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

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Cladophialophora carrionii complex 117905 dH 14505 EU137300, –, – Chromoblastomycosis, hand, male Falcon State, Venezuela 117900 dH 14493 EU137284, –, EU137227 Chromoblastomycosis, hand, male Falcon State, Venezuela 114392 UNEFM 82267 = dH 13261 EU137267, EU137150, EU137211 Chromoblastomycosis, leg, female Falcon State, Venezuela – FMC 248 AF397181, –, – Chromoblastomycosis Venezuela – IFM 41807 AB109175, –, – Group mt-I – Venezuela – IFM 4812 AB109168, –, – Group mt-I – Venezuela – IMTSP 690 AF397180, –, – Chromoblastomycosis Brazil 410.96 UAMH 4392 = NCMH 1010 = DUKE 2403 EU137310, EU137195, EU137250 Chromoblastomycosis – 163.54 EU137304, EU137186, EU137243 Chromoblastomycosis Australia 117903 dH 14482 EU137282, –, EU137225 Chromoblastomycosis, forearm, male – 362.70 M.J. Campos 4555 = dH 15806 EU137302, EU137184, EU137242 Human Mozambique 260.83 CDC B-1352 = FMC 282 = ATCC 44535 (ex-T of C. ajelloi) EU137292, EU137175, EU137234 Group mt-I Skin lesion in human Uganda 986.96 UAMH 5717 EU137297, EU137180, – Clinical material – – IFM 4805 AB087204, –, – – – – IFM 4811 AB109178, –, – – – – IFM 41814 AB109176, –, – – – B / II / 2: C. carrionii 160.54 ATCC 16264 = CDC A-835 = MUCL 40053 = IFM 4808 (ex-LT of C. carrionii) AB109177 / EU137266, EU137201, EU137210 Group mt-II Chromoblastomycosis, human Australia – Todd Pryce 200867 = dH 13218 Human Australia 406.96 MRL 1114 = UAMH 4366 = dH 15847 EU137317, EU137202, EU137256 Human Queensland, Australia 100434 ATCC 32279 = dH 10745 = IP 518 = RV 16499 EU137289, EU137172, EU137232 Human Madagascar – IFM 4810 AB109170, –, – – – – IFM 41446 = DCU 606 AB109171, –, – – – C: C. carrionii – IFM 41651 AB109174, –, – Group mt-I – China – IFM 41650 AB109173, –, – Group mt-I – China – IFM 41641 AB109172, –, – Group mt-I – China – IFM 4985 AB109179, –, – – – – IFM 4986 AB109180, –, – – – D / III / 3: C. yegresii 114406 UNEFM SgSR1 = dH 13275 EU137323, EU137208, EU137263 Stenocereus griseus asymptomatic plant Falcon State, Venezuela 114407 UNEFM SgSR2 = dH 13276 EU137324, –, EU137264 Stenocereus griseus asymptomatic plant Falcon State, Venezuela 114405** UNEFM SgSR3 = dH 13274 (ex-T of C. yegresii) EU137322, EU137209, EU137262 Stenocereus griseus asymptomatic plant Falcon State, Venezuela 1 Abbreviations: ATCC = American Type Culture Collection, Manassas, U.S.A.; CBS = Centraalbureau voor Schimmelcultures, Utrecht, The Netherlands; CDC = Centers for Disease Control and Prevention, Atlanta, U.S.A.; DCU = Department of Dermatology, School of Medicine, Chiba, Japan; dH = G.S. de Hoog working collection; FMC = Faculdade de Medicina, Caracas, Venezuela; ITMSP = Instituto de Medicina Tropical de São Paulo, São Paulo, Brazil; IFM = Research Center for Pathogenic Fungi and Microbial Toxicoses, Chiba University, Chiba, Japan; IP = Institut Pasteur, Paris, France; MUCL = Mycotheque de l’Université de Louvain, Louvain-la-Neuve, Belgium; RV = Prince Leopold Institute of Tropical Medicine, Antwerp, Belgium; UAMH = The University of Alberta Microfungus Collection and Herbarium, Edmonton, Canada; UNEFM = Universidade Nacional Experimental Francisco de Miranda, Coro, Falcon, Venezuela. Ex-T = Type strain; ex-LT = Lectotype strain. *Type I and II groups based on mitochondrial DNA restriction fragment length polymorphism: H-1 and H-2 = restriction patterns 1 and 2, respectively, with HaeIII enzyme; M-1 and M-2 = restriction patterns 1 and 2, respectively, with MspI enzyme; S-1 and S-2 = restriction patterns 1 and 2, respectively, with Sau3AI enzyme. ** Used in plant and mouse inoculation experiments. www.studiesinmycology.org 221
De Hoog et al. Table 2. Results from MrAic using corrected Akaike Information Criterion (AICc). Fragment/Gene Model df* lnL* AICc* wAICc* rRNA ITS TrNG 89 -21.840.556 4575.9992” 0.3080 EF-1α HKYG 88 -19.392.355 41.147.171 0.5242 ß-Tubulin SYMIG 90 -28.547.745 59.261.933 0.1913 *df = degrees of freedom; lnL = log likelihood; AICc = corrected AIC; wAICc = weighted corrected AIC. DNA extraction Approximately 1 cm 2 mycelium of 30-d-old cultures was transferred to a 2 mL Eppendorf tube containing 300 µL TES-buffer (Tris 1.2 % w/v, Na-EDTA 0.38% w/v, SDS 2 % w/v, pH 8.0) and about 80 mg of a silica mixture (Silica gel H, Merck 7736, Darmstadt, Germany / Kieselguhr Celite 545, Machery, Düren, Germany, 2 : 1, w/w). Cells were disrupted mechanically in a tight-fitting sterile pestle for approximately 1 min. Subsequently 200 µL TES-buffer was added, the mixture was vortexed, 10 µL proteinase K was added and incubated for 10 min at 65 °C. After addition of 140 µL of 5 M NaCl and 1/10 vol CTAB 10 % (cetyltrimethylammoniumbromide) buffer, the material was incubated for 30 min at 65 °C. Subsequently 700 µL SEVAG (24 : 1, chloroform : isoamylalcohol) was mixed to solution, incubated during 30 min on ice water and centrifuged for 10 min at 14 000 rpm. The supernatant was transferred to a new tube with 225 µL 5 M NH 4 -acetate, incubated on ice water and centrifuged again for 10 min at 14 000 rpm. The supernatant was transferred to another Eppendorf tube with 0.55 vol isopropanol and spun for 5 min at 14 000 rpm. Subsequently, the pellet was washed with ice cold 70 % ethanol. After drying at room temperature it was re-suspended in 48.5 µL TE buffer (Tris 0.12 % w/v, Na-EDTA 0.04 % w/v) plus 1.5 µL RNAse 20 U/mL and incubated for 15–30 min at 37 °C. Sequencing and phylogenetic reconstruction Three loci, namely the internal transcribed spacers (ITS), ß- tubulin (BT2) and translation elongation factor 1-α (EF1), were sequenced. For ITS sequencing, amplification was performed with V9G (5’-TTACGTCCCTGCCCTTTGTA-3’) and LS266 (5’- GCATTCCCAAACAACTCGACTC-3’). Sequencing reactions were conducted with ITS1 and ITS4 primers (White et al. 1990). For BT2 amplification and sequencing, primers Bt2a (5’-GGTAACCAAATCGGTGCTGCTTTC-3’) and Bt2b (5’- ACCCTCAGTGTAGTGACCCTTGGC-3’) were used (Glass & Donaldson 1995) and for EF1 amplification and sequencing, primers EF1-728F (5’CATCGAGAAGTTCGAGAAGG-3’) and EF1-986R (5’-TACTTGAAGGAACCCTTACC-3’) (Carbone & Kohn, 1999). Sequences were aligned in BioNumerics v. 4.5 (Applied Maths, Kortrijk, Belgium), exported and converted into Phylip interleaved format (Felsenstein 1993). Calculation of ILD (incongruence length difference) was performed in PAUP v. 4.0b10 (Swofford 2003). A combined data set of ITS, EF1 and BT2 sequences was created. Optimality criterion was set to parsimony. The total number of characters was 1 263 with equal weight, while 677 characters were constant, and 396 parsimony-informative. Gaps were treated as missing, and treebisection-reconnection (TBR) was used as branch-swapping algorithm. Maximum number of trees was set to 100 and left unchanged. Substitution model testing The program MrAic (www.abc.se/~nylander/; Nylander 2004) was used to select a substitution model. MrAic is a Perl script for calculating the Akaike Information Criterion (AIC), corrected Akaike Information Criterion (AICc), Bayesian Information Criterion (BIC), and Akaike weights for nucleotide substitution models and model uncertainty. Using an ML algorithm, likelihood scores under different models were estimated using Phyml (http://atgc.lirmm.fr/phyml/). All 56 models implemented in Modeltest (Posada & Crandall 1998) were evaluated. These models were also combined with proportion of invariable sites (I) and/or gamma distribution shape parameter (G). A difference between Modeltest and MrAic is that the latter does not evaluate all models on the same, approximate topology as in PAUP (Swofford 1981). Instead, Phyml was used to try to find the maximum of the likelihood function under all models. This is necessary for finding AIC, AICc, or BIC for the models. The AICc calculation (Table 2) was used to select the right model for the ratio of parameters to characters (Nchar/Nparameters < 40; Burnham & Anderson 2002) for all loci. The substitution matrix of the models is printed next to the trees. Another advantage of using MrAic in combination with Phyml was the obtained accuracy of tree topology and the greater calculation speed (Guindon & Gascuel 2003). Population genetic analyses In order to confirm the intraspecific diversity shown in the MP trees, the number of populations in the C. carrionii complex was inferred with Structure v. 2.2 (Pritchard et al. 2000) using genotype data of the ITS regions of rRNA gene and of the partial EF1 and BT2 genes. Genotypes of these three loci of 43 isolates were sorted on the basis of sequence similarity. Structure is a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. The parameters were as follows: the length of burn-in period was set to 10 6 , number of MCMC repeats after burn-in 30 000; the ancestry model: admixture (individuals have mixed ancestry and is recommended as starting point for most analyses). Uniform prior for ALPHA was set to 1.0 (default) and all allele frequencies were taken as independent among populations with λ set to 1.0 (default). Probability of the data (for estimating K) was also computed (Falush et al. 2003). The burn-in period length and number of MCMC repetitions after burn-in were set as 10 000 and 100 000, and admixture model and allele frequencies correlated model were chosen for analysis. The number of populations (K) was assumed from two to four. Association of multilocus genotypes was screened with the multilocus option in BioNumerics. To test for reproductive mode in each population, index of association (I A , a measure of multilocus linkage disequilibrium) was calculated with Multilocus v. 1.2.2 (www. bio.ic.ac.uk/evolve/software/multilocus). The null hypothesis for this analysis was complete panmixia. The values of I A were compared between observed and randomised data sets. The hypothesis would be rejected when p < 0.05. Population differentiation (index: theta, θ) was also detected using the same software and a null hypothesis for this analysis is no population differentiation. When observed θ is statistically significantly different from those of random datasets (p < 0.05), population differentiation should be considered. 222
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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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Crous et al. Treatment of phylogene
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Crous et al. Teratosphaeria bellula
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Crous et al. 6. Conidiophores short
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Crous et al. Habit plant pathogenic
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Crous et al. Fig. 7. Catenulostroma
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Crous et al. system, consisting of
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Crous et al. Fig. 9. Penidiella col
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Crous et al. Fig. 12. Penidiella ri
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Crous et al. conidiophores, about 1
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Crous et al. have conidiomata rangi
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Crous et al. Schizothyriaceae clade
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Crous et al. Fig. 21. Stigmidium sc
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Crous et al. Gams W, Verkley GJM, C
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Crous et al. Table 1. Isolates for
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Crous et al. 100 61 100 52 100 10 c
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Crous et al. Fig. 3. Rachicladospor
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Crous et al. Fig. 4. Toxicocladospo
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Crous et al. Fig. 5. Verrucocladosp
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Crous et al. Fig. 7. Stenella aragu
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Crous et al. Helotiales, incertae s
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Crous et al. Fig. 10. Ochrocladospo
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Crous et al. Fig. 12. Rhizocladospo
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Crous et al. 7. Conidiophores unbra
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Crous et al. 33. Terminal conidioge
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Crous et al. Crous PW, Kang JC, Bra
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Arzanlou et al. To date 26 species
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Arzanlou et al. Table 1. (Continued
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Arzanlou et al. 10 changes Athelia
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Arzanlou et al. Athelia epiphylla A
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Arzanlou et al. Fig. 3. Periconiell
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Arzanlou et al. Cultural characteri
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Arzanlou et al. Fig. 10. A. Ramichl
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Arzanlou et al. Ramichloridium musa
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Arzanlou et al. Fig. 20. Rhinocladi
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Arzanlou et al. Fig. 22. Rhinocladi
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Arzanlou et al. Rhinocladiella mack
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Arzanlou et al. Fig. 26. Veronaea c
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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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Page 180 and 181: Cladosporium sphaerospermum species
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Page 222 and 223: Crous et al. Fusicladium rhodense C
Page 224 and 225: Crous et al. Excluded taxa Polyscyt
Page 226 and 227: Crous et al. the conidial tips are
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Page 232 and 233: Cladophialophora carrionii complex
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Page 246 and 247: Hormoconis resinae and morphologica
Page 252 and 253: Fig. 6 Hormoconis resinae and morph
Page 256 and 257: Cladophialophora, 52 k , 54 k -55,
Page 258 and 259: Fusicladium phillyreae, 189 c , 191
Page 260 and 261: Ramichloridium epichloës, 60, 89 P
Page 262: Trimmatostroma salicis, 3 t , 5, 6
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