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

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Arzanlou et al. To date 26 species have been named in Ramichloridium; they not only differ in morphology, but also in life style. Ramichloridium mackenziei C.K. Campb. & Al-Hedaithy is a serious human pathogen, causing cerebral phaeohyphomycosis (Al-Hedaithy et al. 1988, Campbell & Al-Hedaithy 1993), whereas R. musae causes tropical speckle disease on members of the Musaceae (Stahel 1937, Jones 2000). Another plant-pathogenic species, R. pini de Hoog & Rahman, causes a needle disease on Pinus contorta (de Hoog et al. 1983). Other clinically relevant species of Ramichloridium are R. basitonum de Hoog and occasionally R. schulzeri (Sacc.) de Hoog, while the remaining species tend to be common soil saprobes. No teleomorph has thus far been linked to species of Ramichloridium. The main question that remains is whether shared morphology among the species in this genus reflects common ancestry (Seifert 1993, Untereiner & Naveau 1999). To delineate anamorphic genera adequately, morphology and conidial ontogeny alone are no longer satisfactory (Crous et al. 2006a, b), and DNA data provide additional characters to help delineate species and genera (Taylor et al. 2000, Mostert et al. 2006, Zipfel et al. 2006). The aim of the present study was to integrate morphological and cultural features with DNA sequence data to resolve the species concepts and generic limits of the taxa currently placed in Periconiella, Ramichloridium, Rhinocladiella and Veronaea, and to resolve the status of several new cultures that were isolated during the course of this study. Materials and Methods Isolates Species names, substrates, geographical origins and GenBank accession numbers of the isolates included in this study are listed in Table 1. Fungal isolates are maintained in the culture collection of the Centraalbureau voor Schimmelcultures (CBS) in Utrecht, the Netherlands. DNA extraction, amplification and sequence analysis Genomic DNA was extracted from colonies grown on 2 % malt extract agar (MEA, Difco) (Gams et al. 2007) using the FastDNA kit (BIO101, Carlsbad, CA, U.S.A.). The primers ITS1 and ITS4 (White et al. 1990) were used to amplify the internal transcribed spacer region (ITS) of the nuclear ribosomal RNA operon, including: the 3’ end of the 18S rRNA gene, the first internal transcribed spacer region (ITS1), the 5.8S rRNA gene, the second internal transcribed spacer region (ITS2) and the 5’ end of 28S rRNA gene. Part of the large subunit 28S rRNA (LSU) gene was amplified with primers LR0R (Rehner & Samuels 1994) and LR5 (Vilgalys & Hester 1990). The ITS region was sequenced only for those isolates for which these data were not available. The ITS analyses confirmed the proposed classification based on LSU analysis for each major clade and are not presented here in detail; but the sequences are deposited in GenBank where applicable. The PCR reaction was performed in a mixture with 0.5 units Taq polymerase (Bioline, London, U.K.), 1× PCR buffer, 0.5 mM MgCl 2 , 0.2 mM of each dNTP, 5 pmol of each primer, approximately 10–15 ng of fungal genomic DNA, with the total volume adjusted to 25 µL with sterile water. Reactions were performed on a GeneAmp PCR System 9700 (Applied Biosystems, Foster City, CA) with cycling conditions consisting of 5 min at 96 °C for primary denaturation, followed by 36 cycles at 96 °C (30 s), 52 °C (30 s), and 72 °C (60 s), with a final 7 min extension step at 72 °C to complete the reaction. The amplicons were sequenced using BigDye Terminator v. 3.1 (Applied Biosystems, Foster City, CA) or DYEnamicET Terminator (Amersham Biosciences, Freiburg, Germany) Cycle Sequencing Kits and analysed on an ABI Prism 3700 (Applied Biosystems, Foster City, CA) under conditions recommended by the manufacturer. Newly generated sequences were subjected to a Blast search of the NCBI databases, sequences with high similarity were downloaded from GenBank and comparisons were made based on the alignment of the obtained sequences. Sequences from GenBank were also selected for similar taxa. The LSU tree was rooted using sequences of Athelia epiphylla Pers. and Paullicorticium ansatum Liberta as outgroups. Phylogenetic analysis was performed with PAUP (Phylogenetic Analysis Using Parsimony) v. 4.0b10 (Swofford 2003), using the neighbour-joining algorithm with the uncorrected (“p”), the Kimura 2-parameter and the HKY85 substitution models. Alignment gaps longer than 10 bases were coded as single events for the phylogenetic analyses; the remaining gaps were treated as missing data. Any ties were broken randomly when encountered. Phylogenetic relationships were also inferred with the parsimony algorithm using the heuristic search option with simple taxon additions and tree bisection and reconstruction (TBR) as the branch-swapping algorithm; alignment gaps were treated as a fifth character state and all characters were unordered and of equal weight. Branches of zero length were collapsed and all multiple, equally parsimonious trees were saved. Only the first 5 000 equally most parsimonious trees were saved. Other measures calculated included tree length, consistency index, retention index and rescaled consistency index (TL, CI, RI and RC, respectively). The robustness of the obtained trees was evaluated by 1 000 bootstrap replications. Bayesian analysis was performed following the methods of Crous et al. (2006c). The best nucleotide substitution model was determined using MrModeltest v. 2.2 (Nylander 2004). MrBayes v. 3.1.2 (Ronquist & Huelsenbeck 2003) was used to perform phylogenetic analyses, using a general time-reversible (GTR) substitution model with inverse gamma rates, dirichlet base frequencies and the temp value set to 0.5. New sequences were lodged with NCBI’s GenBank (Table 1) and the alignment and trees with TreeBASE (www.treebase.org). Morphology Cultural growth rates and morphology were recorded from colonies grown on MEA for 2 wk at 24 ºC in the dark, and colony colours were determined by reference to the colour charts of Rayner (1970). Microscopic observations were made from colonies cultivated on MEA and OA (oatmeal agar, Gams et al. 2007), using a slide culture technique. Slide cultures were set up in Petri dishes containing 2 mL of sterile water, into which a U-shaped glass rod was placed, extending above the water surface. A block of freshly growing fungal colony, approx. 1 cm square was placed onto a sterile microscope slide, covered with a somewhat larger, sterile glass cover slip, and incubated in the moist chamber. Fungal sporulation was monitored over time, and when optimal, images were captured by means of a Nikon camera system (Digital Sight DS-5M, Nikon Corporation, Japan). Structures were mounted in lactic acid, and 30 measurements (× 1 000 magnification) determined wherever possible, with the extremes of spore measurements given in parentheses. 58
Ramichloridium and allied genera Table 1. Isolates of Ramichloridium and similar genera used for DNA analysis and morphological studies. Species Accession number 1 Source Origin GenBank numbers (LSU, ITS) Myrmecridium flexuosum CBS 398.76*; IMI 203547 Soil Suriname EU041825, EU041768 Myrmecridium schulzeri CBS 100.54; JCM 6974 Soil Zaire EU041826, EU041769 CBS 134.68; ATCC 16310 Soil Germany EU041827, EU041770 CBS 156.63 Homo sapiens Netherlands EU041828, EU041771 CBS 188.96 Soil Papua New Guinea EU041829, EU041772 CBS 304.73 Wheat straw South Africa EU041830, EU041773 CBS 305.73; JCM 6967 Wheat straw South Africa EU041831, EU041774 CBS 325.74; JCM 7234 Triticum aestivum Netherlands EU041832, EU041775 CBS 381.87 — Australia EU041833, EU041776 CBS 642.76 Malus sylvestris Switzerland EU041834, EU041777 CBS 114996 Cannomois virgata South Africa EU041835, EU041778 Periconiella arcuata CBS 113477* Ischyrolepsis subverticellata South Africa EU041836, EU041779 Periconiella levispora CBS 873.73* Turpinia pomifera Sri Lanka EU041837, EU041780 Periconiella velutina CBS 101948*; CPC 2262 Brabejum stellatifolium South Africa EU041838, EU041781 CBS 101949; CPC 2263 Brabejum stellatifolium South Africa EU041839, EU041782 CBS 101950; CPC 2264 Brabejum stellatifolium South Africa EU041840, EU041783 Pleurothecium obovoideum CBS 209.95*; MFC 12477 Pasania edulis Japan EU041841, EU041784 Pseudovirgaria hyperparasitica CBS 121735; CPC 10702 On Phragmidium sp. on Rubus coreanus Korea EU041822, EU041765 CBS 121738; CPC 10704 On Phragmidium sp. on Rubus coreanus Korea EU041823, EU041766 CBS 121739*; CPC 10753 On Pucciniastrum agrimoniae on Korea EU041824, EU041767 Agrimonia pilosa Radulidium epichloës CBS 361.63*; MUCL 3124 Epichloë typhina U.S.A. EU041842, EU041785 Radulidium sp. CBS 115704 Poaceae Guyana EU041843, EU041786 Radulidium subulatum CBS 287.84 Puccinia allii U.K. EU041844, EU041787 Ramichloridium apiculatum CBS 405.76* Phragmites australis Czech Republic EU041845, EU041788 CBS 912.96 Incubator for cell cultures Germany EU041846, EU041789 CBS 101010 Lasioptera arundinis Czech Republic EU041847, EU041790 CBS 156.59*; ATCC 13211; IMI Forest soil U.S.A. EU041848, EU041791 100716; JCM 6972; MUCL 7991; MUCL 15753; QM 7716 CBS 390.67 Cucumis sativus South Africa EU041849, EU041792 CBS 391.67; JCM 6966 Aloe sp. South Africa EU041850, EU041793 CBS 400.76; IMI 088021 Soil Pakistan EU041851, EU041794 Ramichloridium australiense CBS 121710 Musa banksii Australia EU041852, EU041795 Ramichloridium biverticillatum CBS 335.36 Musa sapientum — EU041853, EU041796 Ramichloridium brasilianum CBS 283.92* Forest soil Brazil EU041854, EU041797 Ramichloridium cerophilum CBS 103.59* Sasa sp. Japan EU041855, EU041798 Ramichloridium indicum CBS 171.96 — — EU041856, EU041799 Ramichloridium musae CBS 190.63; MUCL 9557 Musa sapientum — EU041857, EU041800 CBS 365.36*; JCM 6973; MUCL 9556 Musa sapientum Surinam EU041858, EU041801 Ramichloridium pini CBS 461.82*; MUCL 28942 Pinus contorta U.K. EU041859, EU041802 Ramichloridium strelitziae CBS 121711 Strelitzia sp. South Africa EU041860, EU041803 Rhinocladiella anceps CBS 157.54; ATCC 15680; MUCL Fagus sylvatica France EU041861, EU041804 1081; MUCL 7992; MUCL 15756 CBS 181.65*; ATCC 18655; DAOM Soil Canada EU041862, EU041805 84422; IMI 134453; MUCL 8233; OAC 10215 Rhinocladiella basitona CBS 101460*; IFM 47593 Homo sapiens Japan EU041863, EU041806 Rhinocladiella fasciculata CBS 132.86* Decayed wood India EU041864, EU041807 Rhinocladiella mackenziei CBS 367.92; NCPF 2738; UTMB 3169 Homo sapiens Israel EU041865, EU041808 www.studiesinmycology.org 59
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Studies in Mycology 58 (2007) The g
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Studies in Mycology The Studies in
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CONTENTS P.W. Crous, U. Braun and J
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lectotype for the genus by Clements
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Schubert K (2005a). Morphotaxonomic
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Crous et al. Table 1. Isolates for
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Crous et al. Table 1. (Continued).
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Crous et al. 100 10 changes 65 100
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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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Page 108 and 109: Dichocladosporium gen. nov. 10 chan
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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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