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.

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

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PLoS One. 2013;8(11). doi:10.1371/annotation/acfe0686-dd9d-4673-8cc9-3bb9f457a8c4 PubMed

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Medlar JM (1915) A new fungus, Phialophora verrucosa, pathogenic for man. Mycologia 7: 200–203.

Iwatsu T, Miyaji M (1977) Subcutaneous cystic granuloma caused by Phialophora verrucosa . Mycopathologia 64: 165–168. PubMed

Haase G, Sonntag L, Melzer-Krick B, de Hoog GS (1999) Phylogeny inference by SSU gene analysis of members of the Herpotrichiellaceae with special reference to human pathogenic species. Stud Mycol 43: 80–97.

Hoog GS de, Guarro J, Gené J, Figueras MJ (2000) Atlas of clinical fungi 2nd ed. Centraalbureau voor Schimmelcultures, Utrecht and Universitat Rovira I Virgili, Reus. 1124 p.

Hoog GS de, Mayser P, Haase G, Horré R, Horrevorts AM (2000) A new species, Phialophora europaea, causing superficial infections in humans. Mycoses 43: 409–416. PubMed

Vries GA de (1962) Cyphellophora laciniata nov. gen. nov. sp. and Dactylium fusarioides Fragoso et Ciferri. Mycopat Mycol Appl 16: 47–54.

Walz A, Hoog GS de (1987) A new species of Cyphellophora . Anton Leeuw Int J G 53: 143–146. PubMed

Ajello L, Padhye AA, Payne M (1980) Phaeohyphomycosis in a dog caused by Pseudomicrodochium suttonii sp. nov. Mycotaxon 12: 131–136.

Vries GA de, Elders M, Luykx MHF (1986) Description of Cyphellophora pluriseptata sp. nov. Anton Leeuw Int J G 52: 141–143. PubMed

Sutton BC, Campbell CK, Goldschmied-Reouven A (1991) Pseudomicrodochium fusarioides sp. nov. isolated from human bronchial fluid. Mycopathologia 114: 159–161. PubMed

Feng P, Lu Q, Najafzadeh MJ, Gerrits van den Ende AHG, Sun J, et al.. (2012) Cyphellophora and its relatives in Phialophora: biodiversity and possible role in human infection. Fung Diver. Available: DOI 10.1007/s13225-012-0194-5.

Nunes AT, Cavalcanti MA, Queiroz Aciole de L (1999) Occurrence of Pseudomicrodochium suttonii in Brazil. Rev Microbiol 30: 52–53.

Decock C, Delgado-Rodríguez G, Buchet S, Seng JM (2003) A new species and three new combinations in Cyphellophora, with a note on the taxonomic affinities of the genus, and its relation to Kumbhamaya and Pseudomicrodochium . Anton Leeuw Int J G 84: 209–216. PubMed

Crous PW, Schubert K, Braun U, Hoog GS de, Hocking AD, et al. (2007) Opportunistic, human-pathogenic species in the Herpotrichiellaceae are phenotypically similar to saprobic or phytopathogenic species in the Venturiaceae. Stud Mycol 58: 185–217. PubMed PMC

Jacob M, Bhat DJ (2000) Two new endophytic fungi from India. Cryptogamie Mycol 21: 81–88.

Geiser DM, Gueidan C, Miadlikowska J, Lutzoni F, Kauff F, et al. (2006) Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae. Mycologia 98: 1053–1064. PubMed

Crous PW, Braun U, Wingfield MJ, Wood AR, Shin HD, et al. (2009) Phylogeny and taxonomy of obscure genera of microfungi. Persoonia 22: 139–161. PubMed PMC

Untereiner WA, Angus A, Réblová M, Orr M-J (2008) The systematics of the Phialophora verrucosa complex: new insights from β-tubulin, large subunit nuclear rDNA and ITS sequence data. Botany 86: 742–750.

Gams W, Holubová-Jechová V (1976) Chloridium and some other dematiaceous hyphomycetes growing on decaying wood. Stud Mycol 13: 1–99.

Constantinescu O, Holm K, Holm J (1995) Teleomorph-anamorph connections in Ascomycetes: the anamorphs of three species of Chaetosphaeria . Mycol Res 99: 585–592.

Untereiner WA, Naveau FA, Bachewich J, Angus A (2006) Evolutionary relationships of Hyphodiscus hymeniophilus (anamorph Catenulifera rhodogena) inferred from β-tubulin and nuclear ribosomal DNA sequences. Can J Bot 84: 243–253.

Bogale M, Orr M-J, O'Hara MJ, Untereiner WA ( 2010) Systematic of Catenulifera (anamorphic Hyaloscyphaceae) with an assessment of the phylogenetic position of Phialophora hyalina . Fung Biol 114: 396–409. PubMed

Réblová M, Gams W, Seifert KA (2011) Monilochaetes and allied genera of the Glomerellales, and a reconsideration of families in the Microascales . Stud Mycol 68: 163–191. PubMed PMC

Hoog GS de, Weenink O, Gerrits van den Ende AHG (1999) Taxonomy of the Phialophora verrucosa complex with the description of two new species. Stud Mycol 43: 107–122.

Caretta G, Tosi S, Piontelli E, Hoog de GS (2006) Phialophora sessilis, a lithobiont fungus. Mycotaxon 95: 281–284.

Côté CA, Greer CL, Peculis BA (2002) Dynamic conformational model for the role of ITS2 in pre-rRNA processing in yeast. RNA 8: 786–797. PubMed PMC

Mai JC, Coleman AW (1997) The internal transcribed spacer 2 exhibits a common secondary structure in green algae and flowering plants. J Mol Evol 44: 258–271. PubMed

Joseph N, Krauskopf E, Vera MI, Michot B (1999) Ribosomal internal transcribed spacer 2 (ITS2) exhibits a common core of secondary structure in vertebrates and yeast. Nucleic Acids Res 27: 4533–4540. PubMed PMC

Coleman AW (2007) Pan-eukaryote ITS2 homologies revealed by RNA secondary structure. Nucleic Acids Res 35: 3322–3329. PubMed PMC

Coleman AW, Mai JC (1997) Ribosomal DNA ITS-1 and ITS-2 sequence comparisons as a tool for predicting genetic relatedness. J Mol Evol 45: 168–177. PubMed

Coleman AW (2000) The significance of a coincidence between evolutionary landmarks found in mating affinity and a DNA sequence. Protist 151: 1–9. PubMed

Gams W, Hoekstra ES, Aptroot A (1998) CBS course of mycology, 4th edn. Baarn, The Netherlands: Centraalbureau voor Schimmelcultures. 165 p.

Untereiner WA, Straus NA, Malloch D (1995) A molecular-morphotaxonomic approach to the systematics of the Herpotrichiellaceae and allied black yeasts. Mycol Res 99: 897–913.

Lee SB, Taylor JW (1990) 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. Academic, San Diego. 282–287.

Schmitt I, Crespo A, Divakar PK, Frankhauser JD, Herman-Sackett E, et al. (2009) New primers for promising single-copy genes in fungal phylogenetics and systematics. Persoonia 23: 35–40. PubMed PMC

Crous PW, Schroers H-J, Groenewald JZ, Braun U, Schubert K (2006) Metulocladosporiella gen. nov. for the causal organism of Cladosporium speckle disease of banana. Mycol Res 110: 264–275. PubMed

Tsuneda A, Hambleton S, Currah RS (2011) The anamorph genus Knufia and its phylogenetically allied species in Coniosporium, Sarcinomyces, and Phaeococcomyces . Botany 89: 523–536.

Chomnunti P, Ko Ko TW, Chukeatirote E, Cai L, Jones EBG, et al. (2012) Phylogeny of Chaetothyriaceae in northern Thailand including three new species. Mycologia 104: 382–395. PubMed

Chomnunti P, Bhat DJ, Gareth Jones EB, Chukeatirote K, Bahkali AH, et al. (2012) Trichomeriaceae, a new sooty mould family of Chaetothyriales. Fung Diver 56: 63–76.

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

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

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

Réblová M, Réblová K (2012) RNA secondary structure, an important bioinformatics tool to enhance multiple sequence alignment: a case study (Sordariomycetes, Fungi). Mycol Prog. Available: DOI 10.1007/s11557-012-0836-8.

Nylander J (2008) MrModeltest2 v. 2.3. C program for selecting DNA substitution models using PAUP*.

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

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

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

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

Sukosd Z, Knudsen B, Kjems J, Pedersen CNS (2012) PPfold 3.0: Fast RNA secondary structure prediction using phylogeny and auxiliary data. Bioinformatics 28: 2691–2692. PubMed

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

Darty K, Denise A, Ponty Y (2009) VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics 25: 1974–1975. PubMed PMC

Koetschan C, Förster F, Keller A, Schleicher T, Ruderisch B, et al. (2010) The ITS2 Database III–sequences and structures for phylogeny. Nucleic Acids Research 38: D275–D279. PubMed PMC

Leontis NB, Stombaugh J, Westhof E (2002) The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res 30: 3497–3531. PubMed PMC

Stombaugh J, Zirbel CL, Westhof E, Leontis NB (2009) Frequency and isostericity of RNA base pairs. Nucleic Acids Res 37: 2294–2312. PubMed PMC

Wrona B, Grabowski M (2004) Etiology of apple sooty blotch in Poland. J Plant Protection Res 44: 294–297.

Zhuang J, Zhu M, Zhang M, Lin H, Lei Y, et al. (2010) Phialophora sessilis, a species causing flyspeck signs on bamboo in China. Mycotaxon 113: 405–413.

Sutton BC (1975) Hyphomycetes on cupules of Castanea sativa . Trans Brit Mycol Soc 64: 405–426.

Hoog GS de, Hogeweg P, Meuzelaar HLC, Weijman ACM (1977) Rhinocladiella and allied genera. Stud Mycol 15: 1–136.

Perfect JR, Schell WA (1996) The new fungal opportunists are coming. Clin Infect Dis 22 (Suppl. 2)8112–8118. PubMed

Hamada N, Abe N (2010) Growth characteristics of four fungal species in bathrooms. Biocontrol Sci 15: 111–115. PubMed

Lian X, Hoog GS de (2010) Indoor wet cells harbour melanized agents of cutaneous infection. Med Mycol 48: 622–628. PubMed

Summerbell R, Cooper E, Bunn U, Jamieson F, Gupta AK (2005) Onychomycosis: a critical study of techniques and criteria for confirming the etiologic significance of nondermatophytes. Medical Mycology 43: 39–59. PubMed

Nag Raj TR (1977) Ypsilonia, Acanthotheciella, and Kazulia gen. nov. Can J Bot 55: 1599–1622.

Hughes SJ (1976) Sooty molds. Mycologia 68: 693–820.

Constantinescu O, Holm K, Holm L (1989) Teleomorph-anamorph connections in Ascomycetes. 1–3. Stanhughesia (Hyphomycetes) new genus, the anamorph of Ceramothyrium . Stud Mycol 31: 71–84.

Fuckel L (1874) Symbolae Mycologicae. Zweiter Nachtrag. Jahrbücher des Nassauischen Vereins für Naturkunde 27(28): 1–99.

Hawksworth DL (1980) Notes on some fungi occurring on Peltigera, with a key to accepted species. Trans Br Mycol Soc 74: 363–386.

Untereiner WA, Gueidan C, Orr M-J, Diederich P (2011) The phylogenetic position of the lichenicolous ascomycete Capronia peltigerae . Fung Diver 49: 225–233.

Crous PW, Groenewald JZ, Summerell B (2007) Exophiala placitae Crous & Summerell, sp. nov. Fungal Planet, 17. Centraalbureau voor Schimmelcultures, Utrecht, Netherlands.

Hibbett DS, Binder M, Bischoff JF, Blackwell M, Cannon PF, et al. (2007) A higher-level phylogenetic classification of the Fungi. Mycol Res 111: 509–547. PubMed

Barr ME (1976) Perspectives in the Ascomycotina. Mem. New York Bot. Gard. 28: 1–8.

Barr ME (1987) Prodromus to class Loculoascomycetes. Published by the author. Amherst, Massachusetts. 168 p.

Winka K, Eriksson OE, Bång Å (1998) Molecular evidence for recognizing the Chaetothyriales. Mycologia 90: 822–830.

Kirk PM, Cannon PF, Minter DW, Stalpers JA (2008). Dictionary of the Fungi (10th ed). Wallingford, UK: CABI. 446 p.

Untereiner WA, Naveau F (1999) Molecular systematics of the Herpotrichiellaceae with an assessment of the phylogenetic positions of Exophiala dermatitidis and Phialophora americana . Mycologia 91: 67–83.

Untereiner WA (2000) Capronia and its anamorphs: exploring the value of morphological and molecular characters in the systematics of the Herpotrichiellaceae. Stud Mycol 45: 141–148.

Gueidan C, Ruibal CV, de Hoog GS, Gorbushina AA, Untereiner WA, et al. (2008) A rock-inhabiting ancestor for mutualistic and pathogen-rich fungal lineages. Stud Mycol 61: 111–119. PubMed PMC

Schol-Schwarz MB (1968) Rhinocladiella, its synonym Fonsecaea and its relation to Phialophora . Anton Leeuw Int J G 34: 119–152. PubMed

Samuels GJ, Müller E (1978) Life-history studies of Brazilian ascomycetes. 3. Melanomma radicans sp. nov. and its Apiosphaeria anamorph, Trematosphaeria perrumpens sp. nov, and Berlesiella fungicola sp. nov. and its Ramichloridium anamorph. Sydowia 31: 142–156.

Müller E, Petrini O, Fisher PJ, Samuels GJ, Rossman AY (1987) Taxonomy and anamorphs of the Herpotrichiellaceae with notes on generic synonomy. Trans Br Mycol Soc 88: 63–74.

Untereiner WA (1995) Fruiting studies in species of Capronia (Herpotrichiellaceae). Anton Leeuw Int J G 68: 3–17. PubMed

Untereiner WA (1997) Taxonomy of selected members of the ascomycete genus Capronia with notes on anamorph-teleomorph connections. Mycologia 89: 120–131.

Okada G, Seifert KA, Takematsu A, Yamaoka Y, Miyazaki S, et al. (1998) A molecular phylogenetic reappraisal of the Graphium complex based on 18 S rDNA sequences. Can J Bot 76: 1495–1506.

Cheewangkoon R, Groenewald JZ, Summerell BA, Hyde KD, To-anun C, et al. (2009) Myrtaceae, a cache of fungal biodiversity. Persoonia 23: 55–85. PubMed PMC

Sterflinger K, De Baere R, de Hoog GS, De Wachter R, Krumbein WE, et al. (1997) Coniosporium perforans and C. apollinis, two new rock-inhabiting fungi isolated from marble in the Sanctuary of Delos (Cyclades, Greece). Anton Leeuw Int J G 72: 349–363. PubMed

Sert HC, Sterflinger K (2010) A new Coniosporium species from historical marble monuments. Mycol Prog 9: 353–359.

Li DM, Hoog GS de, Lindhardt Saunte DM, Gerrits van den Ende AHG, Chen XR (2008) Coniosporium epidermidis sp. nov., a new species from human skin. Stud Mycol 61: 131–136. PubMed PMC

Hutchison LJ, Untereiner WA, Hiratsuka Y (1995) Knufia cryptophialidica gen. et sp. nov., a dematiaceous hyphomycete isolated from black galls of trembling aspen (Populus tremuloides). Mycologia 87: 902–908.

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

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

Goertzen LR, Can JJ, Gutell RR, Jasen RK (2003) ITS secondary structure derived from comparative analysis: implications for sequence alignment and phylogeny of the Asteraceae. Mol Phylogenet Evol 29: 216–234. PubMed

Thornhill DJ, Lord JB (2010) Secondary structure models for the internal transcribed spacer (ITS) region 1 from symbiotic dinoflagellates. Protist 161: 434–451. PubMed

Bridge PD, Schlitt T, Cannon PF, Buddie AG, Baker M, et al. (2008) Domain II hairpin structure in ITS1 sequences as an aid in differentiating recently evolved animal and plant pathogenic fungi. Mycopathologia 166: 1–16. PubMed

Rodriguez-Martínez R, Rocap G, Logares R, Romac S, Massana R (2012) Low evolutionary diversification in a widespread and abundant uncultured protist (MAST-4). Mol Biol Evol 29: 1393–1406. PubMed

Réblová M, Winka K (2000) Phylogeny of Chaetosphaeria and its anamorphs based on morphological and molecular data. Mycologia 92: 939–954.

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

Caisová L, Marin B, Melkonian M (2011) A close-up view on ITS2 evolution and speciation – a case study in the Ulvophyceae (Chlorophyta, Viridiplantae). BMC Evol Biol 11: 262. Available: http://www.biomedcentral.com/1471-2148/11/262. Accessed 20 September 2011. PubMed PMC

Schultz J, Maisel S, Gerlach D, Müller T, Wolf M (2005) A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota. RNA 11: 361–364. PubMed PMC

Coleman AW, van Oppen MJH (2008) Secondary structure of the rRNA ITS2 region reveals key evolutionary patterns in acroporid corals. J Mol Evol 67: 389–396. PubMed

Gould IR, Kollman PA (1994) Theoretical Investigation of the Hydrogen Bond Strengths in Guanine-Cytosine and Adenine-Thymine Base Pairs. J Am Chem Soc 116: 2493–2499.

Sykes MT, Levitt M (2005) Describing RNA structure by libraries of clustered nucleotide doublets. J Mol Biol 351: 26–38. PubMed PMC

Fabry S, Köhler A, Coleman AW (1999) Intraspecies analysis: comparison of ITS sequence data and gene intron sequence data with breeding data for a worldwide collection of Gonium pectorale . Journal of Molecular Evolution 48: 94–101. PubMed

Coleman AW (2005) Paramecium aurelia revisited. J Eukaryot Microbiol 52: 68–77. PubMed

Amato A, Kooistra WHCF, Ghiron JHL, Mann DG, Pröschold T, et al. (2007) Reproductive isolation among sympatric cryptic species in marine diatoms. Protist 158: 193–207. PubMed

Coleman AW (2003) ITS2 is a double-edged tool for eukaryote evolutionary comparisons. Trends Genet 19: 370–375. PubMed

Coleman AW, Vacquier VD (2002) Exploring the phylogenetic utility of ITS sequences for animals: a test case for abalone (Haliotis). J Mol Evol 54: 246–257. PubMed

Schultz J, Muller T, Achtziger M, Seibel P, Dandekar T, et al. (2006) The internal transcribed spacer 2 database-a web server for (not only) low level phylogenetic analyses. Nucleic Acids Res 34: W704. PubMed PMC

Selig C, Wolf M, Muller T, Dandekar T, Schultz J (2007) The ITS2 Database II: homology modeling RNA structure for molecular systematics. Nucleic Acids Res 36: D377–D380. PubMed PMC

Müller T, Philippi N, Dandekar T, Schultz J, Wolf M (2007) Distinguishing species. RNA 13: 1469. PubMed PMC

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