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.

Central European Institute of Technology Masaryk University Brno Czech Republic

Department of Botany and Biodiversity Research Division of Systematic and Evolutionary Botany University of Vienna Vienna Austria

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 Taxonomy Institute of Botany of the Academy of Sciences of the Czech Republic Průhonice Czech Republic

Faculty of Medicine Masaryk University Brno Czech Republic

Laboratory of Enzyme Technology Institute of Microbiology of the Academy of Sciences of the Czech Republic Prague Czech Republic

Zobrazit více v PubMed

Munk A. Danish Pyrenomycetes. A preliminary flora. Dan Bot Ark 1957;17: 1–491.

Barr ME. The ascomycete connection. Mycologia 1983;75: 1–13.

Barr ME. Notes on the Calosphaeriales. Mycologia 1985;77: 549–565.

Réblová M, Mostert L, Gams W, Crous PW. New genera in the Calosphaeriales:

Vijaykrishna D, Mostert L, Jeewon R, Gams W, Hyde KD et al.

Mostert L, Groenewald JZ, Summerbell RC, Gams W, Crous PW. Taxonomy and pathology of Togninia (Diaporthales) and its Phaeoacremonium anamorphs. Studies in Mycology 2006;54: 1–115.

Damm U, Crous PW, Fourie PH. A fissitunicate ascus mechanism in the Calosphaeriaceae, and novel species of PubMed DOI PMC

Réblová M. New insights into the systematics and phylogeny of the genus

Trouillas FP, Lorber JD, Peduto F, Grant J, Coates WW, Anderson KK et al. First report of PubMed

Meyer WM, Dooley JR, Kwon-Chung KJ. Mycotic granuloma caused by PubMed

Hironaga M, Nakano K, Yokoyama I, Kitajima J. PubMed PMC

De Hoog GS, Guarro J, Gené J, Figueras MJ. Hyphomycetes. Genus:

Mhmoud NA, Ahmed SA, Fahal AH, de Hoog GS, Gerrits van den Ende AHG, van de Sande WWJ. PubMed DOI PMC

Mostert L, Crous PW, Groenewald (Ewald) JZ, Gams W, Summerbell RC. PubMed

Damm U, Mostert L, Crous PW, Fourie PH. Novel PubMed DOI PMC

Essakhi S, Mugnai L, Crous PW, Groenewald JZ, Surico G. Molecular and phenotypic characterisation of novel PubMed DOI PMC

Graham AB, Johnston PR, Weir BS. Three new

Gramaje D, Armengol J, Mohammadi H, Banihashemi Z, Mostert L. Novel PubMed

Gramaje D, Agustí-Brisach C, Pérez-Sierra A, Moralejo E, Olmo D, Mostert L et al. Fungal trunk pathogens associated with wood decay of almond trees on Mallorca (Spain). Persoonia 2012;28: 1–13. 10.3767/003158512X626155 PubMed DOI PMC

Gramaje D, Leon M, Pérez-Sierra A, Burgess T, Armengol J. New PubMed DOI PMC

Raimondo ML, Lops F, Carlucci A. PubMed DOI

Ajello L, Georg LK, Steigbigel RT, Wang CJK. A case of phaeohyphomycosis caused by a new species of PubMed

Weitzman I, Gordon MA, Henderson RW, Lapa EW. PubMed

Padhye AA, Davis MS, Baer D, Reddick A, Sinha KK, Ott J. Phaeohyphomycosis caused by PubMed PMC

Matsui T, Nishimoto K, Udagawa S, Ishihara H, Ono T. Subcutaneous phaeohyphomycosis caused by PubMed

Guarro J, Alves SH, Gené J, Grazziotin NA, Mazzuco R, Dalmagro C Two cases of subcutaneous infection due to PubMed PMC

Mostert L, Groenewald JZ, Summerbell RC, Robert V, Sutton DA, Padhye AA et al. Species of PubMed PMC

Hausner G, Eyjólfsdóttir GG, Reid J, Klassen GR. Two additional species of the genus Togninia. Can J Bot 1992;70: 724−734.

Gramaje D, Mostert L, Groenewald JZ, Crous PW. PubMed DOI

Leontis NB, Westhof E. Analysis of RNA motifs. Curr Opin Struc Biol 2003;13: 300–308. PubMed

Holbrook SR. RNA structure: the long and the short of it. Curr Opin Struc Biol 2005;15: 302−308. PubMed PMC

Leontis NB, Lescoute A, Westhof E. The building blocks and motifs of RNA architecture. Curr Opin Struc Biol 2006;16: 279–287. PubMed PMC

Malloch D. Moulds: their isolation, cultivation and identification Toronto, Ontario: University of Toronto Press; 1981.

Gams W, Hoekstra ES, Aptroot A. CBS course of mycology, 4th edn. Baarn, The Netherlands: Centraalbureau voor Schimmelcultures; 1998.

Online Auction Color Chart Co. The Online auction color chart The new language of color for buyers and sellers. Online Auction Color Chart Company; 2004.

Réblová M, Gams W, Seifert KA. 2011. PubMed DOI PMC

Lee SB, Taylor JW. Isolation of DNA from fungal mycelium and single spores In: Innis MA, Gelfand DH, Snisky JJ, White TJ (eds.) PCR protocols: a guide to methods and applications. San Diego: Academic; 1990.

Glass NL, Donaldson GC.Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous ascomycetes. Appl Environ Microbiol 1995;61: 1323–1330. PubMed PMC

Geiser DM, Frisvad JC, Taylor JW. Evolutionary relationships in

Hall TA. BioEdit 5.0.9: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999;41: 95–98.

Gutell RR. Collection of small subunit (16 S- and 16 S-like) ribosomal RNA structures. Nucleic Acids Res 1993;21: 3051–3054. PubMed PMC

Gutell RR, Gray MW, Schnare MN. A compilation of large subunit (23 S and 23 S-like) ribosomal RNA structures. Nucleic Acids Res 1993;21: 3055–3074. PubMed PMC

Réblová M, Réblová K. RNA secondary structure, an important bioinformatics tool to enhance multiple sequence alignment: a case study (Sordariomycetes, Fungi). Mycol Prog 2013;12: 305–319.

Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006;22: 2688–2690. PubMed

Stamatakis A, Ludwig T, Meier H. RaxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 2005;21: 456–463. PubMed

Mason-Gamer RJ, Kellogg EA. Testing for phylogenetic conflict among molecular data sets in the tribe Triticeae (Gramineae). Syst Biol 1996;45: 524–545.

Huelsenbeck JP, Ronquist F. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 2001;17: 754–755. PubMed

Nylander J. MrModeltest2 v. 2.3 (Program for selecting DNA substitution models using PAUP*). Uppsala, Sweden: Evolutionary Biology Centre; 2008.

Rambaut A, Suchard MA, Xie D & Drummond AJ. MCMC Trace Analysis Tool Version v1.6.0. 2013. Available: http://beast.bio.ed.ac.uk/Tracer.

Larget B, Simon DL. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol Biol Evol 1999;16: 750–759.

Sukosd Z, Knudsen B, Kjems J, Pedersen CNS. PPfold 3.0: Fast RNA secondary structure prediction using phylogeny and auxiliary data. Bioinformatics 2012;28: 2691–2692. 10.1093/bioinformatics/bts488 PubMed DOI

Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003;31: 3406–3415. PubMed PMC

Darty K, Denise A, Ponty Y. VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics 2009;25: 1974–1975. 10.1093/bioinformatics/btp250 PubMed DOI PMC

Laing C, Wen D, Wang JTL, Schlick T. Predicting coaxial helical stacking in RNA junctions. Nucleic Acid Res 2012;40: 487–498. 10.1093/nar/gkr629 PubMed DOI PMC

Lamiable A, Barth D, Denise A, Quessette F, Vial S, Westhof E. Automated prediction of three-way junction topological families in RNA secondary structures. Comput Biol Chem 2012;37: 1–5. 10.1016/j.compbiolchem.2011.11.001 PubMed DOI

Ellis JB, Everhart BM. The North American Pyrenomycetes. Newfield, New Jersey; 1892.

Marincowitz S, Crous PW, Groenewald JZ, Wingfield MJ. CBS Biodiversity Series 7 Utrecht, the Netherlands: CBS Fungal Biodiversity Centre; 2008.

Romero AI, Samuels GJ. Studies on xylophilous fungi from Argentina. VI. Ascomycotina on

Nitschke TRJ. Pyrenomycetes Germanici Die Kernpilze Deutschlands Bearbeitet von Dr. Th. Nitschke. Erster Band. Erste Lieferung. i–ii. Germany, Bresalau: Verlag von Eduard Trewendt; 1867.

Saccardo PA. Fungi Italici Autographice delineati. Fascs. 9−12, Tabs. 321–480. Patavii, Italy; 1878.

Barr ME, Rogers JD, Ju MJ. Revisionary studies in the Calosphaeriales. Mycotaxon 1993;48: 529–535.

Berlese AN. Icones Fungorum omnium hucusque cognitorum Volume 3 Padova, Italy; 1900.

Ellis JB, Everhart BM. 1890. New species of fungi from various localities. Proc Acad Nat Sci Philadelphia 1890;42: 219–249.

Hawksworth DL. A new dawn for the naming of fungi: impacts of decisions made in Melbourne in July 2011 on the future publication and regulation of fungal names. MycoKeys 2011;1: 7–20. PubMed PMC

Hawksworth DL, Crous PW, Redhead SA, Reynolds DR, Samson RA, Seifert KA et al. The Amsterdam Declaration on fungal nomenclature. IMA Fungus 2011;2: 105–112. 10.5598/imafungus.2011.02.01.14 PubMed DOI PMC

Wingfield MJ, de Beer ZW, Slippers B, Wingfield BD, Groenewald JZ, Lombard L et al. One fungus, one name promotes progressive plant pathology. Mol Plant Pathol 2012;212: 604–613. PubMed PMC

Tulasne LR, Tulasne C. Selecta Fungorum Carpologia. Vol. 2. Paris; 1863.

Samuels GJ, Candoussau F. Heterogeneity in the Calosphaeriales: a new

Smith GJD, Liew ECY, Hyde KD. The Xylariales: a monophyletic order containing 7 families. Fung Diver 2003;13: 185–218.

Pirozynski KA.

Fernández FA, Rogers JD, Ju YM, Huhndorf SM, Umaña L. PubMed

Huhndorf SM, Miller AN, Greif M, Samuels GJ. PubMed

Réblová M, Mostert L. PubMed

Crous PW, Gams W, Wingfield MJ, Van Wyk PS. 1996.

Rappaz F. Taxonomie et nomenclature des Diatrypacées à asques octosporés (1). Mycol Helv 1987;2: 285–648.

Barr ME.

Eriksson OE, Hawksworth DL. Notes on ascomycete systematics—Nos 1769–1884. Syst Ascom 1994;13: 183–214.

Lumbsch HT, Huhndorf SM (2010) Myconet Volume 14. Part One. Outline of Ascomycota—2009. Part Two. Notes on Ascomycete Systematics. Nos. 4751–5113. Fieldiana Life Earth Sci 1: 1–64.

Spegazzini CL. Fungi Guaranitici. Pugillus II. Reprint pagination 72 p. [nos 1–202]; 1888.

Ramaley AW.

Eriksson OE. The families of bitunicate ascomycetes. Opera Bot 1981;60: 1–220.

Réblová M. PubMed

Réblová M, Réblová K, Štěpánek V. Molecular systematics of PubMed PMC

Réblová M, Štěpánek V. New fungal genera, PubMed DOI

Cui J-L, Guo S-X, Dong H, Xiao P. Endophytic Fungi from Dragon’s Blood Specimens: Isolation, Identification, Phylogenetic Diversity and Bioactivity. Phytother Res 2011;25: 1189–1195. 10.1002/ptr.3361 PubMed DOI

Réblová M. Molecular systematics of PubMed

Schol-Schwarz MB. Revision of the genus

Gams W.

Hu DM, Lei C, Hyde KD. Three new ascomycetes from freshwater in China. Mycologia 2012;104: 1478–1489. 10.3852/11-430 PubMed DOI

Tegli S, Bertelli E, Surico G. Sequence analysis of ITS ribosomal DNA in five

Dupont J, Laloui W, Magnin S, Larignon P, Roquebert MF.

Groenewald M, Kang JC, Crous PW, Gams W. ITS and beta-tubulin phylogeny of

Choi J, Lee Y, Chung HS, Koo JS, Yong D, Kim YS et al. Subcutaneous phaeohyphomycosis caused by PubMed DOI PMC

Yan ZH, Rogers SO, Wang CJK. Assessment of

Rodrigues A, Mueller UG, Ishak HD, Bacci M Jr, Pagnocca FC. Ecology of microfungal communities in gardens of fungus-growing ants Hymenoptera: Formicidae): a year-long survey of three species of attine ants in Central Texas. FEMS Microbiol Ecol 2011;78: 244–255. 10.1111/j.1574-6941.2011.01152.x PubMed DOI

To KKW, Lau SKP, Wu AKL, Lee RA, Ngan AHY, Tsang CCC et al. PubMed

Takamatsu S, Hirata T, Sato Y. Phylogenetic analysis and predicted secondary structures of the rDNA internal transcribed spacers of the powdery mildew fungi (Erysiphaceae). Mycoscience 1998;39: 441–453.

Coleman AW, Maria Preparata R, Mehrotra B, Mai JC. Derivation of the secondary structure of the ITS-1 transcript in Volvocales and its taxonomic correlations. Protist 1998;149: 135–146. 10.1016/S1434-4610(98)70018-5 PubMed DOI

Coleman AW, van Oppen MJH. Secondary structure of the rRNA ITS2 region reveals key evolutionary patterns in acroporid corals. J Mol Evol 2008;67: 389–96. 10.1007/s00239-008-9160-y PubMed DOI

Réblová M, Winka K. Phylogeny of

Réblová M, Untereiner W, Réblová K (2013) Novel evolutionary lineages revealed in the Chaetothyriales (Fungi) based on multigene phylogenetic analyses and comparison of ITS secondary structure. PLOS One 2013. May 28;8(5). PubMed PMC

Gottschling M, Plötner J. Secondary structure models of the nuclear internal transcribed spacer regions and 5.8S rRNA in Calciodinelloideae (Peridiniaceae) and other dinoagellates. Nucleic Acids Res 2004;32: 307–315. PubMed PMC

Gottschling M, Hilger H, Wolf M, Diane N. Secondary structure of the ITS1 transcript and its application in a reconstruction of the phylogeny of Boraginales. Plant Biol 2001;3: 629–636.

Chen CA, Chang CC, Wei NV, Chen CH, Lein YT, Lin HE et al. Secondary structure and phylogenetic utility of the ribosomal internal transcribed spacer 2 (ITS2) in Scleractinian Corals. Zool Stud 2004;43: 759–771.

Krüger D, Gargas A. The basidiomycete genus

Krüger D, Gargas A. Secondary structure of ITS2 rRNA provides taxonomic characters for systematic studies ‒ a case in Lycoperdaceae (Basidiomycota). Mycol Res 2008;112: 316–330. 10.1016/j.mycres.2007.10.019 PubMed DOI

Aguilar C, Sánchez JA. Phylogenetic hypotheses of gorgoniid octocorals according to ITS2 and their predicted RNA secondary structures. Mol Phyl Evol 2007;43: 784–786. PubMed

Bridge PD, Schlitt T, Cannon PF, Buddie AG, Baker M, Borman AM. Domain II hairpin structure in ITS1 sequences as an aid in differentiating recently evolved animal and plant pathogenic fungi. Mycopathologia 2008;166: 1–16. 10.1007/s11046-008-9094-3 PubMed DOI

Ullrich B, Reinhold K, Niehuis O, Misof B. Secondary structure and phylogenetic analysis of the internal transcribed spacers 1 and 2 of bush crickets (Orthoptera: Tettigoniidae: Barbitistini). J Zool Syst Evol Res 2010;48: 219–228.

Noller HF. Structure of ribosomal RNA. Annu Rev Biochem 1984;53: 119–162. PubMed

Noller HF. Ribosomal RNA and translation. Annu Rev Biochem 1991;60: 191–227. PubMed

Leontis NB, Hills MT, Piotto M, Ouporov IE, Malhotra A, Gorenstein DG, Helical Stacking in DNA three-way junctions containing two unpaired pyrimidines: Proton NMR studies. Biophys J 1994;68: 251–265. PubMed PMC

Lilley DM, Clegg RM, Diekmann S, Seeman NC, von Kitzing E, Hagerman PJ. A nomenclature of junctions and branch points in nucleic acids. Nucleic Acids Res 1995;23: 3363–3364. PubMed PMC

Forster AC, Symons RH. Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites. Cell 1987;49: 211–220. PubMed

Wieland M, Gfell M, Hartig J. Expanded hammerhead ribozymes containing addressable three-way junctions. RNA 2009;15: 968–976. 10.1261/rna.1220309 PubMed DOI PMC

Scott WG, Murray JB, Arnold JR, Stoddard BL, Klug A. Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science 1996;274: 2065–2069. PubMed

Batey RT, Gilbert SD, Montange RK. Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature 2004;432: 411–415. PubMed

Lescoute A, Westhof E. Topology of three-way junctions in folded RNAs. RNA 2006;12: 83–93. PubMed PMC

Walter AE, Turner DH. Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces. Biochemistry 1994;33: 12715–12719. PubMed

Aalberts DP, Nandagopal N. A two-length-scale polymer theory for RNA loop free energies and helix stacking. RNA 2010;16: 1350–1355. 10.1261/rna.1831710 PubMed DOI PMC

Besseová I, Réblová K, Leontis NB, Šponer J. Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome. Nucleic Acids Res 2010;38: 6247–6264. 10.1093/nar/gkq414 PubMed DOI PMC

Réblová K, Šponer J, Lankaš F. Structure and mechanical properties of the ribosomal L1 stalk three-way junction Nucleic Acids Res 2012;40: 6290–6303. 10.1093/nar/gks258 PubMed DOI PMC

Yang JH, Usman N, Chartrand P, Cedergren R. Minimum ribonucleotide requirement for catalysis by the RNA hammerhead domain. Biochemistry 1992;31: 5005–5009. PubMed

Re-evaluation of Ceratostomella and Xylomelasma with introduction of two new species (Sordariomycetes)

The root-symbiotic Rhizoscyphus ericae aggregate and Hyaloscypha (Leotiomycetes) are congeneric: Phylogenetic and experimental evidence

Phylogenetic classification and generic delineation of Calyptosphaeria gen. nov., Lentomitella, Spadicoides and Torrentispora (Sordariomycetes)

Recommendations for competing sexual-asexually typified generic names in Sordariomycetes (except Diaporthales, Hypocreales, and Magnaporthales)