Colletotrichum: complex species or species ... - CBS - KNAW

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Damm et al.Table 1. (Continued).GenBank No.Species Accession No. 1 Host/Substrate Country ITS GAPDH CHS-1 HIS3 ACT TUB2 CALC. karstii CBS 124969, LCM 232 Quercus salicifolia, leaf endophyte Panama JQ005179 JQ005266 JQ005353 JQ005440 JQ005527 JQ005613 JQ005700CBS 127591 Sapium integerrimium Australia JQ005186 JQ005273 JQ005360 JQ005447 JQ005534 JQ005620 JQ005707CBS 129815, T.A.7 Solanum betaceum, fruit Colombia JQ005187 JQ005274 JQ005361 JQ005448 JQ005535 JQ005621 JQ005708CBS 128548, ICMP 18589 Solanum lycopersicum New Zealand JQ005205 JQ005292 JQ005379 JQ005466 JQ005553 JQ005639 JQ005726CBS 508.97, LARS 168 Stylosanthes sympodialis Australia JQ005193 JQ005280 JQ005367 JQ005454 JQ005541 JQ005627 JQ005714CBS 128552, ICMP 18276 Synsepalum dulcificum, leaves Taiwan JQ005188 JQ005275 JQ005362 JQ005449 JQ005536 JQ005622 JQ005709CBS 124951 Theobroma cacao, leaf endophyte Panama JQ005180 JQ005267 JQ005354 JQ005441 JQ005528 JQ005614 JQ005701CBS 128540, STE-U 698 Triticum sp. South Africa JQ005210 JQ005297 JQ005384 JQ005471 JQ005558 JQ005644 JQ005731CBS 124956 Zamia obliqua, leaf endophyte Panama JQ005216 JQ005303 JQ005390 JQ005477 JQ005564 JQ005650 JQ005737CBS 124956 Zamia obliqua, leaf endophyte Panama JQ005216 JQ005303 JQ005390 JQ005477 JQ005564 JQ005650 JQ005737CBS 125388 Zamia obliqua, leaf endophyte Panama JQ005185 JQ005272 JQ005359 JQ005446 JQ005533 JQ005619 JQ005706C. novae-zelandiae CBS 128505, ICMP 12944* Capsicum annuum, fruit rot New Zealand JQ005228 JQ005315 JQ005402 JQ005489 JQ005576 JQ005662 JQ005749CBS 130240, ICMP 12064 Citrus sp. (grapefruit) New Zealand JQ005229 JQ005316 JQ005403 JQ005490 JQ005577 JQ005663 JQ005750C. oncidii CBS 129828* Oncidium sp., leaf Germany JQ005169 JQ005256 JQ005343 JQ005430 JQ005517 JQ005603 JQ005690CBS 130242 Oncidium sp., leaf Germany JQ005170 JQ005257 JQ005344 JQ005431 JQ005518 JQ005604 JQ005691C. parsonsiae CBS 128525, ICMP 18590* Parsonsia capsularis, leaf endophyte New Zealand JQ005233 JQ005320 JQ005407 JQ005494 JQ005581 JQ005667 JQ005754C. petchii CBS 378.94* Dracaena marginata, spotted leaves Italy JQ005223 JQ005310 JQ005397 JQ005484 JQ005571 JQ005657 JQ005744CBS 379.94 Dracaena marginata, spotted leaves Italy JQ005224 JQ005311 JQ005398 JQ005485 JQ005572 JQ005658 JQ005745CBS 118193, AR 3658 Dracaena sanderana, living leaves China JQ005227 JQ005314 JQ005401 JQ005488 JQ005575 JQ005661 JQ005748CBS 118774, AR 3751 Dracaena sanderana, living stems China JQ005225 JQ005312 JQ005399 JQ005486 JQ005573 JQ005659 JQ005746CBS 125957, NB 145 Dracaena, leaf spots Netherlands JQ005226 JQ005313 JQ005400 JQ005487 JQ005574 JQ005660 JQ005747C. phyllanthi CBS 175.67, MACS 271* Phyllanthus acidus, anthracnose India JQ005221 JQ005308 JQ005395 JQ005482 JQ005569 JQ005655 JQ005742C. torulosum CBS 128544, ICMP 18586* Solanum melongena New Zealand JQ005164 JQ005251 JQ005338 JQ005425 JQ005512 JQ005598 JQ005685CBS 102667 Passiflora edulis, leaf blotch New Zealand JQ005165 JQ005252 JQ005339 JQ005426 JQ005513 JQ005599 JQ005686Colletotrichum sp. CBS 123921, MAFF 238642 Dendrobium kingianum Japan JQ005163 JQ005250 JQ005337 JQ005424 JQ005511 JQ005597 JQ0056841 CBS: Culture collection of the Centraalbureau voor Schimmelcultures, Fungal Biodiversity Centre, Utrecht, The Netherlands; IMI: Culture collection of CABI Europe UK Centre, Egham, UK; MAFF: MAFF Genebank Project, Ministry of Agriculture, Forestryand Fisheries, Tsukuba, Japan; BRIP: Plant Pathology Herbarium, Department of Employment, Economic, Development and Innovation, Queensland, Australia; ICMP: International Collection of Microorganisms from Plants, Auckland, New Zealand; STE-U:Culture collection of the Department of Plant Pathology, University of Stellenbosch, South Africa; MACS: MACS Collection of Microorganisms, Pune, India; * ex-holotype or ex-epitype cultures.4
The Colletotrichum boninense species complexcomplex were detected in blastn searches in GenBank. Yang et al.(2011) recently reported C. boninense from Pleione bulbocodioidesand Oncidium flexuosum (Orchidaceae) in China and described arelated species, C. karstii that occurs on several orchids in China.Conidia of C. boninense s. lat. are similar to those of C.gloeosporioides, differing only slightly in length/width ratio andin the presence of a prominent scar at the base of the conidium(Moriwaki et al. 2003). Isolates of C. boninense have often beenidentified as C. gloeosporioides in the past (Moriwaki et al. 2002,2003, Johnston et al. 2005). Von Arx (1957) listed approximately600 synonyms of C. gloeosporioides and nine formae speciales,and it is likely that some of these refer to C. boninense.The ITS1 phylogeny in the paper of Moriwaki et al. (2003) showsconsiderable infraspecific variation. Some of the strains acceptedby these authors as C. boninense are referable to the segregatespecies recognised in this paper. Lubbe et al. (2004) recognisedtwo subgroups but considered both as C. boninense. Groupingwithin C. boninense was also detected by phylogenies of strainsfrom New Zealand (Johnston & Jones 1997, Johnston et al. 2005)showing several clades, with some developing sexual morphs (seeHyde et al. 2009). These data indicate that C. boninense representsa species complex. In this paper, we characterise species withinthe C. boninense species complex morphologically and by meansof multi-gene analysis.MATERIALS AND METHODSIsolatesIsolates comprised those previously identified as C. boninenseas well as other related cultures from the CBS culture collection.The type specimens of the species studied are located in thefungaria (dried fungus collections) of the Centraalbureau voorSchimmelcultures (CBS), Utrecht, The Netherlands, the BotanischeStaatssammlung München (M), Germany and the Royal BotanicGardens, Kew (K(M)), United Kingdom which now incorporatesthe CABI dried collection (IMI). The culture dried down to serveas epitype specimen of C. petchii, was selected from the culturecollection of the CBS. All descriptions are based on either the exholotypeor ex-epitype culture. Features of other isolates are addedif they deviated from the ex-holotype and ex-epitype isolates.Subcultures of the types and epitypes, as well as all other isolatesused for morphological and sequence analyses, are maintainedin the culture collections of CBS, IMI and/or ICMP (InternationalCollection of Microorganisms from Plants, Landcare Research,Auckland, New Zealand), and their data are presented in Table 1.Morphological analysisTo enhance sporulation, 5-mm-diam plugs from the margin ofactively growing cultures were transfered to the centre of 9-cmdiamPetri dishes containing synthetic nutrient-poor agar medium(SNA; Nirenberg 1976) amended with autoclaved filter paper anddouble-autoclaved stems of Anthriscus sylvestris placed onto theagar surface. The strains were also studied after growth on OA(oatmeal agar, Crous et al. 2009) or 2 % PDA (Difco potato-dextroseagar). Cultures were incubated at 20 °C under near UV light witha 12 h photoperiod for 10 d. Measurements and photographsof characteristic structures were made according to methodsdescribed by Damm et al. (2007). Appressoria on hyphae wereobserved on the reverse side of colonies grown on SNA plates.Microscopic preparations were made in clear lactic acid, with 30measurements per structure, and observed with a Nikon SMZ1000dissecting microscope (DM) or with a Nikon Eclipse 80i microscopeusing differential interference contrast (DIC) illumination. Colonycharacters and pigment production on SNA and OA incubated at20 °C were noted after 10 d. Colony colours were rated accordingto Rayner (1970). Growth rates were measured after 7 and 10 d.Phylogenetic analysisGenomic DNA of the isolates was extracted using the method ofDamm et al. (2008). The 5.8S nuclear ribosomal gene with the twoflanking internal transcribed spacers (ITS), a 200-bp intron of theglyceraldehyde-3-phosphate dehydrogenase (GAPDH), and partialsequences of the actin (ACT), chitin synthase 1 (CHS-1), betatubulin(TUB2), histone3 (HIS3) and calmodulin (CAL) genes wereamplified and sequenced using the primer pairs ITS-1F (Gardes &Bruns 1993) + ITS-4 (White et al. 1990) or V9G (de Hoog & Gerritsvan den Ende 1998) + ITS-4, GDF1 + GDR1 (Guerber et al. 2003),ACT-512F + ACT-783R (Carbone & Kohn 1999), CHS-354R +CHS-79F (Carbone & Kohn 1999), BT2Fd + BT4R (Woudenberget al. 2009) or T1 (O’Donnell & Cigelnik 1997) + Bt-2b (Glass &Donaldson 1995), CYLH3F + CYLH3R (Crous et al. 2004b) andCAL 228F + CAL 737R (Carbone & Kohn 1999), respectively.The PCRs were performed in a 2720 Thermal Cycler (AppliedBiosystems, Foster City, California) in a total volume of 12.5 μL.The GAPDH, ACT, CHS-1, TUB2, HIS3 and CAL PCR mixturecontained 1 μL 20x diluted genomic DNA, 0.2 μM of each primer,1x PCR buffer (Bioline, Luckenwalde, Germany), 2 mM MgCl 2, 20μM of each dNTP, 0.7 μL DMSO and 0.25 U Taq DNA polymerase(Bioline). Conditions for amplification were an initial denaturationstep of 5 min at 94 o C, followed by 40 cycles of 30 s at 94 o C, 30 sat 52 o C and 30 s at 72 o C, and a final denaturation step of 7 min at72 o C. The ITS PCR was performed as described by Woudenberget al. (2009). The DNA sequences obtained from forward andreverse primers were used to obtain consensus sequences usingBionumerics v. 4.60 (Applied Maths, St-Martens-Latem, Belgium),which were added to the outgroup (C. gloeosporioides CBS112999) and the alignment assembled and manually adjustedusing Sequence Alignment Editor v. 2.0a11 (Rambaut 2002).To determine whether the seven sequence datasets werecongruent and combinable, tree topologies of 70 % reciprocalNeighbour-Joining bootstrap with Maximum Likelihood distances(10000 replicates) with substitution models determined separatelyfor each partition using MrModeltest v. 2.3 (Nylander 2004) werecompared visually (Mason-Gamer & Kellogg 1996). A maximumparsimony analysis was performed on the multilocus alignment (ITS,ACT, TUB2, CHS-1, GAPDH, HIS3, CAL) with PAUP (PhylogeneticAnalysis Using Parsimony) v. 4.0b10 (Swofford, 2000) using theheuristic search option with 100 random sequence additions andtree bisection and reconstruction (TBR) as the branch-swappingalgorithm. Alignment gaps were treated as missing and allcharacters were unordered and of equal weight. The robustness ofthe trees obtained was evaluated by 500 bootstrap replications withtwo random sequence additions (Hillis & Bull 1993). Tree length,consistency index (CI), retention index (RI), rescaled consistencyindex (RC) and homoplasy index (HI) were calculated for theresulting tree. A Markov Chain Monte Carlo (MCMC) algorithm wasused to generate phylogenetic trees with Bayesian probabilitiesusing MrBayes v. 3.1.1 (Ronquist & Huelsenbeck 2003) for thewww.studiesinmycology.org5
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The Colletotrichum acutatum species
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Damm et al.Table 3. Appressoria mea
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Damm et al.Fig. 25. Colletotrichum
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Damm et al.to olivaceous grey, filt
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Damm et al.are formed directly from
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Damm et al.Arx JA von (1957). Die A
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Damm et al.Masaba DM, Waller JM (19
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Weir et al.Table 1. A list of strai
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Weir et al.Table 1. (Continued).Spe
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Weir et al.11ICMP 17789 Malus USA1I
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Weir et al.Kahawae cladeC. alataeC.
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Weir et al.A0.991ICMP 17905 Coffea
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Weir et al.Conidial width variation
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Weir et al.G. c.“f.sp. camelliae
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Weir et al.Fig. 10. Colletotrichum
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Weir et al.Fig. 18. Glomerella cing
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Weir et al.Notes: First described f
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Weir et al.gossypii var. cephalospo
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Weir et al.Simmonds JH (1968). Type
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Cannon et al.182
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Cannon et al.In rare instances, Col
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Cannon et al.Table 1. (Continued).P
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Cannon et al.Table 2. Colletotrichu
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Cannon et al.as did those for Colle
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Cannon et al.Table 3. Authentic seq
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Cannon et al.110.74 C. cuscutae IMI
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Cannon et al.C. lindemuthianum AB08
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Cannon et al.Hawksworth DL (2011).
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Studies in MycologyStudies in Mycol
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CBS Biodiversity SeriesNo. 11:Taxon
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Studies in Mycology (ISSN 0166-0616
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