Resolving the Lophiostoma bipolare complex: generic delimitations within Lophiostomataceae Stud. Mycol. (IF 14) Pub Date : 2018-03-07 A. Hashimoto, K. Hirayama, H. Takahashi, M. Matsumura, G. Okada, C.Y. Chen, J.W. Huang, M. Kakishima, T. Ono, K. Tanaka
Lophiostoma bipolare was taxonomically revised based on the morphological observations and phylogenetic analyses of molecular data from nuclear rDNA SSU-ITS-LSU, TUB, tef1, and rpb2 genes. Twenty-nine strains were morphologically similar to Lo. bipolare. A total of 174 sequences were generated from the Lo. bipolare complex. Phylogenetic analyses based on TUB sequence revealed 11 distinct species within the Lo. bipolare complex. Morphological features of the ascospores and the anatomical structure of the ascomata from both field collections as well as axenic culture, which have been reported previously as variable features at intraspecific levels, were compared to evaluate the taxonomic reliability of these features. To clarify the generic position of the 11 species, phylogenetic analyses were done on SSU-ITS-LSU-tef1-rpb2 gene sequences. The Lo. bipolare complex shared phylogenetic relationships with Pseudolophiostoma and Vaginatispora, and formed an additional five distinct clades from other members of Lophiostomataceae. According to its phylogenetic position, Lo. bipolare sensu stricto was distantly related to Lophiostoma s. str., and formed an independent clade within Lophiostomataceae. Lophiostoma bipolare s. str. could be distinguished from the other lophiostomataceous genera by the clypeus around the ostiolar neck and by the thin and uniformly thick peridium. A novel genus described as Lentistoma was established to accommodate this species, and the epitypification of Lentistoma bipolare (basionym: Massarina bipolaris) was proposed. Other lineages of the Lo. bipolare complex could not be separated on the basis of the ascospore size and sheath variations, but were distinguished based on ascomatal features, such as the existence of the clypeus, brown hyphae surrounding the peridium, and the contexture of the peridium, which were stable indicators of generic boundaries in Lophiostomataceae. Four additional new genera with five new species were recognised based on these morphological differences: Crassiclypeus (C. aquaticus), Flabellascoma (F. cycadicola and F. minimum), Leptoparies (Lep. palmarum), and Pseudopaucispora (Pseudop. brunneospora). Three new species were added to Pseudolophiostoma (Pseudol. cornisporum, Pseudol. obtusisporum, and Pseudol. tropicum) and two new species were added to Vaginatispora (V. amygdali and V. scabrispora). The re-evaluation of the validity of several previously recognised genera resulted in the introduction of two new genera with new combinations for Lophiostoma pseudoarmatisporum as Parapaucispora pseudoarmatispora and Vaginatispora fuckelii as Neovaginatispora fuckelii.
Cladosporium species in indoor environments Stud. Mycol. (IF 14) Pub Date : 2018-03-07 K. Bensch, J.Z. Groenewald, M. Meijer, J. Dijksterhuis, Ž. Jurjevic, J. Houbraken, P.W. Crous, R.A. Samson
As part of a worldwide survey of the indoor mycobiota about 520 new Cladosporium isolates from indoor environments mainly collected in China, Europe, New Zealand, North America and South Africa were investigated by using a polyphasic approach to determine their species identity. All Cladosporium species occurring in indoor environments are fully described and illustrated. Fourty-six Cladosporium species are treated of which 16 species are introduced as new. A key for the most common Cladosporium species isolated from indoor environments is provided. Cladosporium halotolerans proved to be the most frequently isolated Cladosporium species indoors.
Deconstructing the evolutionary complexity between rust fungi (Pucciniales) and their plant hosts Stud. Mycol. (IF 14) Pub Date : 2018-03-01 M. Catherine Aime, Charles D. Bell, Andrew W. Wilson
The rust fungi (Pucciniales) are the most speciose natural group of plant pathogens, members of which possess some of the most complex lifecycles in biology. How natural selection works on the Pucciniales has been the subject of several hypotheses in mycology. This study uses molecular age estimation using sequence data from multiple loci, and cophylogeny reconciliation analyses to test hypotheses regarding how the aecial and telial stages in the lifecycle of rust fungi may have differentially impacted diversification in the Pucciniales. Molecular age estimates show that the timing of diversification in the Pucciniales correlates with the diversification of their gymnosperm and angiosperm hosts. Host reconciliation analyses suggest that systematic relationships of hosts from the aecial stage of the Pucciniales lifecycle better reflect the systematic relationships among the Pucciniales. The results demonstrate the relative importance of this stage on the overall evolution of the Pucciniales and supports hypotheses made by Leppik over half a century ago. However, these hypotheses are not as strongly supported in more recently derived lineages of rust fungi because codiversification patterns with hosts are not as clear. This study represents the first evaluation of how different life stages in the Pucciniales shape the evolution of these fungi.
Phylogeny of dermatophytes with genomic character evaluation of clinically distinct Trichophyton rubrum and T. violaceum Stud. Mycol. (IF 14) Pub Date : 2018-02-21 Ping Zhan, K. Dukik, D. Li, J. Sun, J.B. Stielow, B. Gerrits van den Ende, B. Brankovics, S.B.J. Menken, H. Mei, W. Bao, G. Lv, W. Liu, G.S. de Hoog
Trichophyton rubrum and T. violaceum are prevalent agents of human dermatophyte infections, the former being found on glabrous skin and nail, while the latter is confined to the scalp. The two species are phenotypically different but are highly similar phylogenetically. The taxonomy of dermatophytes is currently being reconsidered on the basis of molecular phylogeny. Molecular species definitions do not always coincide with existing concepts which are guided by ecological and clinical principles. In this article, we aim to bring phylogenetic and ecological data together in an attempt to develop new species concepts for anthropophilic dermatophytes. Focus is on the T. rubrum complex with analysis of rDNA ITS supplemented with LSU, TUB2, TEF3 and ribosomal protein L10 gene sequences. In order to explore genomic differences between T. rubrum and T. violaceum, one representative for both species was whole genome sequenced. Draft sequences were compared with currently available dermatophyte genomes. Potential virulence factors of adhesins and secreted proteases were predicted and compared phylogenetically. General phylogeny showed clear gaps between geophilic species of Arthroderma, but multilocus distances between species were often very small in the derived anthropophilic and zoophilic genus Trichophyton. Significant genome conservation between T. rubrum and T. violaceum was observed, with a high similarity at the nucleic acid level of 99.38 % identity. Trichophyton violaceum contains more paralogs than T. rubrum. About 30 adhesion genes were predicted among dermatophytes. Seventeen adhesins were common between T. rubrum and T. violaceum, while four were specific for the former and eight for the latter. Phylogenetic analysis of secreted proteases reveals considerable expansion and conservation among the analyzed species. Multilocus phylogeny and genome comparison of T. rubrum and T. violaceum underlined their close affinity. The possibility that they represent a single species exhibiting different phenotypes due to different localizations on the human body is discussed.
Fungus wars: basidiomycete battles in wood decay Stud. Mycol. (IF 14) Pub Date : 2018-02-21 J. Hiscox, J. O’Leary, L. Boddy
Understanding the mechanisms underlying wood decay basidiomycete community dynamics is crucial for fully understanding decomposition processes, and for modelling ecosystem function and resilience to environmental change. Competition drives community development in decaying woody resources, with interactions occurring at a distance, following physical contact, and through specialised relationships such as mycoparasitism. Outcomes of combative interactions range from replacement, where one mycelium displaces another, to deadlock, where neither combatant captures territory from the other; and a spectrum of intermediate outcomes (i.e. partial or mutual replacement) lie between these extremes. Many wood decay basidiomycetes coexist within a resource, in a complex and dynamic community, and new research techniques are focusing on spatial orientation of interactions in 3 dimensions, as opposed to historical two-dimensional research. Not only do interactions drive changes in species composition and thus wood decomposition rate, they also may have industrial applications in biocontrol of pathogenic or nuisance fungi, enzyme production, and in the production of novel antifungals and antibiotics. Altogether, fungal interactions are a fascinating and important field of study.
Novel and interesting Ophiocordyceps spp. (Ophiocordycipitaceae, Hypocreales) with superficial perithecia from Thailand Stud. Mycol. (IF 14) Pub Date : 2018-02-17 J. Luangsa-ard, K. Tasanathai, D. Thanakitpipattana, A. Khonsanit, M. Stadler
Ophiocordyceps is a heterogeneous, species-rich genus in the order Hypocreales (Sordariomycetes, Ascomycota) that includes invertebrate-pathogenic taxa. In this study, seven new species in Ophiocordyceps producing superficial perithecia infecting various insect hosts (Lepidoptera, Hemiptera) are described from Thailand – Ophiocordyceps brunneinigra, O. brunneiperitheciata, O. geometridicola, O. multiperitheciata, O. pauciovoperitheciata, O. pseudoacicularis and O. spataforae. Phylogenetic analyses based on multigene loci comprising the large subunit of the ribosomal DNA (LSU), partial sequences of elongation factor 1-alpha (TEF) and the largest and second largest subunit of the RNA polymerase (RPB1, PRB2) strongly support these new species of Ophiocordyceps in the Ophiocordycipitaceae. They differ from species previously described species Ophiocordyceps acicularis, O. atewensis, O. cochlidiicola, and O. crinalis, in the shape and sizes of distinguishing characters such as perithecia, ascospores and conidia. We also report a new record of O. macroacicularis in Thailand.
Temporal variation of fungal diversity in a mosaic landscape in Germany Stud. Mycol. (IF 14) Pub Date : 2018-02-07 S. Rudolph, J.G. Maciá-Vicente, H. Lotz-Winter, M. Schleuning, M. Piepenbring
This study aims at characterizing the diversity and temporal changes of species richness and composition of fungi in an ecotone of a forest border and a meadow in the Taunus mountain range in Germany. All macroscopically visible, epigeous fungi and vascular plants were sampled monthly over three years, together with climatic variables like humidity and temperature that influence fungal diversity and composition as shown by previous studies. In this mosaic landscape, a total of 855 fungal species were collected and identified based on morphological features, the majority of which belonged to Ascomycota (51 %) and Basidiomycota (45 %). Records of fungal species and plant species (218) for this area yielded a fungus to plant species ratio of 4:1, with a plant species accumulation curve that reached saturation. The three years of monitoring, however, were not sufficient to reveal the total fungal species richness and estimation factors showed that a fungus to plant species ratio of 6:1 may be reached by further sampling efforts. The effect of climatic conditions on fungal species richness differed depending on the taxonomic and ecological group, with temporal patterns of occurrence of Basidiomycota and mycorrhizal fungi being strongly associated with temperature and humidity, whereas the other fungal groups were only weakly related to abiotic conditions. In conclusion, long-term, monthly surveys over several years yield a higher diversity of macroscopically visible fungi than standard samplings of fungi in autumn. The association of environmental variables with the occurrence of specific fungal guilds may help to improve estimators of fungal richness in temperate regions.
Two different R gene loci co-evolved with Avr2 of Phytophthora infestans and confer distinct resistance specificities in potato Stud. Mycol. (IF 14) Pub Date : 2018-02-07 C. Aguilera-Galvez, N. Champouret, H. Rietman, X. Lin, D.t Wouters, Z. Chu, J.D.G. Jones, J.H. Vossen, R.G.F. Visser, P.J. Wolters, V.G.A.A. Vleeshouwers
Late blight caused by the oomycete pathogen Phytophthora infestans is the most devastating disease in potato. For sustainable management of this economically important disease, resistance breeding relies on the availability of resistance (R) genes. Such R genes against P. infestans have evolved in wild tuber-bearing Solanum species from North, Central and South America, upon co-evolution with cognate avirulence (Avr) genes. Here, we report how effectoromics screens with Avr2 of P. infestans revealed defence responses in diverse Solanum species that are native to Mexico and Peru. We found that the response to AVR2 in the Mexican Solanum species is mediated by R genes of the R2 family that resides on a major late blight locus on chromosome IV. In contrast, the response to AVR2 in Peruvian Solanum species is mediated by Rpi-mcq1, which resides on chromosome IX and does not belong to the R2 family. The data indicate that AVR2 recognition has evolved independently on two genetic loci in Mexican and Peruvian Solanum species, respectively. Detached leaf tests on potato cultivar Désirée transformed with R genes from either the R2 or the Rpi-mcq1 locus revealed an overlapping, but distinct resistance profile to a panel of 18 diverse P. infestans isolates. The achieved insights in the molecular R - Avr gene interaction can lead to more educated exploitation of R genes and maximize the potential of generating more broad-spectrum, and potentially more durable control of the late blight disease in potato.
RXLR effector diversity in Phytophthora infestans isolates determines recognition by potato resistance proteins; the case study AVR1 and R1 Stud. Mycol. (IF 14) Pub Date : 2018-02-07 Y. Du, R. Weide, Z. Zhao, P. Msimuko, F. Govers, K. Bouwmeester
Late blight disease caused by the plant pathogenic oomycete pathogen Phytophthora infestans is one of the most limiting factors in potato production. P. infestans is able to overcome introgressed late blight resistance by adaptation of effector genes. AVR1 is an RXLR effector that triggers immune responses when recognized by the potato resistance protein R1. P. infestans isolates avirulent on R1 plants were found to have AVR1 variants that are recognized by R1. Virulent isolates though, lack AVR1 but do contain a close homologue of AVR1, named A-L, of which all variants escape recognition by R1. Co-expression of AVR1 and R1 in Nicotiana benthamiana results in a hypersensitive response (HR). In contrast, HR is not activated when A-L is co-expressed with R1. AVR1 and A-L are highly similar in structure. They share two W motifs and one Y motif in the C-terminal part but differ in the T-region, a 38 amino acid extension at the carboxyl-terminal tail of AVR1 lacking in A-L. To pinpoint what determines R1-mediated recognition of AVR1 we tested elicitor activity of AVR1 and A-L chimeric and deletion constructs by co-expression with R1. The T-region is important as it enables R1-mediated recognition of A-L, not only when fused to A-L but also via trans-complementation. Yet, AVR1 lacking the T-region is still active as an elicitor of HR, but this activity is lost when certain motifs are swapped with A-L. These data show that A-L circumvents R1 recognition not only because it lacks the T-region, but also because of differences in the conserved C-terminal effector motifs.
Scopulariopsis and scopulariopsis-like species from indoor environments Stud. Mycol. (IF 14) Pub Date : 2017-03-18 J.H.C. Woudenberg, M. Meijer, J. Houbraken, R.A. Samson
Scopulariopsis-like species are often reported from the indoor environment, as well as from clinical samples. The lack of type isolates and thorough phylogenetic studies in the Microascaceae hampered the correct identification of these isolates. Based on recent phylogenetic studies, which resulted in multiple name changes, the aim is to molecularly identify the Scopulariopsis and scopulariopsis-like species which occur in the indoor environment and give an overview of the current species in these genera and their habitats. Strains from the CBS culture collection were supplemented with almost 80 indoor strains of which the internal transcribed spacer 1 and 2 and intervening 5.8S nrDNA (ITS), beta-tubulin (tub2) and translation elongation factor 1-alpha (tef1) gene regions were sequenced for phylogenetic inference. The multi-gene phylogenies recognise 33 Microascus species and 12 Scopulariopsis species and showed that the recently established genus Fuscoannellis, typified by Scopulariopsis carbonaria, should be synonymized with the genus Yunnania. Seven new Microascus species, four new Scopulariopsis species, and one new Yunnania species, are described, and a new name in Microascus and two new name combinations (one in Microascus, and one in Yunnania) are proposed. In the indoor environment 14 Microascus species and three Scopulariopsis species were found. Scopulariopsis brevicaulis (22 indoor isolates) and Microascus melanosporus (19 indoor isolates) are the most common indoor species, in number of isolates, followed by M. paisii (8 indoor isolates) and S. candida (7 indoor isolates). A genus phylogeny based on the ITS, tef1 and the large subunit 28S nrDNA (LSU) of the type or representative isolates of all here recognised species is provided depicting all species habitats. No correlation between phylogenetic relationship and habitat preference could be observed. Ten species which are found indoor are also found in relation with human-derived samples. A table showing recent name changes and a key to common species of Scopulariopsis and scopulariopsis-like genera found indoors is included.
Polyphasic taxonomy of Aspergillus section Aspergillus (formerly Eurotium), and its occurrence in indoor environments and food Stud. Mycol. (IF 14) Pub Date : 2017-07-12 A.J. Chen, V. Hubka, J.C. Frisvad, C.M. Visagie, J. Houbraken, M. Meijer, J. Varga, R. Demirel, Ž. Jurjević, A. Kubátová, F. Sklenář, Y.G. Zhou, R.A. Samson
Aspergillus section Aspergillus (formerly the genus Eurotium) includes xerophilic species with uniseriate conidiophores, globose to subglobose vesicles, green conidia and yellow, thin walled eurotium-like ascomata with hyaline, lenticular ascospores. In the present study, a polyphasic approach using morphological characters, extrolites, physiological characters and phylogeny was applied to investigate the taxonomy of this section. Over 500 strains from various culture collections and new isolates obtained from indoor environments and a wide range of substrates all over the world were identified using calmodulin gene sequencing. Of these, 163 isolates were subjected to molecular phylogenetic analyses using sequences of ITS rDNA, partial β-tubulin (BenA), calmodulin (CaM) and RNA polymerase II second largest subunit (RPB2) genes. Colony characteristics were documented on eight cultivation media, growth parameters at three incubation temperatures were recorded and micromorphology was examined using light microscopy as well as scanning electron microscopy to illustrate and characterize each species. Many specific extrolites were extracted and identified from cultures, including echinulins, epiheveadrides, auroglaucins and anthraquinone bisanthrons, and to be consistent in strains of nearly all species. Other extrolites are species-specific, and thus valuable for identification. Several extrolites show antioxidant effects, which may be nutritionally beneficial in food and beverages. Important mycotoxins in the strict sense, such as sterigmatocystin, aflatoxins, ochratoxins, citrinin were not detected despite previous reports on their production in this section. Adopting a polyphasic approach, 31 species are recognized, including nine new species. ITS is highly conserved in this section and does not distinguish species. All species can be differentiated using CaM or RPB2 sequences. For BenA, Aspergillus brunneus and A. niveoglaucus share identical sequences. Ascospores and conidia morphology, growth rates at different temperatures are most useful characters for phenotypic species identification.
Cephalotrichum and related synnematous fungi with notes on species from the built environment Stud. Mycol. (IF 14) Pub Date : 2017-09-21 J.H.C. Woudenberg, M. Sandoval-Denis, J. Houbraken, K.A. Seifert, R.A. Samson
A recent taxonomic revision of Microascaceae with an emphasis on synnematous fungi enabled re-identification of previously isolated indoor strains of Cephalotrichum. All available Cephalotrichum strains from the culture collection of the Westerdijk Institute were studied, 20 originating from the built environment. Phylogenetic relationships were inferred from DNA sequence data from the internal transcribed spacer 1 and 2 and intervening 5.8S nrDNA (ITS), and parts of β-tubulin (tub2) and translation elongation factor 1-α (tef1) genes. Additionally, herbarium material of 14 Cephalotrichum species described from soil in China was studied, and the taxonomy of C. album, not considered in recent revisions, was reevaluated. Sixteen phylogenetic species in Cephalotrichum are distinguished, five described as new species: C. domesticum, C. lignatile, C. telluricum, C. tenuissimum and C. transvaalense. Five Cephalotrichum species occur in the built environment: C. domesticum, C. gorgonifer (formerly known as Trichurus spiralis), C. microsporum, C. purpureofuscum, and C. verrucisporum. Based on the number of isolates, C. gorgonifer (nine strains) is the most common indoor species. The study of the Chinese herbarium material resulted in the acceptance of three additional Cephalotrichum species: C. casteneum, C. ellipsoideum, and C. spirale. Four species are considered nomena dubia (C. cylindrosporum, C. macrosporum, C. ovoideum, and C. robustum), five are placed in synonymy with other Cephalotrichum species (C. acutisporum, C. inflatum, C. longicollum, C. oblongum, C. terricola) and one species, C. verrucipes, is probably a synonym of Penicillium clavigerum. Cephalotrichum columnare, former Doratomyces columnaris, is transferred to Kernia. Cephalotrichum album, formerly known as Doratomyces putredinis, is transferred to Acaulium and redescribed.
Phylogeny of xerophilic aspergilli (subgenus Aspergillus) and taxonomic revision of section Restricti Stud. Mycol. (IF 14) Pub Date : 2017-09-27 F. Sklenář, Ž. Jurjević, P. Zalar, J.C. Frisvad, C.M. Visagie, M. Kolařík, J. Houbraken, A.J. Chen, N. Yilmaz, K.A. Seifert, M. Coton, F. Déniel, N. Gunde-Cimerman, R.A. Samson, S.W. Peterson, V. Hubka
Aspergillus section Restricti together with sister section Aspergillus (formerly Eurotium) comprises xerophilic species, that are able to grow on substrates with low water activity and in extreme environments. We adressed the monophyly of both sections within subgenus Aspergillus and applied a multidisciplinary approach for definition of species boundaries in sect. Restricti. The monophyly of sections Aspergillus and Restricti was tested on a set of 102 isolates comprising all currently accepted species and was strongly supported by Maximum likelihood (ML) and Bayesian inferrence (BI) analysis based on β-tubulin (benA), calmodulin (CaM) and RNA polymerase II second largest subunit (RPB2) loci. More than 300 strains belonging to sect. Restricti from various isolation sources and four continents were characterized by DNA sequencing, and 193 isolates were selected for phylogenetic analyses and phenotypic studies. Species delimitation methods based on multispecies coalescent model were employed on DNA sequences from four loci, i.e., ID region of rDNA (ITS + 28S), CaM, benA and RPB2, and supported recognition of 21 species, including 14 new. All these species were also strongly supported in ML and BI analyses. All recognised species can be reliably identified by all four examined genetic loci. Phenotype analysis was performed to support the delimitation of new species and includes colony characteristics on seven cultivation media incubated at several temperatures, growth on an osmotic gradient (six media with NaCl concentration from 0 to 25 %) and analysis of morphology including scanning electron microscopy. The micromorphology of conidial heads, vesicle dimensions, temperature profiles and growth parameters in osmotic gradient were useful criteria for species identification. The vast majority of species in sect. Restricti produce asperglaucide, asperphenamate or both in contrast to species in sect. Aspergillus. Mycophenolic acid was detected for the first time in at least six members of the section. The ascomata of A. halophilicus do not contain auroglaucin, epiheveadride or flavoglaucin which are common in sect. Aspergillus, but shares the echinulins with sect. Aspergillus.
Aspergillus subgenus Polypaecilum from the built environment Stud. Mycol. (IF 14) Pub Date : 2017-11-13 J.B. Tanney, C.M. Visagie, N. Yilmaz, K.A. Seifert
Xerophilic fungi, especially Aspergillus species, are prevalent in the built environment. In this study, we employed a combined culture-independent (454-pyrosequencing) and culture-dependent (dilution-to-extinction) approach to investigate the mycobiota of indoor dust collected from 93 buildings in 12 countries worldwide. High and low water activity (aw) media were used to capture mesophile and xerophile biodiversity, resulting in the isolation of approximately 9 000 strains. Among these, 340 strains representing seven putative species in Aspergillus subgenus Polypaecilum were isolated, mostly from lowered aw media, and tentatively identified based on colony morphology and internal transcribed spacer rDNA region (ITS) barcodes. Further morphological study and phylogenetic analyses using sequences of ITS, β-tubulin (BenA), calmodulin (CaM), RNA polymerase II second largest subunit (RPB2), DNA topoisomerase 1 (TOP1), and a pre-mRNA processing protein homolog (TSR1) confirmed the isolation of seven species of subgenus Polypaecilum, including five novel species: A. baarnensis, A. keratitidis, A. kalimae sp. nov., A. noonimiae sp. nov., A. thailandensis sp. nov., A. waynelawii sp. nov., and A. whitfieldii sp. nov. Pyrosequencing detected six of the seven species isolated from house dust, as well as one additional species absent from the cultures isolated, and three clades representing potentially undescribed species. Species were typically found in house dust from subtropical and tropical climates, often in close proximity to the ocean or sea. The presence of subgenus Polypaecilum, a recently described clade of xerophilic/xerotolerant, halotolerant/halophilic, and potentially zoopathogenic species, within the built environment is noteworthy.
Phylogeny and taxonomy of the scab and spot anthracnose fungus Elsinoë (Myriangiales, Dothideomycetes) Stud. Mycol. (IF 14) Pub Date : 2017-02-24 X.L. Fan, R.W. Barreto, J.Z. Groenewald, J.D.P. Bezerra, O.L. Pereira, R. Cheewangkoon, L. Mostert, C.M. Tian, P.W. Crous
Species of Elsinoë are phytopathogens causing scab and spot anthracnose on many plants, including some economically important crops such as avocado, citrus, grapevines, and ornamentals such as poinsettias, field crops and woody hosts. Disease symptoms are often easily recognisable, and referred to as signature-bearing diseases, for the cork-like appearance of older infected tissues with scab-like appearance. In some Elsinoë-host associations the resulting symptoms are better described as spot anthracnose. Additionally the infected plants may also show mild to severe distortions of infected organs. Isolation of Elsinoë in pure culture can be very challenging and examination of specimens collected in the field is often frustrating because of the lack of fertile structures. Current criteria for species recognition and host specificity in Elsinoë are unclear due to overlapping morphological characteristics, and the lack of molecular and pathogenicity data. In the present study we revised the taxonomy of Elsinoë based on DNA sequence and morphological data derived from 119 isolates, representing 67 host genera from 17 countries, including 64 ex-type cultures. Combined analyses of ITS, LSU, rpb2 and TEF1-α DNA sequence data were used to reconstruct the backbone phylogeny of the genus Elsinoë. Based on the single nomenclature for fungi, 26 new combinations are proposed in Elsinoë for species that were originally described in Sphaceloma. A total of 13 species are epitypified with notes on their taxonomy and phylogeny. A further eight new species are introduced, leading to a total of 75 Elsinoë species supported by molecular data in the present study. For the most part species of Elsinoë appear to be host specific, although the majority of the species treated are known only from a few isolates, and further collections and pathogenicity studies will be required to reconfirm this conclusion.
Corynespora, Exosporium and Helminthosporium revisited – New species and generic reclassification Stud. Mycol. (IF 14) Pub Date : 2017-05-13 H. Voglmayr, W.M. Jaklitsch
Molecular phylogenetic analyses of a multigene matrix of partial nuSSU-ITS-LSU rDNA, rpb2 and tef1 sequences were performed to investigate the phylogenetic relationships of Corynespora, Exosporium and Helminthosporium species. Based on phylogenetic analyses and morphology, the genus Exosporium is synonymised with Helminthosporium, and the genus Corynespora is revealed as polyphyletic. Corynespora smithii is confirmed to be closely related to the generic type C. cassiicola and its morphology is described and illustrated. Exosporium tiliae, Corynespora caespitosa, C. endiandrae, C. leucadendri and C. olivacea are recognised in Helminthosporium, and Splanchnonema quercicola and S. kalakadense are combined in Helminthosporium. Based on pure culture studies and DNA sequence data, Massaria heterospora and Massarinula italica are shown to be the sexual morphs of Helminthosporium tiliae and H. microsorum, respectively. European accessions of Splanchnonema quercicola are recognised to differ from the North American type and are described as Helminthosporium quercinum. The sexual morph of H. oligosporum is recorded and described for the first time. The generic type of Helminthosporium, H. velutinum, is epitypified with a recent collection from the type host, Fagus sylvatica. Based on sequence data, Helminthosporium genistae is recognised as a distinct species. Several species for which subperidermal stromata have been reported are shown to be fungicolous on Diaporthales, the “stromata” representing aborted and transformed host stromata or conidiomata: H. caespitosum, H. microsorum, H. quercicola and H. quercinum on Coryneum spp.; H. hispanicum on conidiomata of Juglanconis juglandina; H. juglandinum on conidiomata of Diaporthe sp.; H. oligosporum and H. tiliae on Hercospora tiliae. The newly described H. austriacum is fungicolous on Amphisphaeria cf. millepunctata (Xylariales).
Stemphylium revisited Stud. Mycol. (IF 14) Pub Date : 2017-06-06 J.H.C. Woudenberg, B. Hanse, G.C.M. van Leeuwen, J.Z. Groenewald, P.W. Crous
In 2007 a new Stemphylium leaf spot disease of Beta vulgaris (sugar beet) spread through the Netherlands. Attempts to identify this destructive Stemphylium sp. in sugar beet led to a phylogenetic revision of the genus. The name Stemphylium has been recommended for use over that of its sexual morph, Pleospora, which is polyphyletic. Stemphylium forms a well-defined monophyletic genus in the Pleosporaceae, Pleosporales (Dothideomycetes), but lacks an up-to-date phylogeny. To address this issue, the internal transcribed spacer 1 and 2 and intervening 5.8S nr DNA (ITS) of all available Stemphylium and Pleospora isolates from the CBS culture collection of the Westerdijk Institute (N = 418), and from 23 freshly collected isolates obtained from sugar beet and related hosts, were sequenced to construct an overview phylogeny (N = 350). Based on their phylogenetic informativeness, parts of the protein-coding genes calmodulin and glyceraldehyde-3-phosphate dehydrogenase were also sequenced for a subset of isolates (N = 149). This resulted in a multi-gene phylogeny of the genus Stemphylium containing 28 species-clades, of which five were found to represent new species. The majority of the sugar beet isolates, including isolates from the Netherlands, Germany and the UK, clustered together in a species clade for which the name S. beticola was recently proposed. Morphological studies were performed to describe the new species. Twenty-two names were reduced to synonymy, and two new combinations proposed. Three epitypes, one lectotype and two neotypes were also designated in order to create a uniform taxonomy for Stemphylium.
Didymellaceae revisited Stud. Mycol. (IF 14) Pub Date : 2017-06-09 Q. Chen, L.W. Hou, W.J. Duan, P.W. Crous, L. Cai
The Didymellaceae is one of the most species-rich families in the fungal kingdom, and includes species that inhabit a wide range of ecosystems. The taxonomy of Didymellaceae has recently been revised on the basis of multi-locus DNA sequence data. In the present study, we investigated 108 Didymellaceae isolates newly obtained from 40 host plant species in 27 plant families, and various substrates from caves, including air, water and carbonatite, originating from Argentina, Australia, Canada, China, Hungary, Israel, Italy, Japan, South Africa, the Netherlands, the USA and former Yugoslavia. Among these, 68 isolates representing 32 new taxa are recognised based on the multi-locus phylogeny using sequences of LSU, ITS, rpb2 and tub2, and morphological differences. Within the Didymellaceae, five genera appeared to be limited to specific host families, with other genera having broader host ranges. In total 19 genera are recognised in the family, with Heracleicola being reduced to synonymy under Ascochyta. This study has significantly improved our understanding on the distribution and biodiversity of Didymellaceae, although the placement of several genera still need to be clarified.
First report of Phyllosticta citricarpa and description of two new species, P. paracapitalensis and P. paracitricarpa, from citrus in Europe Stud. Mycol. (IF 14) Pub Date : 2017-05-29 V. Guarnaccia, J.Z. Groenewald, H. Li, C. Glienke, E. Carstens, V. Hattingh, P.H. Fourie, P.W. Crous
The genus Phyllosticta occurs worldwide, and contains numerous plant pathogenic, endophytic and saprobic species. Phyllosticta citricarpa is the causal agent of Citrus Black Spot disease (CBS), affecting fruits and leaves of several citrus hosts (Rutaceae), and can also be isolated from asymptomatic citrus tissues. Citrus Black Spot occurs in citrus-growing regions with warm summer rainfall climates, but is absent in countries of the European Union (EU). Phyllosticta capitalensis is morphologically similar to P. citricarpa, but is a non-pathogenic endophyte, commonly isolated from citrus leaves and fruits and a wide range of other hosts, and is known to occur in Europe. To determine which Phyllosticta spp. occur within citrus growing regions of EU countries, several surveys were conducted (2015–2017) in the major citrus production areas of Greece, Italy, Malta, Portugal and Spain to collect both living plant material and leaf litter in commercial nurseries, orchards, gardens, backyards and plant collections. A total of 64 Phyllosticta isolates were obtained from citrus in Europe, of which 52 were included in a multi-locus (ITS, actA, tef1, gapdh, LSU and rpb2 genes) DNA dataset. Two isolates from Florida (USA), three isolates from China, and several reference strains from Australia, South Africa and South America were included in the overall 99 isolate dataset. Based on the data obtained, two known species were identified, namely P. capitalensis (from asymptomatic living leaves of Citrus spp.) in Greece, Italy, Malta, Portugal and Spain, and P. citricarpa (from leaf litter of C. sinensis and C. limon) in Italy, Malta and Portugal. Moreover, two new species were described, namely P. paracapitalensis (from asymptomatic living leaves of Citrus spp.) in Italy and Spain, and P. paracitricarpa (from leaf litter of C. limon) in Greece. On a genotypic level, isolates of P. citricarpa populations from Italy and Malta (MAT1-2-1) represented a single clone, and those from Portugal (MAT1-1-1) another. Isolates of P. citricarpa and P. paracitricarpa were able to induce atypical lesions (necrosis) in artificially inoculated mature sweet orange fruit, while P. capitalensis and P. paracapitalensis induced no lesions. The Phyllosticta species recovered were not found to be widespread, and were not associated with disease symptoms, indicating that the fungi persisted over time, but did not cause disease.
Pseudodidymellaceae fam. nov.: Phylogenetic affiliations of mycopappus-like genera in Dothideomycetes Stud. Mycol. (IF 14) Pub Date : 2017-07-13 A. Hashimoto, M. Matsumura, K. Hirayama, R. Fujimoto, K. Tanaka
The familial placement of four genera, Mycodidymella, Petrakia, Pseudodidymella, and Xenostigmina, was taxonomically revised based on morphological observations and phylogenetic analyses of nuclear rDNA SSU, LSU, tef1, and rpb2 sequences. ITS sequences were also provided as barcode markers. A total of 130 sequences were newly obtained from 28 isolates which are phylogenetically related to Melanommataceae (Pleosporales, Dothideomycetes) and its relatives. Phylogenetic analyses and morphological observation of sexual and asexual morphs led to the conclusion that Melanommataceae should be restricted to its type genus Melanomma, which is characterised by ascomata composed of a well-developed, carbonaceous peridium, and an aposphaeria-like coelomycetous asexual morph. Although Mycodidymella, Petrakia, Pseudodidymella, and Xenostigmina are phylogenetically related to Melanommataceae, these genera are characterised by epiphyllous, lenticular ascomata with well-developed basal stroma in their sexual morphs, and mycopappus-like propagules in their asexual morphs, which are clearly different from those of Melanomma. Pseudodidymellaceae is proposed to accommodate these four genera. Although Mycodidymella and Xenostigmina have been considered synonyms of Petrakia based on sexual morphology, we show that they are distinct genera. Based on morphological observations, these genera in Pseudodidymellaceae are easily distinguished by their synasexual morphs: sigmoid, multi-septate, thin-walled, hyaline conidia (Mycodidymella); globose to ovoid, dictyosporus, thick-walled, brown conidia with cellular appendages (Petrakia); and clavate with a short rostrum, dictyosporus, thick-walled, brown conidia (Xenostigmina). A synasexual morph of Pseudodidymella was not observed. Although Alpinaria was treated as member of Melanommataceae in a previous study, it has hyaline cells at the base of ascomata and pseudopycnidial, confluent conidiomata which is atypical features in Melanommataceae, and is treated as incertae sedis.
Phylogenetic revision of Camarosporium (Pleosporineae, Dothideomycetes) and allied genera Stud. Mycol. (IF 14) Pub Date : 2017-08-23 D.N. Wanasinghe, K.D. Hyde, R. Jeewon, P.W. Crous, N.N. Wijayawardene, E.B.G. Jones, D.J. Bhat, A.J.L. Phillips, J.Z. Groenewald, M.C. Dayarathne, C. Phukhamsakda, K.M. Thambugala, T.S. Bulgakov, E. Camporesi, Y.S. Gafforov, P.E. Mortimer, S.C. Karunarathna
A concatenated dataset of LSU, SSU, ITS and tef1 DNA sequence data was analysed to investigate the taxonomic position and phylogenetic relationships of the genus Camarosporium in Pleosporineae (Dothideomycetes). Newly generated sequences from camarosporium-like taxa collected from Europe (Italy) and Russia form a well-supported monophyletic clade within Pleosporineae. A new genus Camarosporidiella and a new family Camarosporidiellaceae are established to accommodate these taxa. Four new species, Neocamarosporium korfii, N. lamiacearum, N. salicorniicola and N. salsolae, constitute a strongly supported clade with several known taxa for which the new family, Neocamarosporiaceae, is introduced. The genus Staurosphaeria based on S. lycii is resurrected and epitypified, and shown to accommodate the recently introduced genus Hazslinszkyomyces in Coniothyriaceae with significant statistical support. Camarosporium quaternatum, the type species of Camarosporium and Camarosporomyces flavigena cluster together in a monophyletic clade with significant statistical support and sister to the Leptosphaeriaceae. To better resolve interfamilial/intergeneric level relationships and improve taxonomic understanding within Pleosporineae, we validate Camarosporiaceae to accommodate Camarosporium and Camarosporomyces. The latter taxa along with other species are described in this study.
Mycosphaerellaceae – Chaos or clarity? Stud. Mycol. (IF 14) Pub Date : 2017-09-28 S.I.R. Videira, J.Z. Groenewald, C. Nakashima, U. Braun, R.W. Barreto, P.J.G.M. de Wit, P.W. Crous
The Mycosphaerellaceae represent thousands of fungal species that are associated with diseases on a wide range of plant hosts. Understanding and stabilising the taxonomy of genera and species of Mycosphaerellaceae is therefore of the utmost importance given their impact on agriculture, horticulture and forestry. Based on previous molecular studies, several phylogenetic and morphologically distinct genera within the Mycosphaerellaceae have been delimited. In this study a multigene phylogenetic analysis (LSU, ITS and rpb2) was performed based on 415 isolates representing 297 taxa and incorporating ex-type strains where available. The main aim of this study was to resolve the phylogenetic relationships among the genera currently recognised within the family, and to clarify the position of the cercosporoid fungi among them. Based on these results many well-known genera are shown to be paraphyletic, with several synapomorphic characters that have evolved more than once within the family. As a consequence, several old generic names including Cercosporidium, Fulvia, Mycovellosiella, Phaeoramularia and Raghnildiana are resurrected, and 32 additional genera are described as new. Based on phylogenetic data 120 genera are now accepted within the family, but many currently accepted cercosporoid genera still remain unresolved pending fresh collections and DNA data. The present study provides a phylogenetic framework for future taxonomic work within the Mycosphaerellaceae.
Exploring the genomic diversity of black yeasts and relatives (Chaetothyriales, Ascomycota) Stud. Mycol. (IF 14) Pub Date : 2017-01-27 M.M. Teixeira, L.F. Moreno, B.J. Stielow, A. Muszewska, M. Hainaut, L. Gonzaga, A. Abouelleil, J.S.L. Patané, M. Priest, R. Souza, S. Young, K.S. Ferreira, Q. Zeng, M.M.L. da Cunha, A. Gladki, B. Barker, V.A. Vicente, E.M. de Souza, G. Sybren de Hoog
The order Chaetothyriales (Pezizomycotina, Ascomycetes) harbours obligatorily melanised fungi and includes numerous etiologic agents of chromoblastomycosis, phaeohyphomycosis and other diseases of vertebrate hosts. Diseases range from mild cutaneous to fatal cerebral or disseminated infections and affect humans and cold-blooded animals globally. In addition, Chaetothyriales comprise species with aquatic, rock-inhabiting, ant-associated, and mycoparasitic life-styles, as well as species that tolerate toxic compounds, suggesting a high degree of versatile extremotolerance. To understand their biology and divergent niche occupation, we sequenced and annotated a set of 23 genomes of main the human opportunists within the Chaetothyriales as well as related environmental species. Our analyses included fungi with diverse life-styles, namely opportunistic pathogens and closely related saprobes, to identify genomic adaptations related to pathogenesis. Furthermore, ecological preferences of Chaetothyriales were analysed, in conjuncture with the order-level phylogeny based on conserved ribosomal genes. General characteristics, phylogenomic relationships, transposable elements, sex-related genes, protein family evolution, genes related to protein degradation (MEROPS), carbohydrate-active enzymes (CAZymes), melanin synthesis and secondary metabolism were investigated and compared between species. Genome assemblies varied from 25.81 Mb (Capronia coronata) to 43.03 Mb (Cladophialophora immunda). The bantiana-clade contained the highest number of predicted genes (12 817 on average) as well as larger genomes. We found a low content of mobile elements, with DNA transposons from Tc1/Mariner superfamily being the most abundant across analysed species. Additionally, we identified a reduction of carbohydrate degrading enzymes, specifically many of the Glycosyl Hydrolase (GH) class, while most of the Pectin Lyase (PL) genes were lost in etiological agents of chromoblastomycosis and phaeohyphomycosis. An expansion was found in protein degrading peptidase enzyme families S12 (serine-type D-Ala-D-Ala carboxypeptidases) and M38 (isoaspartyl dipeptidases). Based on genomic information, a wide range of abilities of melanin biosynthesis was revealed; genes related to metabolically distinct DHN, DOPA and pyomelanin pathways were identified. The MAT (MAting Type) locus and other sex-related genes were recognized in all 23 black fungi. Members of the asexual genera Fonsecaea and Cladophialophora appear to be heterothallic with a single copy of either MAT-1-1 or MAT-1-2 in each individual. All Capronia species are homothallic as both MAT1-1 and MAT1-2 genes were found in each single genome. The genomic synteny of the MAT-locus flanking genes (SLA2-APN2-COX13) is not conserved in black fungi as is commonly observed in Eurotiomycetes, indicating a unique genomic context for MAT in those species. The heterokaryon (het) genes expansion associated with the low selective pressure at the MAT-locus suggests that a parasexual cycle may play an important role in generating diversity among those fungi.
Phylogenetic analysis of Monascus and new species from honey, pollen and nests of stingless bees Stud. Mycol. (IF 14) Pub Date : 2017-04-12 R.N. Barbosa, S.L. Leong, O. Vinnere-Pettersson, A.J. Chen, C.M. Souza-Motta, J.C. Frisvad, R.A. Samson, N.T. Oliveira, J. Houbraken
The genus Monascus was described by van Tieghem (1884) to accommodate M. ruber and M. mucoroides, two species with non-ostiolate ascomata. Species delimitation in the genus is still mainly based on phenotypic characters, and taxonomic studies that include sequence data are limited. The genus is of economic importance. Species are used in fermented Asian foods as food colourants (e.g. ‘red rice’ (ang-kak, angka)) and found as spoilage organisms, and recently Monascus was found to be essential in the lifecycle of stingless bees. In this study, a polyphasic approach was applied combining morphological characters, ITS, LSU, β-tubulin, calmodulin and RNA polymerase II second largest subunit sequences and extrolite data, to delimit species and to study phylogenetic relationships in Monascus. Furthermore, 30 Monascus isolates from honey, pollen and nests of stingless bees in Brazil were included. Based on this polyphasic approach, the genus Monascus is resolved in nine species, including three new species associated with stingless bees (M. flavipigmentosus sp. nov., M. mellicola sp. nov., M. recifensis sp. nov., M. argentinensis, M. floridanus, M. lunisporas, M. pallens, M. purpureus, M. ruber), and split in two new sections (section Floridani sect. nov., section Rubri sect. nov.). Phylogenetic analysis showed that the xerophile Monascus eremophilus does not belong in Monascus and monophyly in Monascus is restored with the transfer of M. eremophilus to Penicillium (P. eremophilum comb. nov.). A list of accepted and excluded Monascus and Basipetospora species is given, together with information on (ex-)types cultures and barcode sequence data.
Phylogeny of saprobic microfungi from Southern Europe Stud. Mycol. (IF 14) Pub Date : 2017-05-17 M. Hernández-Restrepo, J. Gené, R.F. Castañeda-Ruiz, J. Mena-Portales, P.W. Crous, J. Guarro
During a survey of saprophytic microfungi on decomposing woody, herbaceous debris and soil from different regions in Southern Europe, a wide range of interesting species of asexual ascomycetes were found. Phylogenetic analyses based on partial gene sequences of SSU, LSU and ITS proved that most of these fungi were related to Sordariomycetes and Dothideomycetes and to lesser extent to Leotiomycetes and Eurotiomycetes. Four new monotypic orders with their respective families are proposed here, i.e. Lauriomycetales, Lauriomycetaceae; Parasympodiellales, Parasympodiellaceae; Vermiculariopsiellales, Vermiculariopsiellaceae and Xenospadicoidales, Xenospadicoidaceae. One new order and three families are introduced here to accommodate orphan taxa, viz. Kirschsteiniotheliales, Castanediellaceae, Leptodontidiaceae and Pleomonodictydaceae. Furthermore, Bloxamiaceae is validated. Based on morphology and phylogenetic affinities Diplococcium singulare, Trichocladium opacum and Spadicoides atra are moved to the new genera Paradiplococcium, Pleotrichocladium and Xenospadicoides, respectively. Helicoon fuscosporum is accommodated in the genus Magnohelicospora. Other novel genera include Neoascotaiwania with the type species N. terrestris sp. nov., and N. limnetica comb. nov. previously accommodated in Ascotaiwania; Pleomonodictys with P. descalsii sp. nov. as type species, and P. capensis comb. nov. previously accommodated in Monodictys; Anapleurothecium typified by A. botulisporum sp. nov., a fungus morphologically similar to Pleurothecium but phylogenetically distant; Fuscosclera typified by F. lignicola sp. nov., a meristematic fungus related to Leotiomycetes; Pseudodiplococcium typified by P. ibericum sp. nov. to accommodate an isolate previously identified as Diplococcium pulneyense; Xyladictyochaeta typified with X. lusitanica sp. nov., a foliicolous fungus related to Xylariales and similar to Dictyochaeta, but distinguished by polyphialidic conidiogenous cells produced on setiform conidiophores. Other novel species proposed are Brachysporiella navarrica, Catenulostroma lignicola, Cirrenalia iberica, Conioscypha pleiomorpha, Leptodontidium aureum, Pirozynskiella laurisilvatica, Parasympodiella lauri and Zanclospora iberica. To fix the application of some fungal names, lectotypes and/or epitypes are designated for Magnohelicospora iberica, Sporidesmium trigonellum, Sporidesmium opacum, Sporidesmium asperum, Camposporium aquaticum and Psilonia atra.
Genera of phytopathogenic fungi: GOPHY 1 Stud. Mycol. (IF 14) Pub Date : 2017-05-05 Y. Marin-Felix, J.Z. Groenewald, L. Cai, Q. Chen, S. Marincowitz, I. Barnes, K. Bensch, U. Braun, E. Camporesi, U. Damm, Z.W. de Beer, A. Dissanayake, J. Edwards, A. Giraldo, M. Hernández-Restrepo, K.D. Hyde, R.S. Jayawardena, L. Lombard, P.W. Crous
Genera of Phytopathogenic Fungi (GOPHY) is introduced as a new series of publications in order to provide a stable platform for the taxonomy of phytopathogenic fungi. This first paper focuses on 21 genera of phytopathogenic fungi: Bipolaris, Boeremia, Calonectria, Ceratocystis, Cladosporium, Colletotrichum, Coniella, Curvularia, Monilinia, Neofabraea, Neofusicoccum, Pilidium, Pleiochaeta, Plenodomus, Protostegia, Pseudopyricularia, Puccinia, Saccharata, Thyrostroma, Venturia and Wilsonomyces. For each genus, a morphological description and information about its pathology, distribution, hosts and disease symptoms are provided. In addition, this information is linked to primary and secondary DNA barcodes of the presently accepted species, and relevant literature. Moreover, several novelties are introduced, i.e. new genera, species and combinations, and neo-, lecto- and epitypes designated to provide a stable taxonomy. This first paper includes one new genus, 26 new species, ten new combinations, and four typifications of older names.
Families of Diaporthales based on morphological and phylogenetic evidence Stud. Mycol. (IF 14) Pub Date : 2017-08-01 I.C. Senanayake, P.W. Crous, J.Z. Groenewald, S.S.N. Maharachchikumbura, R. Jeewon, A.J.L. Phillips, J.D. Bhat, R.H. Perera, Q.R. Li, W.J. Li, N. Tangthirasunun, C. Norphanphoun, S.C. Karunarathna, E. Camporesi, I.S. Manawasighe, A.M. Al-Sadi, K.D. Hyde
Diaporthales is an important ascomycetous order comprising phytopathogenic, saprobic, and endophytic fungi, but interfamilial taxonomic relationships are still ambiguous. Despite its cosmopolitan distribution and high diversity with distinctive morphologies, this order has received relativelyiaceae, Macrohilaceae, Melanconidaceae, Pseudoplagiostomaceae, Schizoparmaceae, Stilbosporaceae and Sydowiellaceae. Taxonomic uncertainties among genera are also clarified and recurrent discrepancies in the taxonomic position of families within the Diaporthales are discussed. An updated outline and key to families and genera of the order is presented.
Revising the Schizoparmaceae: Coniella and its synonyms Pilidiella and Schizoparme Stud. Mycol. (IF 14) Pub Date : 2016-09-23 L.V. Alvarez, J.Z. Groenewald, P.W. Crous
The asexual genera Coniella (1918) and Pilidiella (1927), including their sexual morphs in Schizoparme (1923), have a cosmopolitan distribution and are associated with foliar, fruit, leaf, stem and root diseases on a wide variety of hosts. Species of these genera sometimes occur as secondary invaders of plant tissues infected by other organisms or that are injured by other causes. Several studies published over the last few decades had conflicting ideas as to whether Coniella, Pilidiella and Schizoparme should be regarded as synonymous or as separate genera. The present study aims to resolve the generic classification of these genera through phylogenetic analyses of the concatenated alignment of partial LSU nrDNA, rpb2, ITS nrDNA and tef1 sequence data of 117 isolates, combined with their morphology. Results revealed that all strains cluster in a single well-supported clade. Conidial colour, traditionally the distinguishing character between Coniella and Pilidiella, evolved multiple times throughout the clade, and is not a good character at generic level in Schizoparmaceae. The three genera should therefore be regarded as synonymous, with the older name Coniella having priority. Furthermore, this study delineated 13 new species, and new combinations were proposed for a further 15 species.
Hidden diversity in Thyridaria and a new circumscription of the Thyridariaceae Stud. Mycol. (IF 14) Pub Date : 2016-09-23 W.M. Jaklitsch, H. Voglmayr
A multigene analysis of a combined ITS-LSU-SSU-rpb2-tef1 sequence data matrix was applied to infer the phylogenetic position of the genus Thyridaria in the Pleosporales. The generic type of Thyridaria, T. broussonetiae (syn. T. incrustans), is situated in a clade currently named Roussoellaceae, which becomes a synonym of Thyridariaceae. However, Thyridaria rubronotata does not belong to this clade, but is here recognised as Cyclothyriella rubronotata in its own family Cyclothyriellaceae. The Thyridariaceae contain the genera Thyridaria, Roussoella, Roussoellopsis, Neoroussoella and the new genus Parathyridaria. Roussoella acaciae is combined in Thyridaria and Roussoella percutaenea in Parathyridaria. Ohleria modesta and an additional new thyridaria-like genus, Hobus, are found to represent isolated lineages with unresolved phylogenetic affinites within the Pleosporales. For Ohleria the new family Ohleriaceae is established. Melanomma fuscidulum belongs to Nigrograna, and three new species are described in this genus. A strain named Biatriospora marina clusters with Nigrograna. Based on the newly recognised species in Nigrograna, morphology and ecology do in no way correlate among these genera, therefore we erect the new family Nigrogranaceae for Nigrograna and recommend to discontinue the use of the family name Biatriosporaceae until fresh material of B. marina becomes available for sequencing.
Polyphasic taxonomy of Aspergillus section Cervini Stud. Mycol. (IF 14) Pub Date : 2016-11-09 A.J. Chen, J. Varga, J.C. Frisvad, X.Z. Jiang, R.A. Samson
Species belonging to Aspergillus section Cervini are characterised by radiate or short columnar, fawn coloured, uniseriate conidial heads. The morphology of the taxa in this section is very similar and isolates assigned to these species are frequently misidentified. In this study, a polyphasic approach was applied using morphological characters, extrolite data, temperature profiles and partial BenA, CaM and RPB2 sequences to examine the relationships within this section. Based on this taxonomic approach the section Cervini is resolved in ten species including six new species: A. acidohumus, A. christenseniae, A. novoguineensis, A. subnutans, A. transcarpathicus and A. wisconsinensis. A dichotomous key for the identification is provided.
DNA barcoding analysis of more than 9 000 yeast isolates contributes to quantitative thresholds for yeast species and genera delimitation Stud. Mycol. (IF 14) Pub Date : 2016-11-27 D. Vu, M. Groenewald, S. Szöke, G. Cardinali, U. Eberhardt, B. Stielow, M. de Vries, G.J.M. Verkleij, P.W. Crous, T. Boekhout, V. Robert
DNA barcoding is a global initiative for species identification through sequencing of short DNA sequence markers. Sequences of two loci, ITS and LSU, were generated as barcode data for all (ca. 9k) yeast strains included in the CBS collection, originally assigned to ca. 2 000 species. Taxonomic sequence validation turned out to be the most severe bottleneck due to the large volume of generated trace files and lack of reference sequences. We have analysed and validated CBS strains and barcode sequences automatically. Our analysis shows that there were 6 and 9.5 % of CBS yeast species that could not be distinguished by ITS and LSU, respectively. Among them, ∼3 % were indistinguishable by both loci. Except for those species, both loci were successfully resolving yeast species as the grouping of yeast DNA barcodes with the predicted taxonomic thresholds was more than 90 % similar to the grouping with respect to the expected taxon names. The taxonomic thresholds predicted to discriminate yeast species were 98.41 % for ITS and 99.51 % for LSU. To discriminate current yeast genera, thresholds were 96.31 % for ITS and 97.11 % for LSU. Using ITS and LSU barcodes, we were also able to show that the recent reclassifications of basidiomycetous yeasts in 2015 have made a significant improvement for the generic taxonomy of those organisms. The barcodes of 4 730 (51 %) CBS yeast strains of 1 351 (80 %) accepted yeast species that were manually validated have been released to GenBank and the CBS-KNAW website as reference sequences for yeast identification.
Wood staining fungi revealed taxonomic novelties in Pezizomycotina: New order Superstratomycetales and new species Cyanodermella oleoligni Stud. Mycol. (IF 14) Pub Date : 2016-11-27 E.J. van Nieuwenhuijzen, J.M. Miadlikowska, J.A.M.P. Houbraken, O.C.G. Adan, F.M. Lutzoni, R.A. Samson
A culture-based survey of staining fungi on oil-treated timber after outdoor exposure in Australia and the Netherlands uncovered new taxa in Pezizomycotina. Their taxonomic novelty was confirmed by phylogenetic analyses of multi-locus sequences (ITS, nrSSU, nrLSU, mitSSU, RPB1, RPB2, and EF-1α) using multiple reference data sets. These previously unknown taxa are recognised as part of a new order (Superstratomycetales) potentially closely related to Trypetheliales (Dothideomycetes), and as a new species of Cyanodermella, C. oleoligni in Stictidaceae (Ostropales) part of the mostly lichenised class Lecanoromycetes. Within Superstratomycetales a single genus named Superstratomyces with three putative species: S. flavomucosus, S. atroviridis, and S. albomucosus are formally described. Monophyly of each circumscribed Superstratomyces species was highly supported and the intraspecific genetic variation was substantially lower than interspecific differences detected among species based on the ITS, nrLSU, and EF-1α loci. Ribosomal loci for all members of Superstratomyces were noticeably different from all fungal sequences available in GenBank. All strains from this genus grow slowly in culture, have darkly pigmented mycelia and produce pycnidia. The strains of C. oleoligni form green colonies with slimy masses and develop green pycnidia on oatmeal agar. These new taxa could not be classified reliably at the class and lower taxonomic ranks by sequencing from the substrate directly or based solely on culture-dependent morphological investigations. Coupling phenotypic observations with multi-locus sequencing of fungi isolated in culture enabled these taxonomic discoveries. Outdoor situated timber provides a great potential for culturable undescribed fungal taxa, including higher rank lineages as revealed by this study, and therefore, should be further explored.
The good, the bad and the tasty: The many roles of mushrooms Stud. Mycol. (IF 14) Pub Date : 2016-11-11 K.M.J. de Mattos-Shipley, K.L. Ford, F. Alberti, A.M. Banks, A.M. Bailey, G.D. Foster
Fungi are often inconspicuous in nature and this means it is all too easy to overlook their importance. Often referred to as the “Forgotten Kingdom”, fungi are key components of life on this planet. The phylum Basidiomycota, considered to contain the most complex and evolutionarily advanced members of this Kingdom, includes some of the most iconic fungal species such as the gilled mushrooms, puffballs and bracket fungi. Basidiomycetes inhabit a wide range of ecological niches, carrying out vital ecosystem roles, particularly in carbon cycling and as symbiotic partners with a range of other organisms. Specifically in the context of human use, the basidiomycetes are a highly valuable food source and are increasingly medicinally important. In this review, seven main categories, or ‘roles’, for basidiomycetes have been suggested by the authors: as model species, edible species, toxic species, medicinal basidiomycetes, symbionts, decomposers and pathogens, and two species have been chosen as representatives of each category. Although this is in no way an exhaustive discussion of the importance of basidiomycetes, this review aims to give a broad overview of the importance of these organisms, exploring the various ways they can be exploited to the benefit of human society.
The forgotten Calonectria collection: Pouring old wine into new bags Stud. Mycol. (IF 14) Pub Date : 2016-11-22 L. Lombard, M.J. Wingfield, A.C. Alfenas, P.W. Crous
The genus Calonectria with its Cylindrocladium asexual morphs has been subject to several taxonomic revisions in the past. These have resulted in the recognition of 116 species, of which all but two species (C. hederae and C. pyrochroa) are supported by ex-type cultures and supplemented with DNA barcodes. The present study is based on a large collection of unidentified Calonectria isolates that have been collected over a period of 20 years from various substrates worldwide, which has remained unstudied in the basement of the CBS-KNAW Fungal Biodiversity Centre. Employing a polyphasic approach, the identities of these isolates were resolved and shown to represent many new phylogenetic species. Of these, 24 are newly described, while C. uniseptata is reinstated at species level. We now recognise 141 species that include some of the most important plant pathogens globally.
Aspergillus is monophyletic: Evidence from multiple gene phylogenies and extrolites profiles Stud. Mycol. (IF 14) Pub Date : 2016-11-29 S. Kocsubé, G. Perrone, D. Magistà, J. Houbraken, J. Varga, G. Szigeti, V. Hubka, S.-B. Hong, J.C. Frisvad, R.A. Samson
Aspergillus is one of the economically most important fungal genera. Recently, the ICN adopted the single name nomenclature which has forced mycologists to choose one name for fungi (e.g. Aspergillus, Fusarium, Penicillium, etc.). Previously two proposals for the single name nomenclature in Aspergillus were presented: one attributes the name “Aspergillus” to clades comprising seven different teleomorphic names, by supporting the monophyly of this genus; the other proposes that Aspergillus is a non-monophyletic genus, by preserving the Aspergillus name only to species belonging to subgenus Circumdati and maintaining the sexual names in the other clades. The aim of our study was to test the monophyly of Aspergilli by two independent phylogenetic analyses using a multilocus phylogenetic approach. One test was run on the publicly available coding regions of six genes (RPB1, RPB2, Tsr1, Cct8, BenA, CaM), using 96 species of Penicillium, Aspergillus and related taxa. Bayesian (MrBayes) and Ultrafast Maximum Likelihood (IQ-Tree) and Rapid Maximum Likelihood (RaxML) analyses gave the same conclusion highly supporting the monophyly of Aspergillus. The other analyses were also performed by using publicly available data of the coding sequences of nine loci (18S rRNA, 5,8S rRNA, 28S rRNA (D1-D2), RPB1, RPB2, CaM, BenA, Tsr1, Cct8) of 204 different species. Both Bayesian (MrBayes) and Maximum Likelihood (RAxML) trees obtained by this second round of independent analyses strongly supported the monophyly of the genus Aspergillus. The stability test also confirmed the robustness of the results obtained. In conclusion, statistical analyses have rejected the hypothesis that the Aspergilli are non-monophyletic, and provided robust arguments that the genus is monophyletic and clearly separated from the monophyletic genus Penicillium. There is no phylogenetic evidence to split Aspergillus into several genera and the name Aspergillus can be used for all the species belonging to Aspergillus i.e. the clade comprising the subgenera Aspergillus, Circumdati, Fumigati, Nidulantes, section Cremei and certain species which were formerly part of the genera Phialosimplex and Polypaecilum. Section Cremei and the clade containing Polypaecilum and Phialosimplex are proposed as new subgenera of Aspergillus. The phylogenetic analysis also clearly shows that Aspergillus clavatoflavus and A. zonatus do not belong to the genus Aspergillus. Aspergillus clavatoflavus is therefore transferred to a new genus Aspergillago as Aspergillago clavatoflavus and A. zonatus was transferred to Penicilliopsis as P. zonata. The subgenera of Aspergillus share similar extrolite profiles indicating that the genus is one large genus from a chemotaxonomical point of view. Morphological and ecophysiological characteristics of the species also strongly indicate that Aspergillus is a polythetic class in phenotypic characters.
Aspergillus section Nidulantes (formerly Emericella): Polyphasic taxonomy, chemistry and biology Stud. Mycol. (IF 14) Pub Date : 2016-10-19 A.J. Chen, J.C. Frisvad, B.D. Sun, J. Varga, S. Kocsubé, J. Dijksterhuis, D.H. Kim, S.-B. Hong, J. Houbraken, R.A. Samson
Aspergillus section Nidulantes includes species with striking morphological characters, such as biseriate conidiophores with brown-pigmented stipes, and if present, the production of ascomata embedded in masses of Hülle cells with often reddish brown ascospores. The majority of species in this section have a sexual state, which were named Emericella in the dual name nomenclature system. In the present study, strains belonging to subgenus Nidulantes were subjected to multilocus molecular phylogenetic analyses using internal transcribed spacer region (ITS), partial β-tubulin (BenA), calmodulin (CaM) and RNA polymerase II second largest subunit (RPB2) sequences. Nine sections are accepted in subgenus Nidulantes including the new section Cavernicolus. A polyphasic approach using morphological characters, extrolites, physiological characters and phylogeny was applied to investigate the taxonomy of section Nidulantes. Based on this approach, section Nidulantes is subdivided in seven clades and 65 species, and 10 species are described here as new. Morphological characters including colour, shape, size, and ornamentation of ascospores, shape and size of conidia and vesicles, growth temperatures are important for identifying species. Many species of section Nidulantes produce the carcinogenic mycotoxin sterigmatocystin. The most important mycotoxins in Aspergillus section Nidulantes are aflatoxins, sterigmatocystin, emestrin, fumitremorgins, asteltoxins, and paxillin while other extrolites are useful drugs or drug lead candidates such as echinocandins, mulundocandins, calbistrins, varitriols, variecolins and terrain. Aflatoxin B1 is produced by four species: A. astellatus, A. miraensis, A. olivicola, and A. venezuelensis.
New Talaromyces species from indoor environments in China Stud. Mycol. (IF 14) Pub Date : 2016-11-22 A.J. Chen, B.D. Sun, J. Houbraken, J.C. Frisvad, N. Yilmaz, Y.G. Zhou, R.A. Samson
Talaromyces contains both asexual and sexually reproducing species. This genus is divided in seven sections and currently has 105 accepted species. In this study we investigated the Talaromyces isolates that were obtained during a study of indoor air collected in Beijing, China. These indoor Talaromyces strains are resolved in four sections, seven of them are identified as T. islandicus, T. aurantiacus, T. siamensis and T. albobiverticillius according to BenA sequences, while 14 isolates have divergent sequences and are described here as nine new species. The new species are placed in four sections, namely sections Helici, Islandici, Talaromyces and Trachyspermi. They are described based on sequence data (ITS, BenA, CaM and RPB2) in combination with phenotypic and extrolite characters. Morphological descriptions and notes for distinguishing similar species are provided for each new species. The recently described T. rubrifaciens is synonymised with T. albobiverticillius based on presented phylogenetic results.
Diversity and taxonomy of Chaetomium and chaetomium-like fungi from indoor environments Stud. Mycol. (IF 14) Pub Date : 2016-12-08 X.W. Wang, J. Houbraken, J.Z. Groenewald, M. Meijer, B. Andersen, K.F. Nielsen, P.W. Crous, R.A. Samson
During a study of indoor fungi, 145 isolates belonging to Chaetomiaceae were cultured from air, swab and dust samples from 19 countries. Based on the phylogenetic analyses of DNA-directed RNA polymerase II second largest subunit (rpb2), β-tubulin (tub2), ITS and 28S large subunit (LSU) nrDNA sequences, together with morphological comparisons with related genera and species, 30 indoor taxa are recognised, of which 22 represent known species, seven are described as new, and one remains to be identified to species level. In our collection, 69 % of the indoor isolates with six species cluster with members of the Chaetomium globosum species complex, representing Chaetomium sensu stricto. The other indoor species fall into nine lineages that are separated from each other with several known chaetomiaceous genera occurring among them. No generic names are available for five of those lineages, and the following new genera are introduced here: Amesia with three indoor species, Arcopilus with one indoor species, Collariella with four indoor species, Dichotomopilus with seven indoor species and Ovatospora with two indoor species. The generic concept of Botryotrichum is expanded to include Emilmuelleria and the chaetomium-like species B. muromum (= Ch. murorum) in which two indoor species are included. The generic concept of Subramaniula is expanded to include several chaetomium-like taxa as well as one indoor species. Humicola is recognised as a distinct genus including two indoor taxa. According to this study, Ch. globosum is the most abundant Chaetomiaceae indoor species (74/145), followed by Ch. cochliodes (17/145), Ch. elatum (6/145) and B. piluliferum (5/145). The morphological diversity of indoor Chaetomiaceae as well as the morphological characteristics of the new genera are described and illustrated. This taxonomic study redefines the generic concept of Chaetomium and provides new insight into the phylogenetic relationships among different genera within Chaetomiaceae.
The role of melanin pathways in extremotolerance and virulence of Fonsecaea revealed by de novo assembly transcriptomics using illumina paired-end sequencing Stud. Mycol. (IF 14) Pub Date : 2016-02-28 X.Q. Li, B.L. Guo, W.Y. Cai, J.M. Zhang, H.Q. Huang, P. Zhan, L.Y. Xi, V.A. Vicente, B. Stielow, J.F. Sun, G.S. de Hoog
Melanisation has been considered to be an important virulence factor of Fonsecaea monophora. However, the biosynthetic mechanisms of melanisation remain unknown. We therefore used next generation sequencing technology to investigate the transcriptome and digital gene expression data, which are valuable resources to better understand the molecular and biological mechanisms regulating melanisation in F. monophora. We performed de novo transcriptome assembly and digital gene expression (DGE) profiling analyses of parent (CBS 122845) and albino (CBS 125194) strains using the Illumina RNA-seq system. A total of 17 352 annotated unigenes were found by BLAST search of NR, Swiss-Prot, Gene Ontology, Clusters of Orthologous Groups and Kyoto Encyclopedia of Genes and Genomes (KEGG) (E-value <1e‒5). A total of 2 283 unigenes were judged to be the differentially expressed between the two genotypes. We identified most of the genes coding for key enzymes involved in melanin biosynthesis pathways, including polyketide synthase (pks), multicopper oxidase (mco), laccase, tyrosinase and homogentisate 1,2-dioxygenase (hmgA). DEG analysis showed extensive down-regulation of key genes in the DHN pathway, while up-regulation was noted in the DOPA pathway of the albino mutant. The transcript levels of partial genes were confirmed by real time RT-PCR, while the crucial role of key enzymes was confirmed by either inhibitor or substrate tests in vitro. Meanwhile, numbers of genes involved in light sensing, cell wall synthesis, morphology and environmental stress were identified in the transcriptome of F. monophora. In addition, 3 353 SSRs (Simple Sequence Repeats) markers were identified from 21 600 consensus sequences. Blocking of the DNH pathway is the most likely reason of melanin deficiency in the albino strain, while the production of pheomelanin and pyomelanin were probably regulated by unknown transcription factors on upstream of both pathways. Most of genes involved in environmental tolerance to oxidants, irradiation and extreme temperatures were also assembled and annotated in transcriptomes of F. monophora. In addition, thousands of identified cSSR (combined SSR) markers will favour further genetic linkage studies. In conclusion, these data will contribute to understanding the regulation of melanin biosynthesis and help to improve the studies of pathogenicity of F. monophora.
Take-all or nothing Stud. Mycol. (IF 14) Pub Date : 2016-07-01 M. Hernández-Restrepo, J.Z. Groenewald, M.L. Elliott, G. Canning, V.E. McMillan, P.W. Crous
Take-all disease of Poaceae is caused by Gaeumannomyces graminis (Magnaporthaceae). Four varieties are recognised in G. graminis based on ascospore size, hyphopodial morphology and host preference. The aim of the present study was to clarify boundaries among species and varieties in Gaeumannomyces by combining morphology and multi-locus phylogenetic analyses based on partial gene sequences of ITS, LSU, tef1 and rpb1. Two new genera, Falciphoriella and Gaeumannomycella were subsequently introduced in Magnaporthaceae. The resulting phylogeny revealed several cryptic species previously overlooked within Gaeumannomyces. Isolates of Gaeumannomyces were distributed in four main clades, from which 19 species could be delimited, 12 of which were new to science. Our results show that the former varieties Gaeumannomyces graminis var. avenae and Gaeumannomyces graminis var. tritici represent species phylogenetically distinct from G. graminis, for which the new combinations G. avenae and G. tritici are introduced. Based on molecular data, morphology and host preferences, Gaeumannomyces graminis var. maydis is proposed as a synonym of G. radicicola. Furthermore, an epitype for Gaeumannomyces graminis var. avenae was designated to help stabilise the application of that name.
All that glitters is not Ramularia Stud. Mycol. (IF 14) Pub Date : 2016-06-29 S.I.R. Videira, J.Z. Groenewald, U. Braun, H.D. Shin, P.W. Crous
Ramularia is a species-rich genus that harbours plant pathogens responsible for yield losses to many important crops, including barley, sugar beet and strawberry. Species of Ramularia are hyphomycetes with hyaline conidiophores and conidia with distinct, thickened, darkened, refractive conidiogenous loci and conidial hila, and Mycosphaerella sexual morphs. Because of its simple morphology and general lack of DNA data in public databases, several allied genera are frequently confused with Ramularia. In order to improve the delimitation of Ramularia from allied genera and the circumscription of species within the genus Ramularia, a polyphasic approach based on multilocus DNA sequences, morphological and cultural data were used in this study. A total of 420 isolates belonging to Ramularia and allied genera were targeted for the amplification and sequencing of six partial genes. Although Ramularia and Ramulariopsis proved to be monophyletic, Cercosporella and Pseudocercosporella were polyphyletic. Phacellium isolates clustered within the Ramularia clade and the genus is thus tentatively reduced to synonymy under Ramularia. Cercosporella and Pseudocercosporella isolates that were not congeneric with the ex-type strains of the type species of those genera were assigned to existing genera or to the newly introduced genera Teratoramularia and Xenoramularia, respectively. Teratoramularia is a genus with ramularia-like morphology belonging to the Teratosphaeriaceae, and Xenoramularia was introduced to accommodate hyphomycetous species closely related to Zymoseptoria. The genera Apseudocercosporella, Epicoleosporium, Filiella, Fusidiella, Neopseudocercosporella, and Mycosphaerelloides were also newly introduced to accommodate species non-congeneric with their purported types. A total of nine new combinations and 24 new species were introduced in this study.
The divorce of Sporothrix and Ophiostoma: solution to a problematic relationship Stud. Mycol. (IF 14) Pub Date : 2016-07-27 Z.W. de Beer, T.A. Duong, M.J. Wingfield
One of the causal agents of human sporotrichosis, Sporothrix schenckii, is the type species of the genus Sporothrix. During the course of the last century the asexual morphs of many Ophiostoma spp. have also been treated in Sporothrix. More recently several DNA-based studies have suggested that species of Sporothrix and Ophiostoma converge in what has become known as Ophiostoma s. lat. Were the one fungus one name principles adopted in the Melbourne Code to be applied to Ophiostoma s. lat., Sporothrix would have priority over Ophiostoma, resulting in more than 100 new combinations. The consequence would be name changes for several economically important tree pathogens including O. novo-ulmi. Alternatively, Ophiostoma could be conserved against Sporothrix, but this would necessitate changing the names of the important human pathogens in the group. In this study, we sought to resolve the phylogenetic relationship between Ophiostoma and Sporothrix. DNA sequences were determined for the ribosomal large subunit and internal transcribed spacer regions, as well as the beta-tubulin and calmodulin genes in 65 isolates. The results revealed Sporothrix as a well-supported monophyletic lineage including 51 taxa, distinct from Ophiostoma s. str. To facilitate future studies exploring species level resolution within Sporothrix, we defined six species complexes in the genus. These include the Pathogenic Clade containing the four human pathogens, together with the S. pallida-, S. candida-, S. inflata-, S. gossypina- and S. stenoceras complexes, which include environmental species mostly from soil, hardwoods and Protea infructescences. The description of Sporothrix is emended to include sexual morphs, and 26 new combinations. Two new names are also provided for species previously treated as Ophiostoma.
Phylogeny and taxonomic revision of Microascaceae with emphasis on synnematous fungi Stud. Mycol. (IF 14) Pub Date : 2016-07-29 M. Sandoval-Denis, J. Guarro, J.F. Cano-Lira, D.A. Sutton, N.P. Wiederhold, G.S. de Hoog, S.P. Abbott, C. Decock, L. Sigler, J. Gené
The taxonomy of the synnematous genera Cephalotrichum, Doratomyces and Trichurus, and other related genera Gamsia, Wardomyces and Wardomycopsis, has been controversial and relies mainly on morphological criteria. These are microascaceous saprobic fungi mostly found in air and soil and with a worldwide distribution. In order to clarify their taxonomy and to delineate generic boundaries within the Microascaceae, we studied 57 isolates that include clinical, environmental and all the available ex-type strains of a large set of species by means of morphological, physiological and molecular phylogenetic analyses using DNA sequence data of four loci (the ITS region, and fragments of rDNA LSU, translation elongation factor 1α and β-tubulin). The results demonstrate that Cephalotrichum, Doratomyces and Trichurus are congeneric and the genus Cephalotrichum is accepted here with Echinobotryum as a further synonym. The genera Acaulium and Fairmania, typified by A. albonigrescens and F. singularis, respectively, are distinct from Microascus and Scopulariopsis, Gamsia is distinct from Wardomyces, and Wardomycopsis is confirmed as a separate genus in the Microascaceae. Two new species of Cephalotrichum are described as C. brevistipitatum and C. hinnuleum. Nine new combinations are proposed, i.e. Acaulium acremonium, A. caviariforme, Cephalotrichum asperulum, C. columnare, C. cylindricum, C. dendrocephalum, C. gorgonifer, Gamsia columbina and Wardomyces giganteus. A neotype is designed for C. stemonitis. Lectotypes and epitypes are designated for A. acremonium, A. albonigrescens, C. gorgonifer, C. nanum and W. anomalus. Cephalotrichum cylindricum, C. microsporum, F. singularis and Gamsia columbina are also epitypified with new specimens. Descriptions of the phenotypic features and dichotomous keys for identification are provided for accepted species in the different genera.
Alternaria section Alternaria: Species, formae speciales or pathotypes? Stud. Mycol. (IF 14) Pub Date : 2015-08-25 J.H.C. Woudenberg, M.F. Seidl, J.Z. Groenewald, M. de Vries, J.B. Stielow, B.P.H.J. Thomma, P.W. Crous
The cosmopolitan fungal genus Alternaria consists of multiple saprophytic and pathogenic species. Based on phylogenetic and morphological studies, the genus is currently divided into 26 sections. Alternaria sect. Alternaria contains most of the small-spored Alternaria species with concatenated conidia, including important plant, human and postharvest pathogens. Species within sect. Alternaria have been mostly described based on morphology and / or host-specificity, yet molecular variation between them is minimal. To investigate whether the described morphospecies within sect. Alternaria are supported by molecular data, whole-genome sequencing of nine Alternaria morphospecies supplemented with transcriptome sequencing of 12 Alternaria morphospecies as well as multi-gene sequencing of 168 Alternaria isolates was performed. The assembled genomes ranged in size from 33.3–35.2 Mb within sect. Alternaria and from 32.0–39.1 Mb for all Alternaria genomes. The number of repetitive sequences differed significantly between the different Alternaria genomes; ranging from 1.4–16.5 %. The repeat content within sect. Alternaria was relatively low with only 1.4–2.7 % of repeats. Whole-genome alignments revealed 96.7–98.2 % genome identity between sect. Alternaria isolates, compared to 85.1–89.3 % genome identity for isolates from other sections to the A. alternata reference genome. Similarly, 1.4–2.8 % and 0.8–1.8 % single nucleotide polymorphisms (SNPs) were observed in genomic and transcriptomic sequences, respectively, between isolates from sect. Alternaria, while the percentage of SNPs found in isolates from different sections compared to the A. alternata reference genome was considerably higher; 8.0–10.3 % and 6.1–8.5 %. The topology of a phylogenetic tree based on the whole-genome and transcriptome reads was congruent with multi-gene phylogenies based on commonly used gene regions. Based on the genome and transcriptome data, a set of core proteins was extracted, and primers were designed on two gene regions with a relatively low degree of conservation within sect. Alternaria (96.8 and 97.3 % conservation). Their potential discriminatory power within sect. Alternaria was tested next to nine commonly used gene regions in sect. Alternaria, namely the SSU, LSU, ITS, gapdh, rpb2, tef1, Alt a 1, endoPG and OPA10-2 gene regions. The phylogenies from the two gene regions with a relatively low conservation, KOG1058 and KOG1077, could not distinguish the described morphospecies within sect. Alternaria more effectively than the phylogenies based on the commonly used gene regions for Alternaria. Based on genome and transcriptome comparisons and molecular phylogenies, Alternaria sect. Alternaria consists of only 11 phylogenetic species and one species complex. Thirty-five morphospecies, which cannot be distinguished based on the multi-gene phylogeny, are synonymised under A. alternata. By providing guidelines for the naming and identification of phylogenetic species in Alternaria sect. Alternaria, this manuscript provides a clear and stable species classification in this section.
Common but different: The expanding realm of Cladosporium Stud. Mycol. (IF 14) Pub Date : 2015-11-18 K. Bensch, J.Z. Groenewald, U. Braun, J. Dijksterhuis, M. de Jesús Yáñez-Morales, P.W. Crous
The genus Cladosporium (Cladosporiaceae, Dothideomycetes), which represents one of the largest genera of dematiaceous hyphomycetes, has been intensively investigated during the past decade. In the process, three major species complexes (C. cladosporioides, C. herbarum and C. sphaerospermum) were resolved based on morphology and DNA phylogeny, and a monographic revision of the genus (s. lat.) published reflecting the current taxonomic status quo. In the present study a further 19 new species are described based on phylogenetic characters (nuclear ribosomal RNA gene operon, including the internal transcribed spacer regions ITS1 and ITS2, as well as partial actin and translation elongation factor 1-α gene sequences) and morphological differences. For a selection of the species with ornamented conidia, scanning electron microscopic photos were prepared to illustrate the different types of surface ornamentation. Surprisingly, during this study Cladosporium ramotenellum was found to be a quite common saprobic species, being widely distributed and occurring on various substrates. Therefore, an emended species description is provided. Furthermore, the host range and distribution data for several previously described species are also expanded.
Revision of the Massarineae (Pleosporales, Dothideomycetes) Stud. Mycol. (IF 14) Pub Date : 2015-11-18 K. Tanaka, K. Hirayama, H. Yonezawa, G. Sato, A. Toriyabe, H. Kudo, A. Hashimoto, M. Matsumura, Y. Harada, Y. Kurihara, T. Shirouzu, T. Hosoya
We here taxonomically revise the suborder Massarineae (Pleosporales, Dothideomycetes, Ascomycota). Sequences of SSU and LSU nrDNA and the translation elongation factor 1-alpha gene (tef1) are newly obtained from 106 Massarineae taxa that are phylogenetically analysed along with published sequences of 131 taxa in this suborder retrieved from GenBank. We recognise 12 families and five unknown lineages in the Massarineae. Among the nine families previously known, the monophyletic status of the Dictyosporiaceae, Didymosphaeriaceae, Latoruaceae, Macrodiplodiopsidaceae, Massarinaceae, Morosphaeriaceae, and Trematosphaeriaceae was strongly supported with bootstrap support values above 96 %, while the clades of the Bambusicolaceae and the Lentitheciaceae are moderately supported. Two new families, Parabambusicolaceae and Sulcatisporaceae, are proposed. The Parabambusicolaceae is erected to accommodate Aquastroma and Parabambusicola genera nova, as well as two unnamed Monodictys species. The Parabambusicolaceae is characterised by depressed globose to hemispherical ascomata with or without surrounding stromatic tissue, and multi-septate, clavate to fusiform, hyaline ascospores. The Sulcatisporaceae is established for Magnicamarosporium and Sulcatispora genera nova and Neobambusicola. The Sulcatisporaceae is characterised by subglobose ascomata with a short ostiolar neck, trabeculate pseudoparaphyses, clavate asci, broadly fusiform ascospores, and ellipsoid to subglobose conidia with or without striate ornamentation. The genus Periconia and its relatives are segregated from the Massarinaceae and placed in a resurrected family, the Periconiaceae. We have summarised the morphological and ecological features, and clarified the accepted members of each family. Ten new genera, 22 new species, and seven new combinations are described and illustrated. The complete ITS sequences of nrDNA are also provided for all new taxa for use as barcode markers.
Resolving the Phoma enigma Stud. Mycol. (IF 14) Pub Date : 2015-11-26 Q. Chen, J.R. Jiang, G.Z. Zhang, L. Cai, P.W. Crous
The Didymellaceae was established in 2009 to accommodate Ascochyta, Didymella and Phoma, as well as several related phoma-like genera. The family contains numerous plant pathogenic, saprobic and endophytic species associated with a wide range of hosts. Ascochyta and Phoma are morphologically difficult to distinguish, and species from both genera have in the past been linked to Didymella sexual morphs. The aim of the present study was to clarify the generic delimitation in Didymellaceae by combing multi-locus phylogenetic analyses based on ITS, LSU, rpb2 and tub2, and morphological observations. The resulting phylogenetic tree revealed 17 well-supported monophyletic clades in Didymellaceae, leading to the introduction of nine genera, three species, two nomina nova and 84 combinations. Furthermore, 11 epitypes and seven neotypes were designated to help stabilise the taxonomy and use of names. As a result of these data, Ascochyta, Didymella and Phoma were delineated as three distinct genera, and the generic circumscriptions of Ascochyta, Didymella, Epicoccum and Phoma emended. Furthermore, the genus Microsphaeropsis, which is morphologically distinct from the members of Didymellaceae, grouped basal to the Didymellaceae, for which a new family Microsphaeropsidaceae was introduced.
Zombie-ant fungi across continents: 15 new species and new combinations within Ophiocordyceps. I. Myrmecophilous hirsutelloid species Stud. Mycol. (IF 14) Pub Date : 2018-01-02 João P.M. Araújo, Harry C. Evans, Ryan Kepler, David P. Hughes
Ophiocordyceps species infecting ants – the so-called zombie-ant fungi – comprise one of the most intriguing and fascinating relationships between microbes and animals. They are widespread within tropical forests worldwide, with relatively few reports from temperate ecosystems. These pathogens possess the ability to manipulate host behaviour in order to increase their own fitness. Depending on the fungal species involved the infected ants are manipulated either to leave the nest or ascend understorey shrubs, to die biting onto vegetation, or descend from the canopy to die at the base of trees. Experimental evidence has demonstrated that the behavioural change aids spore dispersal and thus increases the chances of infection, because of the existing behavioural immunity expressed inside ant colonies that limits fungal development and transmission. Despite their undoubted importance for ecosystem functioning, these fungal pathogens are still poorly documented, especially regarding their diversity, ecology and evolutionary relationships. Here, we describe 15 new species of Ophiocordyceps with hirsutella-like asexual morphs that exclusively infect ants. These, form a monophyletic group that we identified in this study as myrmecophilous hirsutelloid species. We also propose new combinations for species previously described as varieties and provide for the first time important morphological and ecological information. The species proposed herein were collected in Brazil, Colombia, USA, Australia and Japan. All species could readily be separated using classic taxonomic criteria, in particular ascospore and asexual morphology.
Naming names: the first women taxonomists in mycology Stud. Mycol. (IF 14) Pub Date : 2017-12-19 Sara Maroske, Tom W. May
The transition from amateur to professional in natural history is generally regarded as having taken place in the nineteenth century, but landmark events such as the 1917 appointment of mycologist Johanna Westerdijk (1883–1961) as the first female professor in the Netherlands indicate that the pattern of change for women was more varied and delayed than for men. We investigate this transition in mycology, and identify only 43 women in the Western World who published scientific mycological literature pre-1900, of whom twelve published new fungal taxa. By charting the emergence of these women over time, and comparing the output of self-taught amateurs and university graduates, we establish the key role of access to higher education in female participation in mycology. Using a suite of strategies, six of the self-taught amateurs managed to overcome their educational disadvantages and name names — Catharina Dörrien (the first to name a fungal taxon), Marie-Anne Libert, Mary Elizabeth Banning, Élise-Caroline Bommer, Mariette Rousseau, and Annie Lorrain Smith. By 1900, the professional era for women in mycology was underway, and increasing numbers published new taxa. Parity with male colleagues in recognition and promotion, however, remains an ongoing issue.
Coelomycetous Dothideomycetes with emphasis on the families Cucurbitariaceae and Didymellaceae Stud. Mycol. (IF 14) Pub Date : 2017-11-21 N. Valenzuela-Lopez, J.F. Cano-Lira, J. Guarro, D.A. Sutton, N. Wiederhold, P.W. Crous, A.M. Stchigel
The taxonomy of the coelomycetes has undergone dramatic changes in recent years, but remains controversial due to the high number of taxa involved, their poor morphological differentiation, the rare occurrence of the sexual morphs, and rapid loss of fertility in vitro. In the present study, we revisited the families Cucurbitariaceae and Didymellaceae (Pleosporales, Dothideomycetes), which include numerous plant pathogens, endophytic species associated with a wide host range, and saprobes. The taxonomy of two of the most relevant genera, i.e. Phoma and Pyrenochaeta, remains ambiguous after several phylogenetic studies, and needs further revision. We have studied a total of 143 strains of coelomycetes from clinical or environmental origin, by combining the LSU, ITS, tub2 and rpb2 sequences for a multi-locus analysis and a detailed morphological comparison. The resulting phylogenetic tree revealed that some fungi previously considered as members of Cucurbitariaceae represented five different families, and four of them, Neopyrenochaetaceae, Parapyrenochaetaceae, Pseudopyrenochaetaceae and Pyrenochaetopsidaceae, are proposed here as new. Furthermore, 13 new genera, 28 new species, and 20 new combinations are proposed within the Pleosporineae. Moreover, four new typifications are introduced to stabilise the taxonomy of these fungi.
Phylogenetic classification and generic delineation of Calyptosphaeria gen. nov., Lentomitella, Spadicoides and Torrentispora (Sordariomycetes) Stud. Mycol. (IF 14) Pub Date : 2017-12-06 M. Réblová, A.N. Miller, K. Réblová, V. Štěpánek
The genus Ceratostomella has a long history of taxonomic confusion. While species with evanescent asci have been transferred to the Microascales and Ophiostomatales, the taxonomic status of species with persistent asci has not been completely resolved. In previous studies using DNA sequence data, cultures and morphology, several Ceratostomella spp. were allocated in 13 genera in the Eurotiomycetes and Sordariomycetes. In our study, the systematics of the remaining Ceratostomella spp. with persistent asci is revisited with new collection data, cultures and phylogeny based on novel DNA sequences from six nuclear loci. Bayesian inference and Maximum Likelihood analyses support the monophyly of several wood-inhabiting species formerly classified in Ceratostomella and other unknown morphologically similar taxa and their division into four genera, i.e. Lentomitella, Spadicoides, Torrentispora and the newly described Calyptosphaeria. This robust clade represents the order Xenospadicoidales in the Sordariomycetidae. Comparative analysis of the ITS2 secondary structure revealed a genetic variation among Lentomitella isolates; 11 species were recognised, of which five are newly introduced and two are new combinations. Other taxonomic novelties include four new species and eight new combinations in Calyptosphaeria, Spadicoides, and Torrentispora. Molecular data suggest that Spadicoides is polyphyletic. The core of the genus is positioned in the Xenospadicoidales; Spadicoides s. str. is experimentally linked with sexual morphs for the first time. Based on DNA sequence data, the monotypic genera Xenospadicoides and Pseudodiplococcium are reduced to synonymy under Spadicoides, while Fusoidispora and Pseudoannulatascus are synonymised with Torrentispora. Members of the Xenospadicoidales inhabit decaying wood in terrestrial and freshwater environments and share a few morphological characters such as the absence of stromatic tissue, ascomata with a cylindrical or rostrate neck, similar anatomies of the ascomatal walls, thin-walled unitunicate asci with a non-amyloid apical annulus, disintegrating paraphyses, usually ellipsoidal to fusiform ascospores and holoblastic-denticulate or tretic conidiogenesis. Revised Ceratostomella spp. with persistent asci are listed and the taxonomic status of each species is re-evaluated based on revision of the holotype and other representative material, published details and available phylogenetic data.
A preliminary account of the Cucurbitariaceae Stud. Mycol. (IF 14) Pub Date : 2017-11-21 W.M. Jaklitsch, J. Checa, M.N. Blanco, I. Olariaga, S. Tello, H. Voglmayr
Fresh collections, type studies and molecular phylogenetic analyses of a multigene matrix of partial nuSSU-ITS-LSU rDNA, rpb2, tef1 and tub2 sequences were used to evaluate the boundaries of Cucurbitaria in a strict sense and of several related genera of the Cucurbitariaceae. Two species are recognised in Cucurbitaria and 19 in Neocucurbitaria. The monotypic genera Astragalicola, Cucitella, Parafenestella, Protofenestella, and Seltsamia are described as new. Fenestella is here included as its generic type F. fenestrata (= F. princeps), which is lecto- and epitypified. Fenestella mackenzei and F. ostryae are combined in Parafenestella. Asexual morphs of Cucurbitariaceae, where known, are all pyrenochaeta- or phoma-like. Comparison of the phylogenetic analyses of the ITS-LSU and combined matrices demonstrate that at least rpb2 sequences should be added whenever possible to improve phylogenetic resolution of the tree backbone; in addition, the tef1 introns should be added as well to improve delimitation of closely related species.
Phylogeny of tremellomycetous yeasts and related dimorphic and filamentous basidiomycetes reconstructed from multiple gene sequence analyses Stud. Mycol. (IF 14) Pub Date : 2015-10-02 X.-Z. Liu, Q.-M. Wang, B. Theelen, M. Groenewald, F.-Y. Bai, T. Boekhout
The Tremellomycetes (Basidiomycota) contains a large number of unicellular and dimorphic fungi with stable free-living unicellular states in their life cycles. These fungi have been conventionally classified as basidiomycetous yeasts based on physiological and biochemical characteristics. Many currently recognised genera of these yeasts are mainly defined based on phenotypical characters and are highly polyphyletic. Here we reconstructed the phylogeny of the majority of described anamorphic and teleomorphic tremellomycetous yeasts using Bayesian inference, maximum likelihood, and neighbour-joining analyses based on the sequences of seven genes, including three rRNA genes, namely the small subunit of the ribosomal DNA (rDNA), D1/D2 domains of the large subunit rDNA, and the internal transcribed spacer regions (ITS 1 and 2) of rDNA including 5.8S rDNA; and four protein-coding genes, namely the two subunits of the RNA polymerase II (RPB1 and RPB2), the translation elongation factor 1-α (TEF1) and the mitochondrial gene cytochrome b (CYTB). With the consideration of morphological, physiological and chemotaxonomic characters and the congruence of phylogenies inferred from analyses using different algorithms based on different data sets consisting of the combined seven genes, the three rRNA genes, and the individual protein-coding genes, five major lineages corresponding to the orders Cystofilobasidiales, Filobasidiales, Holtermanniales, Tremellales, and Trichosporonales were resolved. A total of 45 strongly supported monophyletic clades with multiple species and 23 single species clades were recognised. This phylogenetic framework will be the basis for the proposal of an updated taxonomic system of tremellomycetous yeasts that will be compatible with the current taxonomic system of filamentous basidiomycetes accommodating the ‘one fungus, one name’ principle.
Phylogeny of yeasts and related filamentous fungi within Pucciniomycotina determined from multigene sequence analyses Stud. Mycol. (IF 14) Pub Date : 2015-10-02 Q.-M. Wang, M. Groenewald, M. Takashima, B. Theelen, P.-J. Han, X.-Z. Liu, T. Boekhout, F.-Y. Bai
In addition to rusts, the subphylum Pucciniomycotina (Basidiomycota) includes a large number of unicellular or dimorphic fungi which are usually studied as yeasts. Ribosomal DNA sequence analyses have shown that the current taxonomic system of the pucciniomycetous yeasts which is based on phenotypic criteria is not concordant with the molecular phylogeny and many genera are polyphyletic. Here we inferred the molecular phylogeny of 184 pucciniomycetous yeast species and related filamentous fungi using maximum likelihood, maximum parsimony and Bayesian inference analyses based on the sequences of seven genes, including the small subunit ribosomal DNA (rDNA), the large subunit rDNA D1/D2 domains, the internal transcribed spacer regions (ITS 1 and 2) of rDNA including the 5.8S rDNA gene; the nuclear protein-coding genes of the two subunits of DNA polymerase II (RPB1 and RPB2) and the translation elongation factor 1-α (TEF1); and the mitochondrial gene cytochrome b (CYTB). A total of 33 monophyletic clades and 18 single species lineages were recognised among the pucciniomycetous yeasts employed, which belonged to four major lineages corresponding to Agaricostilbomycetes, Cystobasidiomycetes, Microbotryomycetes and Mixiomycetes. These lineages remained independent from the classes Atractiellomycetes, Classiculomycetes, Pucciniomycetes and Tritirachiomycetes formed by filamentous taxa in Pucciniomycotina. An updated taxonomic system of pucciniomycetous yeasts implementing the ‘One fungus = One name’ principle will be proposed based on the phylogenetic framework presented here.
Multigene phylogeny and taxonomic revision of yeasts and related fungi in the Ustilaginomycotina Stud. Mycol. (IF 14) Pub Date : 2015-12-10 Q.-M. Wang, D. Begerow, M. Groenewald, X.-Z. Liu, B. Theelen, F.-Y. Bai, T. Boekhout
The subphylum Ustilaginomycotina (Basidiomycota, Fungi) comprises mainly plant pathogenic fungi (smuts). Some of the lineages possess cultivable unicellular stages that are usually classified as yeast or yeast-like species in a largely artificial taxonomic system which is independent from and largely incompatible with that of the smut fungi. Here we performed phylogenetic analyses based on seven genes including three nuclear ribosomal RNA genes and four protein coding genes to address the molecular phylogeny of the ustilaginomycetous yeast species and their filamentous counterparts. Taxonomic revisions were proposed to reflect this phylogeny and to implement the ‘One Fungus = One Name’ principle. The results confirmed that the yeast-containing classes Malasseziomycetes, Moniliellomycetes and Ustilaginomycetes are monophyletic, whereas Exobasidiomycetes in the current sense remains paraphyletic. Four new genera, namely Dirkmeia gen. nov., Kalmanozyma gen. nov., Golubevia gen. nov. and Robbauera gen. nov. are proposed to accommodate Pseudozyma and Tilletiopsis species that are distinct from the other smut taxa and belong to clades that are separate from those containing type species of the hitherto described genera. Accordingly, new orders Golubeviales ord. nov. with Golubeviaceae fam. nov. and Robbauerales ord. nov. with Robbaueraceae fam. nov. are proposed to accommodate the sisterhood of Golubevia gen. nov. and Robbauera gen. nov. with other orders of Exobasidiomycetes. The majority of the remaining anamorphic yeast species are transferred to corresponding teleomorphic genera based on strongly supported phylogenetic affinities, resulting in the proposal of 28 new combinations. The taxonomic status of a few Pseudozyma species remains to be determined because of their uncertain phylogenetic positions. We propose to use the term pro tempore or pro tem. in abbreviation to indicate the single-species lineages that are temporarily maintained.
Towards an integrated phylogenetic classification of the Tremellomycetes Stud. Mycol. (IF 14) Pub Date : 2016-01-08 X.-Z. Liu, Q.-M. Wang, M. Göker, M. Groenewald, A.V. Kachalkin, H.T. Lumbsch, A.M. Millanes, M. Wedin, A.M. Yurkov, T. Boekhout, F.-Y. Bai
Families and genera assigned to Tremellomycetes have been mainly circumscribed by morphology and for the yeasts also by biochemical and physiological characteristics. This phenotype-based classification is largely in conflict with molecular phylogenetic analyses. Here a phylogenetic classification framework for the Tremellomycetes is proposed based on the results of phylogenetic analyses from a seven-genes dataset covering the majority of tremellomycetous yeasts and closely related filamentous taxa. Circumscriptions of the taxonomic units at the order, family and genus levels recognised were quantitatively assessed using the phylogenetic rank boundary optimisation (PRBO) and modified general mixed Yule coalescent (GMYC) tests. In addition, a comprehensive phylogenetic analysis on an expanded LSU rRNA (D1/D2 domains) gene sequence dataset covering as many as available teleomorphic and filamentous taxa within Tremellomycetes was performed to investigate the relationships between yeasts and filamentous taxa and to examine the stability of undersampled clades. Based on the results inferred from molecular data and morphological and physiochemical features, we propose an updated classification for the Tremellomycetes. We accept five orders, 17 families and 54 genera, including seven new families and 18 new genera. In addition, seven families and 17 genera are emended and one new species name and 185 new combinations are proposed. We propose to use the term pro tempore or pro tem. in abbreviation to indicate the species names that are temporarily maintained.
Phylogenetic classification of yeasts and related taxa within Pucciniomycotina Stud. Mycol. (IF 14) Pub Date : 2016-01-11 Q.-M. Wang, A.M. Yurkov, M. Göker, H.T. Lumbsch, S.D. Leavitt, M. Groenewald, B. Theelen, X.-Z. Liu, T. Boekhout, F.-Y. Bai
Most small genera containing yeast species in the Pucciniomycotina (Basidiomycota, Fungi) are monophyletic, whereas larger genera including Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces are polyphyletic. With the implementation of the “One Fungus = One Name” nomenclatural principle these polyphyletic genera were revised. Nine genera, namely Bannoa, Cystobasidiopsis, Colacogloea, Kondoa, Erythrobasidium, Rhodotorula, Sporobolomyces, Sakaguchia and Sterigmatomyces, were emended to include anamorphic and teleomorphic species based on the results obtained by a multi-gene phylogenetic analysis, phylogenetic network analyses, branch length-based methods, as well as morphological, physiological and biochemical comparisons. A new class Spiculogloeomycetes is proposed to accommodate the order Spiculogloeales. The new families Buckleyzymaceae with Buckleyzyma gen. nov., Chrysozymaceae with Chrysozyma gen. nov., Microsporomycetaceae with Microsporomyces gen. nov., Ruineniaceae with Ruinenia gen. nov., Symmetrosporaceae with Symmetrospora gen. nov., Colacogloeaceae and Sakaguchiaceae are proposed. The new genera Bannozyma, Buckleyzyma, Fellozyma, Hamamotoa, Hasegawazyma, Jianyunia, Rhodosporidiobolus, Oberwinklerozyma, Phenoliferia, Pseudobensingtonia, Pseudohyphozyma, Sampaiozyma, Slooffia, Spencerozyma, Trigonosporomyces, Udeniozyma, Vonarxula, Yamadamyces and Yunzhangia are proposed to accommodate species segregated from the genera Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces. Ballistosporomyces is emended and reintroduced to include three Sporobolomyces species of the sasicola clade. A total of 111 new combinations are proposed in this study.
Biodiversity of Trichoderma (Hypocreaceae) in Southern Europe and Macaronesia Stud. Mycol. (IF 14) Pub Date : 2015-01-22 W.M. Jaklitsch, H. Voglmayr
The first large-scale survey of sexual and asexual Trichoderma morphs collected from plant and fungal materials conducted in Southern Europe and Macaronesia including a few collections from French islands east of Africa yielded more than 650 specimens identified to the species level. Routine sequencing of tef1 revealed a genetic variation among these isolates that exceeds previous experience and ca. 90 species were recognized, of which 74 are named and 17 species newly described. Aphysiostroma stercorarium is combined in Trichoderma. For the first time a sexual morph is described for T. hamatum. The hitherto most complete phylogenetic tree is presented for the entire genus Trichoderma, based on rpb2 sequences. For the first time also a genus-wide phylogenetic tree based on acl1 sequences is shown. Detailed phylogenetic analyses using tef1 sequences are presented in four separate trees representing major clades of Trichoderma. Discussions involve species composition of clades and ecological and biogeographic considerations including distribution of species.
Diversity and potential impact of Calonectria species in Eucalyptus plantations in Brazil Stud. Mycol. (IF 14) Pub Date : 2015-01-23 R.F. Alfenas, L. Lombard, O.L. Pereira, A.C. Alfenas, P.W. Crous
Species in the genus Calonectria (Hypocreales) represent an important group of plant pathogenic fungi that cause serious losses to plant crops in tropical and subtropical climates. Calonectria leaf blight is currently one of the main impediments to Eucalyptus cultivation in Brazil, and various species of Calonectria have been associated with this disease. Since most previous identifications were solely based on morphological characters, much of the published literature needs to be re-evaluated. The aim of this study was thus to identify and determine the phylogenetic relationships among species that occur in the Eucalyptus growing regions of Brazil by using partial sequences of the β-tubulin, calmodulin, translation elongation factor 1-α and histone H3 gene regions. Based on extensive collections from soil and infected eucalypt leaf samples from plantations, phylogenetic inference revealed the Ca. pteridis complex to be the most common species complex present in Eucalyptus plantations in Brazil. By elucidating taxa in the Ca. pteridis, Ca. cylindrospora and Ca. candelabra species complexes, 20 novel Calonectria species were identified, and a new name in Calonectria provided for Cylindrocladium macrosporum as Ca. pseudopteridis.
Novel taxa in the Fusarium fujikuroi species complex from Pinus spp. Stud. Mycol. (IF 14) Pub Date : 2015-01-23 D.A. Herron, M.J. Wingfield, B.D. Wingfield, C.A. Rodas, S. Marincowitz, E.T. Steenkamp
The pitch canker pathogen Fusarium circinatum has caused devastation to Pinus spp. in natural forests and non-natives in commercially managed plantations. This has drawn attention to the potential importance of Fusarium species as pathogens of forest trees. In this study, we explored the diversity of Fusarium species associated with diseased Pinus patula, P. tecunumanii, P. kesiya and P. maximinoi in Colombian plantations and nurseries. Plants displaying symptoms associated with a F. circinatum-like infection (i.e., stem cankers and branch die-back on trees in plantations and root or collar rot of seedlings) were sampled. A total of 57 isolates were collected and characterised based on DNA sequence data for the translation elongation factor 1-α and β-tubulin gene regions. Phylogenetic analyses of these data allowed for the identification of more than 10 Fusarium species. These included F. circinatum, F. oxysporum, species within the Fusarium solani species complex and seven novel species in the Fusarium fujikuroi species complex (formerly the Gibberella fujikuroi species complex), five of which are described here as new. Selected isolates of the new species were tested for their pathogenicity on Pinus patula and compared with that of F. circinatum. Of these, F. marasasianum, F. parvisorum and F. sororula displayed levels of pathogenicity to P. patula that were comparable with that of F. circinatum. These apparently emerging pathogens thus pose a significant risk to forestry in Colombia and other parts of the world.
Some contents have been Reproduced by permission of The Royal Society of Chemistry.
- Acc. Chem. Res.
- ACS Appl. Mater. Interfaces
- ACS Biomater. Sci. Eng.
- ACS Catal.
- ACS Cent. Sci.
- ACS Chem. Biol.
- ACS Chem. Neurosci.
- ACS Comb. Sci.
- ACS Earth Space Chem.
- ACS Energy Lett.
- ACS Infect. Dis.
- ACS Macro Lett.
- ACS Med. Chem. Lett.
- ACS Nano
- ACS Omega
- ACS Photonics
- ACS Sens.
- ACS Sustainable Chem. Eng.
- ACS Synth. Biol.
- Acta Biomater.
- Acta Crystallogr. A Found. Adv.
- Acta Mater.
- Adv. Colloid Interface Sci.
- Adv. Electron. Mater.
- Adv. Energy Mater.
- Adv. Funct. Mater.
- Adv. Healthcare Mater.
- Adv. Mater.
- Adv. Mater. Interfaces
- Adv. Opt. Mater.
- Adv. Sci.
- Adv. Synth. Catal.
- AlChE J.
- Anal. Bioanal. Chem.
- Anal. Chem.
- Anal. Chim. Acta
- Anal. Methods
- Angew. Chem. Int. Ed.
- Annu. Rev. Anal. Chem.
- Annu. Rev. Biochem.
- Annu. Rev. Environ. Resour.
- Annu. Rev. Food Sci. Technol.
- Annu. Rev. Mater. Res.
- Annu. Rev. Phys. Chem.
- Appl. Catal. A Gen.
- Appl. Catal. B Environ.
- Appl. Clay. Sci.
- Appl. Energy
- Aquat. Toxicol.
- Arab. J. Chem.
- Asian J. Org. Chem.
- Atmos. Environ.
- Carbohydr. Polym.
- Catal. Commun.
- Catal. Rev. Sci. Eng.
- Catal. Sci. Technol.
- Catal. Today
- Cell Chem. Bio.
- Cem. Concr. Res.
- Ceram. Int.
- Chem. Asian J.
- Chem. Bio. Drug Des.
- Chem. Biol. Interact.
- Chem. Commun.
- Chem. Educ. Res. Pract.
- Chem. Eng. J.
- Chem. Eng. Sci.
- Chem. Eur. J.
- Chem. Mater.
- Chem. Phys.
- Chem. Phys. Lett.
- Chem. Phys. Lipids
- Chem. Rev.
- Chem. Sci.
- Chem. Soc. Rev.
- Chin. J. Chem.
- Combust. Flame
- Compos. Part A Appl. Sci. Manuf.
- Compos. Sci. Technol.
- Compr. Rev. Food Sci. Food Saf.
- Comput. Chem. Eng.
- Constr. Build. Mater.
- Coordin. Chem. Rev.
- Corros. Sci.
- Crit. Rev. Food Sci. Nutr.
- Crit. Rev. Solid State Mater. Sci.
- Cryst. Growth Des.
- Curr. Opin. Chem. Eng.
- Curr. Opin. Colloid Interface Sci.
- Curr. Opin. Environ. Sustain
- Curr. Opin. Solid State Mater. Sci.
- Ecotox. Environ. Safe.
- Electrochem. Commun.
- Electrochim. Acta
- Energy Environ. Sci.
- Energy Fuels
- Energy Storage Mater.
- Environ. Impact Assess. Rev.
- Environ. Int.
- Environ. Model. Softw.
- Environ. Pollut.
- Environ. Res.
- Environ. Sci. Policy
- Environ. Sci. Technol.
- Environ. Sci. Technol. Lett.
- Environ. Sci.: Nano
- Environ. Sci.: Processes Impacts
- Environ. Sci.: Water Res. Technol.
- Eur. J. Inorg. Chem.
- Eur. J. Med. Chem.
- Eur. J. Org. Chem.
- Eur. Polym. J.
- J. Acad. Nutr. Diet.
- J. Agric. Food Chem.
- J. Alloys Compd.
- J. Am. Ceram. Soc.
- J. Am. Chem. Soc.
- J. Am. Soc. Mass Spectrom.
- J. Anal. Appl. Pyrol.
- J. Anal. At. Spectrom.
- J. Antibiot.
- J. Catal.
- J. Chem. Educ.
- J. Chem. Eng. Data
- J. Chem. Inf. Model.
- J. Chem. Phys.
- J. Chem. Theory Comput.
- J. Chromatogr. A
- J. Chromatogr. B
- J. Clean. Prod.
- J. CO2 UTIL.
- J. Colloid Interface Sci.
- J. Comput. Chem.
- J. Cryst. Growth
- J. Dairy Sci.
- J. Electroanal. Chem.
- J. Electrochem. Soc.
- J. Environ. Manage.
- J. Eur. Ceram. Soc.
- J. Fluorine Chem.
- J. Food Drug Anal.
- J. Food Eng.
- J. Food Sci.
- J. Funct. Foods
- J. Hazard. Mater.
- J. Heterocycl. Chem.
- J. Hydrol.
- J. Ind. Eng. Chem.
- J. Inorg. Biochem.
- J. Magn. Magn. Mater.
- J. Mater. Chem. A
- J. Mater. Chem. B
- J. Mater. Chem. C
- J. Mater. Process. Tech.
- J. Mech. Behav. Biomed. Mater.
- J. Med. Chem.
- J. Membr. Sci.
- J. Mol. Catal. A Chem.
- J. Mol. Liq.
- J. Nat. Gas Sci. Eng.
- J. Nat. Prod.
- J. Nucl. Mater.
- J. Org. Chem.
- J. Photochem. Photobiol. C Photochem. Rev.
- J. Phys. Chem. A
- J. Phys. Chem. B
- J. Phys. Chem. C
- J. Phys. Chem. Lett.
- J. Polym. Sci. A Polym. Chem.
- J. Porphyr. Phthalocyanines
- J. Power Sources
- J. Solid State Chem.
- J. Taiwan Inst. Chem. E.
- Macromol. Rapid Commun.
- Mass Spectrom. Rev.
- Mater. Chem. Front.
- Mater. Des.
- Mater. Horiz.
- Mater. Lett.
- Mater. Sci. Eng. A
- Mater. Sci. Eng. R Rep.
- Mater. Today
- Meat Sci.
- Med. Chem. Commun.
- Microchem. J.
- Microchim. Acta
- Micropor. Mesopor. Mater.
- Mol. Biosyst.
- Mol. Cancer Ther.
- Mol. Catal.
- Mol. Nutr. Food Res.
- Mol. Pharmaceutics
- Mol. Syst. Des. Eng.
- Nano Energy
- Nano Lett.
- Nano Res.
- Nano Today
- Nano-Micro Lett.
- Nanomed. Nanotech. Biol. Med.
- Nanoscale Horiz.
- Nat. Catal.
- Nat. Chem.
- Nat. Chem. Biol.
- Nat. Commun.
- Nat. Energy
- Nat. Mater.
- Nat. Med.
- Nat. Methods
- Nat. Nanotech.
- Nat. Photon.
- Nat. Prod. Rep.
- Nat. Protoc.
- Nat. Rev. Chem.
- Nat. Rev. Drug. Disc.
- Nat. Rev. Mater.
- Natl. Sci. Rev.
- Neurochem. Int.
- New J. Chem.
- NPG Asia Mater.
- npj 2D Mater. Appl.
- npj Comput. Mater.
- npj Flex. Electron.
- npj Mater. Degrad.
- npj Sci. Food
- Pharmacol. Rev.
- Pharmacol. Therapeut.
- Photochem. Photobiol. Sci.
- Phys. Chem. Chem. Phys.
- Phys. Life Rev.
- PLOS ONE
- Polym. Chem.
- Polym. Degrad. Stabil.
- Polym. J.
- Polym. Rev.
- Powder Technol.
- Proc. Combust. Inst.
- Prog. Cryst. Growth Ch. Mater.
- Prog. Energy Combust. Sci.
- Prog. Mater. Sci.
- Prog. Photovoltaics
- Prog. Polym. Sci.
- Prog. Solid State Chem.