusions:
The phylogenetic tree results showed delimited monophyletic clades in Tulasnella spp., where all 142 Tulasnella sequences were divided into two main clades A and B and assigned to seven species (T. asymmetrica, T. andina, T. eichleriana ECU6, T. eichleriana ECU4 T. pinicola, T. violea), supported by bootstrap values from 72% to 100%. From the 2D secondary structure alignment, three types of consensus models with helices and loops were obtained. Thus, T. albida belongs to type I; T. eichleriana, T. tomaculum, and T. violea belong to type II; and T. asymmetrica, T. andina, T. pinicola, and T. spp. (GER) belong to type III; each type contains four to six domains, with nine CBCs among these that corroborate different species.
An updated account of Fagales-inhabiting Italian Ascomycota and mycogeography, with additions to Pezizomycotina. Abstract Studies of plant-associated Ascomycota are topical, as they have varied life modes depending on their hosts in different ecosystems. In Italy, Fagales are economically and ecologically important plants, especially in the Alps and Apennine mountain ranges. Fagales species host numerous ascomycetous species, comprising endophytes, saprobes, or pathogens. We retrieved data from 308 publications from 1873 to 2021 and listed 776 Ascomycota on Fagales in Italy. Among these, 696 were identified at the species level and 80 at the genus level. Documented taxa belong to Pezizomycotina (746), Saccharomycotina (2), Taphrinomycotina (5), and Ascomycota genera incertae sedis (23). Sordariomycetes are dominant (34%), followed by Dothideomycetes (24%), Lecanoromycetes (16%), and Leotiomycetes (11%). Distribution maps were provided for the occurrence of Fagales trees and Dothideomycetes, Eurotiomycetes, Leotiomycetes, Pezizomycetes, and Sordariomycetes taxa. Lichenized taxa were excluded from the mapping. We provided additions to Valsariaceae (Valsaria rudis) in Dothideomycetes, Coryneaceae (Coryneum modonium), Melanconiellaceae (Melanconiella flavovirens and M. meridionalis), and Woswasiaceae (Woswasia atropurpurea) in Sordariomycetes. These taxa represent a novel host record, a provincial record, and four regional records in Italy. Species boundaries were defined using polyphasic approaches. In addition, taxonomic notes were provided for each reported class, including incertae sedis genera. The study provides information on the taxonomy, hosts, and distribution of Ascomycota in Italy to encourage further research related to important plant species.
Keywords – checklist – host-fungal distribution – morphology – phylogeny – taxonomy
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.
The genus Thyridium , previously known as a saprobic or hemibiotrophic ascomycete on various plants, was revised taxonomically and phylogenetically. Sequences of the following six regions, that is, the nuclear ribosomal internal transcribed spacer (ITS) region, the large subunit (LSU) of rDNA, the second largest RNA polymerase II subunit ( rpb2 ) gene, translation elongation factor 1-alpha ( tef1 ) gene, the actin ( act ) gene, and the beta-tubulin ( tub2 ) gene, were generated for molecular phylogenetic analyses of species of this genus. Phialemoniopsis , a genus encompassing medically important species, is synonymised with Thyridium based on molecular evidence and morphological similarities in their asexual characters. The generic concept for Thyridium is expanded to include species possessing both coelomycetous and hyphomycetous complex asexual morphs. In addition to type species of Thyridium , T. vestitum , nine species were accepted in Thyridium upon morphological comparison and molecular phylogenetic analyses in this study. All seven species of Phialemoniopsis were treated as members of the genus Thyridium and new combinations were proposed. A bambusicolous fungus, Pleospora punctulata , was transferred to Thyridium , and an epitype is designated for this species. A new species, T. flavostromatum , was described from Phyllostachys pubescens . The family Phialemoniopsidaceae, proposed as a familial placement for Phialemoniopsis , was regarded as a synonym of Thyridiaceae. A new order, Thyridiales, was established to accommodate Thyridiaceae; it forms a well-supported, monophyletic clade in Sordariomycetes.
This is the fifth in a series, Mycosphere notes, wherein 50 notes are provided on types of genera and other specimens with descriptions and illustrations. This includes one genus in Arthoniomycetes, one genus in Eurotiomycetes, 38 genera in Dothideomycetes, six genera in Sordariomycetes, two genera in Ascomycota, families incertae sedis, one genus in Pezizomycotina, and one taxon, Angatia rondoniensis, is treated as a doubtful species. Pycnocarpon magnificum is classified in Asterinaceae. We reinstate Eopyrenula in Dacampiaceae on the basis of its Mycosphere 9(4): 647-754 (2018) www.mycosphere.org ISSN 2077 7019
Zanclospora (Chaetosphaeriaceae) is a neglected, phialidic dematiaceous hyphomycete with striking phenotypic heterogeneity among its species. Little is known about its global biogeography due to its extreme scarcity and lack of records verified by molecular data. Phylogenetic analyses of six nuclear loci, supported by phenotypic data, revealed Zanclospora as highly polyphyletic, with species distributed among three distantly related lineages in Sordariomycetes. Zanclospora is a pleomorphic genus with multiple anamorphic stages, of which phaeostalagmus-like and stanjehughesia-like are newly discovered. The associated teleomorphs were previously classified in Chaetosphaeria. The generic concept is emended, and 17 species are accepted, 12 of which have been verified with DNA sequence data. Zanclospora thrives on decaying plant matter, but it also occurs in soil or as root endophytes. Its global diversity is inferred from metabarcoding data and published records based on field observations. Phylogenies of the environmental ITS1 and ITS2 sequences derived from soil, dead wood and root samples revealed seven and 15 phylotypes. The field records verified by DNA data indicate two main diversity centres in Australasia and Caribbean/Central America. In addition, environmental ITS data have shown that Southeast Asia represents a third hotspot of Zanclospora diversity. Our data confirm that Zanclospora is a rare genus.
Dictyochaeta (Chaetosphaeriaceae) is a phialidic dematiaceous hyphomycete with teleomorphs classified in Chaetosphaeria. It is associated with significant variability of asexual morphological traits, which led to its broad delimitation. In the present study, six loci: nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode), nuc 18S rDNA (18S), nuc 28S rDNA (28S), DNA-directed RNA polymerase II second largest subunit gene (RPB2), translation elongation factor 1-α (TEF1-α), and β-tubulin (TUB2), along with comparative morphological and cultivation studies, are used to reevaluate the concept of Dictyochaeta and establish species boundaries. Based on revised species, morphological characteristics of conidia (shape, septation, absence or presence of setulae), collarettes (shape), and setae (presence or absence) and an extension of the conidiogenous cell proved to be important at the generic level. The dual DNA barcoding using ITS and TEF1-α, together with TUB2, facilitated accurate identification of Dictyochaeta species. Thirteen species are accepted, of which seven are characterized in this study; an identification key is provided. It was revealed that D. fuegiana, the type species, is a complex of three distinct species including D. querna and the newly described D. stratosa. Besides, a new species, D. detriticola, and two new combinations, D. callimorpha and D. montana, are proposed. An epitype of D. montana is selected. Dictyochaeta includes saprobes on decaying wood, bark, woody fruits, and fallen leaves. Dictyochaeta is shown to be distantly related to the morphologically similar Codinaea, which is resolved as paraphyletic. Chaetosphaeria talbotii with a Dictyochaeta anamorph represents a novel lineage in the Chaetosphaeriaceae; it is segregated from Dictyochaeta, and a new genus Achrochaeta is proposed. Multigene phylogenetic analysis revealed that D. cylindrospora belongs to the Vermiculariopsiellales, and a new genus Tubulicolla is introduced.
The number of extant freshwater fungi is rapidly increasing, and the published information of taxonomic data are scattered among different online journal archives. The only online repository, http://fungi.life.illinois.edu/, deals with freshwater ascomycetes and their asexual morphs. Other freshwater fungal groups are not included. The newly developed webpage (www.freshwaterfungi.org/) serves as a gateway to freshwater fungal systematics that provides comprehensive and updated information including detailed descriptions, photographic plates and illustrations, notes, phylogenetic trees, estimated and extant list of species, and other related information. The website is developed with user-friendly interfaces, and the usage is discussed in this paper.
In order to more fully elucidate the phylogenetic relationships of the lignicolous, pyrenomycetous genus Chaetosphaeria and its anamorphs and reveal the most reliable molecular data set we sequenced a portion of the large nuclear ribosomal RNA gene (LSU rDNA) and the complete ITS region (ITS1, the 5.8S rRNA gene and ITS2) of 25 members of the Chaetosphaeriaceae including Porosphaerella cordanophora, Striatosphaeria codinaeophora, species of Chaetosphaeria and Melanopsammella, and representatives of eight of the eleven of their anamorph genera. Phylogenetic analyses were performed on four different data sets. The phylogeny inferred from the LSU rDNA sequence data showed two main groups, each with two subgroups, within the monophyletic Chaetosphaeriaceae. These subgroups are easily identified by morphological features of anamorphs and teleomorphs and serve as a background to subdivide the Chaetosphaeria species in to two, respectively, two and four natural groups of taxa. Two sexual species currently referred to Chaetosphaeria and two related asexual species grouped with Hypocreales and Microascales, respectively. Knoxdaviesia is relegated to synonymy with Custingophora. The morphology-based classification of Chaetosphaeria is compared with results from analyses of molecular data. The taxonomic value of morphological characters observed in teleomorphs and dematiaceous hyphomycetous anamorphs is discussed in the light of the results of these analyses.
Members of Aspergillus section Fumigati are important animal pathogens and food contaminants. There is considerable variation among the 16 currently recognized species in this section, particularly in their mating systems: five are known to be strictly mitosporic, nine are homothallic, and two are heterothallic. Phylogenetic relationships were inferred among members of Aspergillus section Fumigati based on partial DNA sequences from the benA β-tubulin and rodA hydrophobin genes. Aspergillus clavatus was chosen as an outgroup. The two gene regions provided nearly equal numbers of phylogenetically informative nucleotide characters. The rodA region possessed a considerably higher level of inferred amino acid variation than did the benA region. The results of a partition homogeneity test showed that the benA and rodA data sets were not in significant conflict, and the topologies of the most parsimonious trees for the two data sets differed only in branches that were not strongly supported by bootstrapping. The data sets in combination showed that morphological and secondary metabolite characters used in taxonomy were not strongly correlated with phylogeny. Mixed interrelationships were found among strictly mitotic, homothallic (selfing and outcrossing) and heterothallic (obligately outcrossing) taxa, suggesting multiple independent losses of the Neosartorya sexual state and possible derivation of heterothallism from homothallism through loss of self compatibility. The food spoiling species N. fischeri was identified as the closest known meiotic relative to the cosmopolitan species most often implicated in human aspergillosis, A. fumigatus.
The new genus Barbatosphaeria is described for a perithecial ascomycete known as Calosphaeria barbirostris occurring on decayed wood of deciduous trees under the periderm. The fungus produces nonstromatic perithecia with hyaline, 1-septate ascospores formed in unitunicate, nonamyloid asci. Anamorphs produced in vitro belong to Sporothrix and Ramichloridium with holoblastic-denticulate conidiogenesis; conidiophores of the two types were formed in succession during the development of the colony. Phylogenetic analyses of nuLSU rDNA sequences indicate that this fungus is distinct from morphologically similar Lentomitella, tentatively placed in the Trichosphaeriales. It groups with freshwater Aquaticola and Cataractispora and terrestrial Cryptadelphia in maximum parsimony analysis; the same grouping but without Cryptadelphia was inferred from Bayesian analysis. Cultivation, morphology and phylogenetic studies of the nuLSU rDNA support the erection of a new genus for C. barbirostris.
The systematic position and phylogenetic relationships of Ceratostomella sensu lato and phenotypically similar fungi using comparative morphological and culture studies and phylogenetic analyses of the nuclear large- and small-subunit ribosomal DNA were explored. In the light of inferred phylogenies and morphological data the genus Ceratostomella is redescribed, the generic concept is emended and four species are accepted (viz. C. cuspidata, C. pyrenaica, C. rhynchophora and C. rostrata). A new genus Xylomelasma is introduced and delimited from Ceratostomella, with two new species described (viz. X. novaezelandiae and X. sordida). In culture species of both Ceratostomella and Xylomelasma produced sterile mycelium. The genus Lentomitella with a phaeoisaria-like anamorph formed in vitro is reinstated to encompass taxa formerly attributed to the broadly perceived Ceratostomella with three accepted species (viz. L. cirrhosa, L. crinigera and L. tomentosa). Lentomitella and Ceratostomella are clearly distinguishable by the morphology of asci, ascospores and centrum. Lentomitella is compared to phenotypically similar Ceratosphaeria, which formed a harpophora-like anamorph in vitro. In the present phylogenies Ceratostomella, Ceratosphaeria, Lentomitella and Xylomelasma are shown as clearly separate genera belonging to three different groups of perithecial ascomycetes. Ceratostomella, Lentomitella and Xylomelasma reside within a large unsupported clade consisting of members the Ophiostomatales, the freshwater Annulatascaceae and a group of nonstromatic, terrestrial taxa. Ceratosphaeria is well supported within the Magnaporthaceae. The systematic value of morphological characters of ascospores, paraphyses, asci, centrum and conidiogenesis in segregating taxa from Ceratostomella sensu lato and their relatives is discussed.
Fluminicola bipolaris is described based on a specimen found on submerged wood collected in a tropical river in the Philippines. The taxon is similar to species of Annulatascus, but differs in having ascospores with bipolar bifurcate or cup-like appendages. The structure of these appendages is unique and is illustrated at the light, scanning and electron microscope levels. Fluminicola bipolaris is compared with species of Annulatascus and Proboscispora.
A major running battle was fought in the 1940s, 1950s and 1960s in the continuing war between advocates of biological species versus taxonomic (morphological) species. The subject was the taxonomic treatment of Paramecium aurelia. At that time, proponents of the newly accredited concept of a biological species (Mayr 1948) demanded that the 16 sexually isolated syngens of Paramecium aurelia be named as separate species. T. M. Sonneborn, who was largely responsible for the mating studies revealing the presence of multiple syngens (isolated mating groups) within the morphologically uniform P. aurelia, felt that species descriptions requiring biochemistry or cell culture for identification were impractical. Finally, in 1975, he capitulated, describing P. primaurelia, P. biaurelia, etc., on isozyme and mating affinity criteria. P. aurelia is not the only taxonomic species encompassing multiple cryptic species. The appropriate taxonomic solution is still moot, but we have obtained DNA sequence data now that reveal the relationships among the P. aurelia syngens, and that can be used to compare with similar cases, both in ciliates and in the microalgae, as well as plants and animals.