The genus Cladosporium and similar dematiaceous ... - CBS - KNAW

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Crous et al. Table 1. Isolates for which new sequences were generated. Anamorph Teleomorph Accession number 1 Host Country Collector GenBank numbers 2 (ITS, LSU) Cladoriella eucalypti CBS 115899*; CPC 10954 Eucalyptus sp. South Africa P.W. Crous EU040224, EU040224 Coniothyrium palmarum CBS 758.73; CMW 5283 Phoenix dactylifera Israel Y. Pinkas DQ240000, EU040225 Devriesia acadiensis CBS 115874; DAOM 232211 Soil Canada N. Nickerson AY692095, EU040226 Devriesia americana CBS 117726; ATCC 96545; CPC 5121 Air U.S.A. F.M. Dugan AY251068, EU040227 Devriesia shelburniensis CBS 115876; DAOM 232217 Soil Canada N. Nickerson AY692093, EU040228 Devriesia thermodurans CBS 115878*; DAOM 225330 Soil Canada N. Nickerson AY692087, EU040229 Hormoconis resinae CBS 365.86 – – – EU040230, EU040230 CBS 184.54; ATCC 11841; CPC 3692; IMI 089837; IFO 31706 Creosote-treated wooden pole U.S.A. – AY251067, EU040231 Hyalodendriella betulae CBS 261.82* Alnus glutinosa Netherlands W. Gams EU040232, EU040232 Ochrocladosporium elatum CBS 146.33*; ATCC 11280; ATHUM 2862; IFO 6372; IMI 049629; Wood pulp Sweden E. Melin EU040233, EU040233 MUCL 10094 Ochrocladosporium frigidarii CBS 103.81* Cooled room Germany B. Ahlert EU040234, EU040234 Parapleurotheciopsis inaequiseptata MUCL 41089; INIFAT C98/30-1 Rotten leaf Brazil R.F. Castañeda EU040235, EU040235 Passalora daleae CBS 113031* Dalea spinosa Mexico L.B. Sparrius EU040236, EU040236 Rachicladosporium luculiae CPC 11407* Luculia sp. New Zealand F. Hill EU040237, EU040237 Ramularia aplospora Mycosphaerella alchemillicola CBS 545.82* Powdery mildew on Alchemilla vulgaris Germany T. Hijwegen EU040238, EU040238 Retroconis fusiformis CBS 330.81; IMI 170799 Gossypium sp. Pakistan – EU040239, EU040239 Rhizocladosporium argillaceum CBS 241.67*; ATCC 38103; IFO 7055; OUT 4262 Decayed myxomycete Japan K. Tubaki EU040240, EU040240 Subramaniomyces fusisaprophyticus CBS 418.95; INIFAT C94/134 Leaf litter Cuba R.F. Castañeda EU040241, EU040241 Thedgonia ligustrina W1877 Ligustrum sp. – H. Evans EU040242, EU040242 Toxicocladosporium irritans CBS 185.58* Mouldy paint Suriname M.B. Schol-Schwarz EU040243, EU040243 Verrucocladosporium dirinae CBS 112794* Dirina massiliensis U.K. A. Aptroot EU040244, EU040244 1 ATCC: American Type Culture Collection, Virginia, U.S.A.; ATHUM: Culture Collection of Fungi, University of Athens, Department of Biology, Section of Ecology and Systematics, Athens, Greece; CBS: Centraalbureau voor Schimmelcultures, Utrecht, The Netherlands; CMW: Culture collection of Mike Wingfield, housed at FABI, Pretoria, South Africa; CPC: Culture collection of Pedro Crous, housed at CBS; DAOM: Plant Research Institute, Department of Agriculture (Mycology), Ottawa, Canada; IFO: Institute For Fermentation, Osaka, Japan; IMI: International Mycological Institute, CABI-Bioscience, Egham, Bakeham Lane, U.K.; INIFAT: Alexander Humboldt Institute for Basic Research in Tropical Agriculture, Ciudad de La Habana, Cuba; MUCL: Mycotheque de l’ Université Catholique de Louvain, Louvain-la-Neuve, Belgium; OUT: Department of Fermentation Technology, Faculty of Engineering, Osaka University, Yamadaue, Suita-shi, Osaka, Japan. 2 ITS: internal transcribed spacer regions and 5.8S rRNA gene; LSU: partial 28S rRNA gene. *Ex-type cultures. 34
Cladosporium and morphologically similar genera The current circumscription of Cladosporium emend. can be summarised as follows: Dematiaceous hyphomycetes; Davidiella anamorphs; mycelium internal and external; hyphae branched, septate, pigmented; stromata lacking or occasionally present; conidiophores mononematous, solitary to fasciculate, cylindrical, geniculate-sinuous to nodulose, simple to branched, subhyaline to usually distinctly pigmented, continuous to septate, smooth to verruculose; conidiogenous cells integrated, terminal and intercalary, usually sympodial, with a single to several scars; conidiogenesis holoblastic; conidiogenous loci coronate, i.e., more or less protuberant, composed of a central convex dome, surrounded by a raised periclinal rim, barely to distinctly darkened; conidia solitary or in short to long, simple to branched acropetal chains, amero- to phragmosporous, subhyaline to usually distinctly pigmented, smooth, verruculose, verrucose, echinulate, cristate, hila coronate, more or less protuberant. The new concept of Cladosporium s. str., supported by molecular data and typical coronate conidiogenous loci and conidial hila, rendered it possible to initiate a comprehensive revision of Cladosporium s. lat. The preparation of a general, annotated check-list of Cladosporium s. lat. was the first step in this direction (Dugan et al. 2004). The aim of the present study, therefore, was to delineate Cladosporium s. str. from other taxa that have in recent years been described in Cladosporium s. lat. To attain this goal isolates were studied under standardised conditions on a set of predescribed media (Schubert et al. 2007b – this volume), and subjected to DNA sequence analysis of the LSU nrRNA gene. were only sequenced for isolates of which these data were not available. The ITS data were not included in the analyses but deposited in GenBank where applicable. Gaps longer than 10 bases were coded as single events for the phylogenetic analyses; the remaining gaps were treated as missing data. Sequence data were deposited in GenBank (Table 1) and alignments in TreeBASE (www.treebase.org). Morphology Wherever possible, 30 measurements (× 1 000 magnification) were made of structures mounted in lactic acid or Shear’s solution (Gams et al. 2007), with the extremes of spore measurements given in parentheses. Microscopic observations were made from colonies cultivated for 7 d under continuous near-ultraviolet light at 25 °C on SNA as explained in Schubert et al. (2007b – this volume). Three classes of conidia are distinguished. Ramoconidia are defined as short apical branches (often conidiogenous cells) of a conidiophore which secede and function as conidia. They are characterised by having a truncate, undifferentiated base, i.e., they differ from true conidia by lacking characteristic basal hila caused by conidiogenesis. Ramoconidia give rise to branched or unbranched conidia. Secondary ramoconidia are branched conidia with a narrowed base, bearing a true hilum, that can occur in chains, giving rise to conidia, which differ from secondary ramoconidia with regards to shape, size and septation. In previous literature on Cladosporium and allied genera, the true ramoconidia have often been classified as “ramoconidia s. str.” whereas the secondary ramoconidia have been named “ramoconidia s. lat.” Materials and methods Isolates Isolates used were obtained from the Centraalbureau voor Schimmelcultures (CBS), or freshly isolated from various substrates (Table 1). Strains were cultured on 2 % malt extract plates (MEA; Gams et al. 2007), by obtaining single conidial colonies as explained in Crous (1998). Colonies were subcultured onto fresh MEA, oatmeal agar (OA), potato-dextrose agar (PDA) and synthetic nutrient-poor agar (SNA) (Gams et al. 2007), and incubated under near-ultraviolet light to study their morphology. Cultural characteristics were assessed after 2–4 wk on OA and PDA at 25 °C in the dark, using the colour charts of Rayner (1970). Nomenclatural novelties and descriptions were deposited in MycoBank (www.MycoBank.org). DNA isolation, sequencing and phylogeny Fungal colonies were established on agar plates, and genomic DNA was isolated following the CTAB-based protocol described in Gams et al. (2007). The primers V9G (de Hoog & Gerrits van den Ende 1998) and LR5 (Vilgalys & Hester 1990) were used to amplify part of the nuclear rDNA operon spanning the 3’ end of the 18S rRNA gene (SSU), the first internal transcribed spacer (ITS1), the 5.8S rRNA gene, the second ITS region and the 5’ end of the 28S rRNA gene (LSU). Four internal primers, namely ITS4 (White et al. 1990), LR0R (Rehner & Samuels 1994), LR3R (www.biology.duke. edu/fungi/mycolab/primers.htm), and LR16 (Moncalvo et al. 1993), were used for sequencing to ensure that good quality overlapping sequences are obtained. The PCR conditions, sequence alignment and subsequent phylogenetic analysis followed the methods of Crous et al. (2006d). The ITS1, ITS2 and 5.8S rRNA gene (ITS) www.studiesinmycology.org Results DNA extraction, amplification and phylogeny Amplicons of approximately 1 700 bases were obtained for the isolates listed in Table 1. The newly generated sequences were used to obtain additional sequences from GenBank, which were added to the alignment. The manually adjusted LSU alignment contained 73 sequences (including the two outgroup sequences) and 996 characters including alignment gaps. Of the 849 characters used in the phylogenetic analysis, 336 were parsimony-informative, 77 were variable and parsimony-uninformative, and 436 were constant. Neighbour-joining analyses using three substitution models on the sequence data yielded trees with identical topologies to one another. The neighbour-joining trees support the same clades as obtained from the parsimony analysis, but with a different arrangement at the deeper nodes, which were poorly supported in the bootstrap analyses or not at all (for example, the Helotiales and Pleosporales are swapped around). Performing a parsimony analysis with gaps treated as new characters increases the number of equally parsimonious trees to 94; the same topology is observed but with less resolution for the taxa in the Helotiales (data not shown). Forty-four equally most parsimonious trees (TL = 1 572 steps; CI = 0.436; RI = 0.789; RC = 0.344), one of which is shown in Fig. 1, were obtained from the parsimony analysis of the LSU sequence data. The cladosporium-like taxa were found to belong to the Helotiales, Pleosporales, Sordariales and as sister taxa to the Davidiellaceae in the Capnodiales. The LSU alignment used for parsimony and distance analysis was supplemented with sequences for Parapleurotheciopsis inaequiseptata (Matsush.) P.M. Kirk and Subramaniomyces fusisaprophyticus (Matsush.) P.M. Kirk, as well as related sequences 35
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Page 7 and 8: CONTENTS P.W. Crous, U. Braun and J
Page 9 and 10: lectotype for the genus by Clements
Page 11: Schubert K (2005a). Morphotaxonomic
Page 14 and 15: Crous et al. Table 1. Isolates for
Page 16 and 17: Crous et al. Table 1. (Continued).
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Page 72 and 73: Arzanlou et al. Table 1. (Continued
Page 74 and 75: Arzanlou et al. 10 changes Athelia
Page 76 and 77: Arzanlou et al. Athelia epiphylla A
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Arzanlou et al. Cultural characteri
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Arzanlou et al. Fig. 30. Myrmecridi
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Arzanlou et al. Fig. 32. Radulidium
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Arzanlou et al. Fig. 34. Rhodoveron
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Arzanlou et al. even further, thoug
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available online at www.studiesinmy
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Dichocladosporium gen. nov. 10 chan
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Dichocladosporium gen. nov. Fig. 3.
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Dichocladosporium gen. nov. to intr
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Dichocladosporium gen. nov. Czechos
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Cladosporium herbarum species compl
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Cladosporium sphaerospermum species
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Crous et al. The aim of the present
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Crous et al. 10 changes Athelia epi
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Crous et al. Table 1. Isolates used
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Crous et al. Table 1. (Continued).
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Crous et al. 0.1 expected changes p
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Crous et al. Fig. 6. Cladophialopho
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Crous et al. Fig. 11. Cladophialoph
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Crous et al. Fig. 13. Cladophialoph
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Crous et al. Fig. 15. Exophiala sp.
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Crous et al. Fig. 18. Cylindrosympo
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Crous et al. Fig. 19. Fusicladium a
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Crous et al. Fig. 22. Fusicladium f
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Crous et al. Fig. 24. Fusicladium p
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Crous et al. Fusicladium rhodense C
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Crous et al. Excluded taxa Polyscyt
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Crous et al. the conidial tips are
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Cladophialophora carrionii complex
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Hormoconis resinae and morphologica
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Fig. 6 Hormoconis resinae and morph
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Cladophialophora, 52 k , 54 k -55,
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Fusicladium phillyreae, 189 c , 191
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Ramichloridium epichloës, 60, 89 P
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Trimmatostroma salicis, 3 t , 5, 6
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