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Sundaresan N, Sahu AK, Jagan EG, Pandi M. Evaluation of ITS2 molecular morphometrics effectiveness in species delimitation of Ascomycota - A pilot study. Fungal Biol 2019; 123:517-527. [PMID: 31196521 DOI: 10.1016/j.funbio.2019.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 04/01/2019] [Accepted: 05/02/2019] [Indexed: 01/19/2023]
Abstract
Exploring the secondary structure information of nuclear ribosomal internal transcribed spacer 2 (ITS2) has been a promising approach in species delimitation. However, Compensatory base changes (CBC) concept employed in this approach turns futile when CBC is absent. This prompted us to investigate the utility of insertion/deletion (INDELs) and substitutions in fungal delineation at species level. Upon this rationale, 116 strains representing 97 species, belonging to 6 genera (Colletotrichum, Boeremia, Leptosphaeria, Peyronellaea, Plenodomus and Stagonosporopsis) of Ascomycota were retrieved from Q-bank for molecular morphometric analysis. CBC, INDELs and substitutions between the species of their respective genus were recorded. Most species combinations lacked CBC. Among the substitution events, transitions were predominant. INDELs were less frequent than the substitutions. These evolutionary events were mapped upon the helices to discern species specific variation sites. In 68 species unique variation sites were recognised. The remaining 29 species shared absolute similarity with distinctly named species. The variation sites catalogued in them overlapped with other distinct species and resulted in the blurring of species boundaries. Species specific variation sites recognized in this study are the preliminary results and they could be discerned with absolute confidence when larger datasets encompassing all described species of genera were investigated. They could be of potential use in barcoding fungi at species level. This study also concludes that the ITS2 molecular morphometric analysis is an efficient third dimensional study of the fungal species delimitation. This may help to avoid the false positives in species delimitations and to alleviate the challenges in molecular characterization.
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Affiliation(s)
- Natesan Sundaresan
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Amit Kumar Sahu
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Enthai Ganeshan Jagan
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Mohan Pandi
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India.
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Réblová M, Hubka V, Thureborn O, Lundberg J, Sallstedt T, Wedin M, Ivarsson M. From the Tunnels into the Treetops: New Lineages of Black Yeasts from Biofilm in the Stockholm Metro System and Their Relatives among Ant-Associated Fungi in the Chaetothyriales. PLoS One 2016; 11:e0163396. [PMID: 27732675 PMCID: PMC5061356 DOI: 10.1371/journal.pone.0163396] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/14/2016] [Indexed: 11/25/2022] Open
Abstract
Rock-inhabiting fungi harbour species-rich, poorly differentiated, extremophilic taxa of polyphyletic origin. Their closest relatives are often well-known species from various biotopes with significant pathogenic potential. Speleothems represent a unique rock-dwelling habitat, whose mycobiota are largely unexplored. Isolation of fungi from speleothem biofilm covering bare granite walls in the Kungsträdgården metro station in Stockholm yielded axenic cultures of two distinct black yeast morphotypes. Phylogenetic analyses of DNA sequences from six nuclear loci, ITS, nuc18S and nuc28S rDNA, rpb1, rpb2 and β-tubulin, support their placement in the Chaetothyriales (Ascomycota). They are described as a new genus Bacillicladium with the type species B. lobatum, and a new species Bradymyces graniticola. Bacillicladium is distantly related to the known five chaetothyrialean families and is unique in the Chaetothyriales by variable morphology showing hyphal, meristematic and yeast-like growth in vitro. The nearest relatives of Bacillicladium are recruited among fungi isolated from cardboard-like construction material produced by arboricolous non-attine ants. Their sister relationship is weakly supported by the Maximum likelihood analysis, but strongly supported by Bayesian inference. The genus Bradymyces is placed amidst members of the Trichomeriaceae and is ecologically undefined; it includes an opportunistic animal pathogen while two other species inhabit rock surfaces. ITS rDNA sequences of three species accepted in Bradymyces and other undescribed species and environmental samples were subjected to phylogenetic analysis and in-depth comparative analysis of ITS1 and ITS2 secondary structures in order to study their intraspecific variability. Compensatory base change criterion in the ITS2 secondary structure supported delimitation of species in Bradymyces, which manifest a limited number of phenotypic features useful for species recognition. The role of fungi in the speleothem biofilm and relationships of Bacillicladium and Bradymyces with other members of the Chaetothyriales are discussed.
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Affiliation(s)
- Martina Réblová
- Department of Taxonomy, Institute of Botany of the Czech Academy of Sciences, 252 43, Průhonice, Czech Republic
- * E-mail:
| | - Vit Hubka
- Department of Botany, Faculty of Science, Charles University in Prague, 128 01, Prague, 2, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, 142 20, Prague, 4, Czech Republic
| | - Olle Thureborn
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91, Stockholm, Sweden
| | - Johannes Lundberg
- Department of Botany, Swedish Museum of Natural History, 104 05, Stockholm, Sweden
| | - Therese Sallstedt
- Department of Biology, University of Southern Denmark, 5230, Odense, Denmark
- Department of Palaeobiology, Swedish Museum of Natural History, 104 05, Stockholm, Sweden
| | - Mats Wedin
- Department of Botany, Swedish Museum of Natural History, 104 05, Stockholm, Sweden
| | - Magnus Ivarsson
- Department of Palaeobiology, Swedish Museum of Natural History, 104 05, Stockholm, Sweden
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Réblová M, Fournier J, Štěpánek V. Two new lineages of aquatic ascomycetes: Atractospora gen. nov. and Rubellisphaeria gen. et sp. nov., and a sexual morph of Myrmecridium montsegurinum sp. nov. Mycol Prog 2016. [DOI: 10.1007/s11557-016-1166-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Réblová M, Jaklitsch WM, Réblová K, Štěpánek V. Phylogenetic Reconstruction of the Calosphaeriales and Togniniales Using Five Genes and Predicted RNA Secondary Structures of ITS, and Flabellascus tenuirostris gen. et sp. nov. PLoS One 2015; 10:e0144616. [PMID: 26699541 PMCID: PMC4689446 DOI: 10.1371/journal.pone.0144616] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 11/20/2015] [Indexed: 11/18/2022] Open
Abstract
The Calosphaeriales is revisited with new collection data, living cultures, morphological studies of ascoma centrum, secondary structures of the internal transcribed spacer (ITS) rDNA and phylogeny based on novel DNA sequences of five nuclear ribosomal and protein-coding loci. Morphological features, molecular evidence and information from predicted RNA secondary structures of ITS converged upon robust phylogenies of the Calosphaeriales and Togniniales. The current concept of the Calosphaeriales includes the Calosphaeriaceae and Pleurostomataceae encompassing five monophyletic genera, Calosphaeria, Flabellascus gen. nov., Jattaea, Pleurostoma and Togniniella, strongly supported by Bayesian and Maximum Likelihood methods. The structural elements of ITS1 form characteristic patterns that are phylogenetically conserved, corroborate observations based on morphology and have a high predictive value at the generic level. Three major clades containing 44 species of Phaeoacremonium were recovered in the closely related Togniniales based on ITS, actin and β-tubulin sequences. They are newly characterized by sexual and RNA structural characters and ecology. This approach is a first step towards understanding of the molecular systematics of Phaeoacremonium and possibly its new classification. In the Calosphaeriales, Jattaea aphanospora sp. nov. and J. ribicola sp. nov. are introduced, Calosphaeria taediosa is combined in Jattaea and epitypified. The sexual morph of Phaeoacremonium cinereum was encountered for the first time on decaying wood and obtained in vitro. In order to achieve a single nomenclature, the genera of asexual morphs linked with the Calosphaeriales are transferred to synonymy of their sexual morphs following the principle of priority, i.e. Calosphaeriophora to Calosphaeria, Phaeocrella to Togniniella and Pleurostomophora to Pleurostoma. Three new combinations are proposed, i.e. Pleurostoma ochraceum comb. nov., P. repens comb. nov. and P. richardsiae comb. nov. The morphology-based key is provided to facilitate identification of genera accepted in the Calosphaeriales.
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Affiliation(s)
- Martina Réblová
- Department of Taxonomy, Institute of Botany of the Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
- * E-mail:
| | - Walter M. Jaklitsch
- Department of Forest and Soil Sciences, Forest Pathology and Forest Protection, Institute of Forest Entomology, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
- Department of Botany and Biodiversity Research, Division of Systematic and Evolutionary Botany, University of Vienna, Vienna, Austria
| | - Kamila Réblová
- Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Václav Štěpánek
- Laboratory of Enzyme Technology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
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Hubka V, Réblová M, Řehulka J, Selbmann L, Isola D, de Hoog SG, Kolařík M. Bradymyces gen. nov. (Chaetothyriales, Trichomeriaceae), a new ascomycete genus accommodating poorly differentiated melanized fungi. Antonie van Leeuwenhoek 2014; 106:979-92. [DOI: 10.1007/s10482-014-0267-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 08/20/2014] [Indexed: 11/29/2022]
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Réblová M, Stěpánek V, Schumacher RK. Xylochrysis lucida gen. et sp. nov., a new lignicolous ascomycete (Sordariomycetidae) with holoblastic conidiogenesis. Mycologia 2014; 106:564-72. [PMID: 24871596 DOI: 10.3852/13-266] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The monotypic genus Xylochrysis is introduced for a lignicolous perithecial ascomycete that possesses golden yellow ascomata with black glabrous necks, a three-layered ascomatal wall, persistent paraphyses, and cylindrical, long-stipitate unitunicate asci with an inamyloid apical annulus, and hyaline, ellipsoidal, unicellular ascospores. In culture it produces hyaline conidiophores with terminally arranged branches bearing metulae, conidiogenous cells and holoblastic conidia. Phylogenetic analysis of two ribosomal (nc18S and nc28S rDNA) and one protein-coding (RPB2) gene position this species within the Sordariomycetidae but without close ordinal or familial affiliation. Morphological and molecular DNA data support the recognition of this new genus and suggest that Xylochrysis is most closely related to the genera Ceratolenta, Cyanoannulus and Woswasia.
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Affiliation(s)
- Martina Réblová
- Department of Taxonomy, Institute of Botany of the Academy of Sciences, CZ-252 43, Průhonice, Czech Republic
| | - Václav Stěpánek
- Laboratory of Enzyme Technology, Institute of Microbiology of the Academy of Sciences, CZ-142 20 Prague, Czech Republic
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Sporoschismopsis angustata sp. nov., a new holomorph species in the Reticulascaceae (Glomerellales), and a reappraisal of Sporoschismopsis. Mycol Prog 2013. [DOI: 10.1007/s11557-013-0949-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Novel evolutionary lineages revealed in the Chaetothyriales (fungi) based on multigene phylogenetic analyses and comparison of its secondary structure. PLoS One 2013; 8:e63547. [PMID: 23723988 PMCID: PMC3665825 DOI: 10.1371/journal.pone.0063547] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 04/01/2013] [Indexed: 11/19/2022] Open
Abstract
Cyphellophora and Phialophora (Chaetothyriales, Pezizomycota) comprise species known from skin infections of humans and animals and from a variety of environmental sources. These fungi were studied based on the comparison of cultural and morphological features and phylogenetic analyses of five nuclear loci, i.e., internal transcribed spacer rDNA operon (ITS), large and small subunit nuclear ribosomal DNA (nuc28S rDNA, nuc18S rDNA), β-tubulin, DNA replication licensing factor (mcm7) and second largest subunit of RNA polymerase II (rpb2). Phylogenetic results were supported by comparative analysis of ITS1 and ITS2 secondary structure of representatives of the Chaetothyriales and the identification of substitutions among the taxa analyzed. Base pairs with non-conserved, co-evolving nucleotides that maintain base pairing in the RNA transcript and unique evolutionary motifs in the ITS2 that characterize whole clades or individual taxa were mapped on predicted secondary structure models. Morphological characteristics, structural data and phylogenetic analyses of three datasets, i.e., ITS, ITS-β-tubulin and 28S-18S-rpb2-mcm7, define a robust clade containing eight species of Cyphellophora (including the type) and six species of Phialophora. These taxa are now accommodated in the Cyphellophoraceae, a novel evolutionary lineage within the Chaetothyriales. Cyphellophora is emended and expanded to encompass species with both septate and nonseptate conidia formed on discrete, intercalary, terminal or lateral phialides. Six new combinations in Cyphellophora are proposed and a dichotomous key to species accepted in the genus is provided. Cyphellophora eugeniae and C. hylomeconis, which grouped in the Chaetothyriaceae, represent another novel lineage and are introduced as the type species of separate genera.
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