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

More documents

Recommendations

Info

Damm et al.combined sequence datasets. Models of nucleotide substitutionfor each gene determined by MrModeltest v. 2.3 were included foreach gene partition. The analyses of two MCMC chains were runfrom random trees for one million generations and sampled every100 generations. The likelihood score of the two runs were 2 730and 2 170 and therefore, the first 2 450 (the average of both) treeswere discarded as the burn-in phase of the analysis and posteriorprobabilities determined from the remaining trees. Sequencesderived in this study were lodged at GenBank, the alignmentin TreeBASE (www.treebase.org), and taxonomic novelties inMycoBank (Crous et al. 2004a).RESULTSPhylogenyThe seven sequence datasets did not show any conflicts in treetopology for the 70 % reciprocal bootstrap trees, which allowed usto combine them. In the multigene analyses (gene boundaries ofITS: 1–561, GAPDH: 572–864, CHS-1: 875–1154, HIS3: 1164–1562, ACT: 1573–1851, TUB2: 1862–2363, CAL: 2374–2823) of87 isolates of C. boninense and related Colletotrichum speciesincluding the outgroup, 2 823 characters including the alignmentgaps were processed, of which 572 characters were parsimonyinformative,247 parsimony-uninformative and 2004 constant. Aftera heuristic search using PAUP, 958 most parsimonious trees wereretained (length = 1423 steps, CI = 0.740, RI = 0.927, RC = 0.686,HI = 0.260) of which one is shown in Fig. 1. The topology of the 958trees was similar, which was verified for a large selection of trees.They differed in the position of taxa within the subclades and in theposition of strain CBS 130241. For Bayesian analysis, a HKY+Gmodel was selected for ACT and CAL, SYM+I+G for ITS, K80+I+Gfor CHS-1, GTR+I+G for HIS3, and HKY+I for GAPDH and TUB2,and incorporated in the analysis. The consensus tree obtainedfrom Bayesian analyses confirmed the tree topology obtained withparsimony as well as the bootstrap support (Fig. 1).The analyses resulted in the detection of 18 clades, whichwe accept as representing different Colletotrichum species.More than half of all strains included cluster in the first clade (C.karstii) with a bootstrap support of 96 % and a Bayesian posteriorprobability value of 1.00. Two single strain clades, representingC. phyllanthi and C. annellatum, group with this big clade with abootstrap support/Bayesian posterior probability value of 96/0.99and 100/1.00, respectively. The C. petchii clade is well supported(100/1.00) and forms a sister clade to the first three species. Theclade representing C. novae-zelandiae consists of two strains ona long branch (100/1.00). In contrast, the following five clades areshort-branched, namely C. boninense s. str. (95/1.00), C. torulosum(100/1.00), C. cymbidiicola (96/1.00), C. oncidii (100/1.00) and aclade containing an unnamed single strain (CBS 123921). Thesefive species form a sister clade (100/1.00) to another well supported(100/1.00) clade formed by two single strain clades, C. beeveriand C. brassicicola, and the C. colombiense clade (100/1.00)containing two strains. The clades representing C. hippeastri andC. brasiliense consist of three and two strains respectively, andare well supported (100/1.00). They group (100/1.00) with a singlestrain clade (C. parsonsiae). The C. constrictum clade (100/1.00)containing two strains and the single strain clade representing C.dacrycarpi are on very long branches and group with a Bayesianposterior probability value of 1.00.The individual alignments and trees of the seven single geneswere compared as well with respect to their performance in speciesrecognition. With ITS and CHS-1 only 7 and 9 species can berecognised, with TUB2 some species close to C. boninense cannot be separated, while with HIS3 and CAL some species onlydiffer in one or two bp and form no or only short-branched clades.With GAPDH all clades are recognised, but some are also shortbranched,especially the single strain clades C. beeveri and C.brassicicola that are well differentiated with almost all other genesexcept for ITS. With ACT the intraspecific variability is very high insome species, which could lead to misidentifications.TaxonomyThe 86 isolates studied (Table 1) are assigned to 18 species withinthe Colletotrichum boninense complex based on DNA sequencedata and morphology, including 12 species that are new to science.Ten species form teleomorph stages in vitro, four species haveknown anamorphs described in Colletotrichum, while one species,G. phyllanthi, has a known teleomorph and is shown here asbelonging to the Colletotrichum boninense species complex. Allspecies studied in culture are characterised below.Species of Colletotrichum represent anamorphic stages ofGlomerella. Anamorph and telemorph names of fungi will haveequal status under the International Code of Nomenclature foralgae, fungi, and plants (formerly the International Code forBotanical Nomenclature), with the deletion of Art. 59, which takeseffect on 1 Jan. 2013. The decision was qualified by a stipulationthat uptake of names of anamorphic genera that predate well-knowncompeting teleomorphic names should be ratified by a committeeof the International Commission for the Taxonomy of Fungi. Thename Colletotrichum (Corda 1831) predates Glomerella (Spauld.& H. Schrenk 1903) and is more commonly used. Consequentlywe name the new holomorphs as species of Colletotrichum and wedo not name the new sexual morphs separately. Furthermore, G.phyllanthi is combined in Colletotrichum as C. phyllanthi. There isprecedent for this as Rojas et al. (2010) described Colletotrichumignotum as having a teleomorph (see Rojas et al. 2010: figs 44–47,table III), although the teleomorphic structures were not included inthe formal species diagnosis.Colletotrichum annellatum Damm, P.F. Cannon & Crous,sp. nov. MycoBank MB560734. Fig. 2.Etymology: The name refers to the proliferation of conidiogenouscells, which appear annellate.Teleomorph developed on SNA. Ascomata ovoid to obpyriform,medium to dark brown, 180–220 × 100–150 µm, glabrous,ostiolate, neck hyaline to pale brown, wall 5–10 µm thick, outerlayer composed of flattened medium brown angular cells, 5–10 µmdiam. Interascal tissue composed of paraphyses, hyaline, septate,branched at the base, disintegrating quickly, 35–55 µm long, base3–4.5 µm diam, apically free, the apex rounded. Asci cylindricalto clavate, 58–74 × 11–16 µm, 8-spored. Ascospores arrangedbiseriately, hyaline, smooth-walled, aseptate, cylindrical to narrowlyfabiform, straight or rarely very slightly curved, both sides rounded,(13.5–)15–17(–18.5) × 5–6 µm, mean ± SD = 16.0 ± 1.1 × 5.6 ±0.4 µm, L/W ratio = 2.9.Teleomorph developed on Anthriscus stem. Ascomata ovoidto obpyriform, medium brown. Asci cylindrical to clavate, 60–706
The Colletotrichum boninense species complex10 changes1001.001.001.00991.001001.001001.00921.00951.00731.0099 CBS 1298331.00 CBS 129834CBS 125468MAFF 305973CBS 128524MAFF 306204CBS 129832CBS 1275950.99 CBS 125388CBS 127591CBS 1298150.99 CBS 128552CBS 1298291.00 CBS 130235MAFF 305998CBS 118401CBS 508.97CBS 124969CBS 1249511.00 CBS 1130871.00 CBS 486.97CBS 112982CBS 861.72CBS 110779CBS 127535CBS 129830CBS 127536CBS 128500CBS 127596CBS 127597CBS 12854896 CBS 1285451.00 CBS 1285510.99 CBS 111860CBS 111998CBS 112762CBS 115535CBS 12992796 CBS 1265320.99 CBS 12854090 CBS 1298241.00 CBS 124956100 CBS 1275521.00 CBS 1298221.001.00CBS 128550CBS 106.91CBS 175.67CBS 129826CBS 378.94CBS 379.94CBS 118774CBS 1181931001.0087 CBS 1259571.00 100 CBS 1285051.00 CBS 13024099 CBS 1237551.00 CBS 123756MAFF 306162CBS 128549CBS 128506CBS 128546CBS 128547CBS 112115CBS 129831CBS 128526CBS 123921C. karstiiC. phyllanthiC. annellatumC. petchiiC. novae-zelandiaeC. boninense861.00Colletotrichum sp.100 CBS 128544100 1.00C. torulosumCBS 1026671.00 IMI 34792396 CBS 128543C. cymbidiicola91 1.00 CBS 1237571.00 100 CBS 129828C. oncidii1.00 CBS 130242CBS 128527C. beeveri100 100 CBS 1298171.00 1.00C. colombienseCBS 129818CBS 101059 C. brassicicola100 CBS 1253771.00 CBS 125376C. hippeastriCBS 241.78CBS 128525C. parsonsiae100 CBS 1285281.00 CBS 128501C. brasilienseCBS 130241C. dacrycarpi100 CBS 1285031.00C. constrictumCBS 128504CBS 112999 C. gloeosporioidesFig. 1. One of 958 most parsimonious trees obtained from a heuristic search of the combined ITS, GAPDH, CHS-1, ACT, HIS3, TUB2 and CAL sequences alignment of theColletotrichum boninense species complex. Bootstrap support values (500 replicates) above 70 % (bold) and Bayesian posterior probability values above 0.95 are shown at thenodes. Colletotrichum gloeosporioides CBS 112999 is used as outgroup. Numbers of ex-type and ex-epitype strains are emphasised in bold.www.studiesinmycology.org7
Page 1: Studies in Mycology 73 (September 2
Page 5 and 6: Colletotrichum: complex species or
Page 10 and 11: Damm et al.Table 1. Strains of Coll
Page 12 and 13: Damm et al.Table 1. (Continued).Gen
Page 16 and 17: Damm et al.Fig. 2. Colletotrichum a
Page 19 and 20: The Colletotrichum boninense specie
Page 45 and 46: available online at www.studiesinmy
Page 47 and 48: The Colletotrichum acutatum species
Page 65 and 66:
The Colletotrichum acutatum species
Page 67 and 68:
Page 69 and 70:
Page 71 and 72:
Page 73 and 74:
Page 75 and 76:
Page 77 and 78:
Page 79 and 80:
Page 81 and 82:
Page 83 and 84:
Page 85 and 86:
Page 87 and 88:
Page 89 and 90:
Page 91:
Page 94 and 95:
Damm et al.µm diam. Setae not obse
Page 96 and 97:
Damm et al.Table 2. Conidia measure
Page 98 and 99:
Damm et al.Table 2. (Continued).Spe
Page 100 and 101:
Damm et al.Table 3. Appressoria mea
Page 102 and 103:
Damm et al.Fig. 25. Colletotrichum
Page 104 and 105:
Page 106 and 107:
Page 108 and 109:
Page 110 and 111:
Page 112 and 113:
Page 114 and 115:
Damm et al.to olivaceous grey, filt
Page 116 and 117:
Damm et al.are formed directly from
Page 118 and 119:
Damm et al.Arx JA von (1957). Die A
Page 120 and 121:
Damm et al.Masaba DM, Waller JM (19
Page 122 and 123:
114
Page 124 and 125:
Weir et al.grass-inhabiting species
Page 126 and 127:
Weir et al.Table 1. A list of strai
Page 128 and 129:
Weir et al.Table 1. (Continued).Spe
Page 130 and 131:
Weir et al.Table 1. (Continued).Spe
Page 132 and 133:
Weir et al.Table 2. Primers used in
Page 134 and 135:
Weir et al.11ICMP 17789 Malus USA1I
Page 136 and 137:
Weir et al.Kahawae cladeC. alataeC.
Page 138 and 139:
Weir et al.A0.991ICMP 17905 Coffea
Page 140 and 141:
Weir et al.Conidial width variation
Page 142 and 143:
Weir et al.G. c.“f.sp. camelliae
Page 144 and 145:
Weir et al.Fig. 10. Colletotrichum
Page 146 and 147:
Page 148 and 149:
Page 150 and 151:
Page 152 and 153:
Page 154 and 155:
Weir et al.Fig. 18. Glomerella cing
Page 156 and 157:
Weir et al.images under C. fructico
Page 158 and 159:
Weir et al.Specimen examined: Thail
Page 160 and 161:
Page 162 and 163:
Weir et al.Notes: First described f
Page 164 and 165:
Weir et al.gossypii var. cephalospo
Page 166 and 167:
Weir et al.to utilise either citrat
Page 168 and 169:
Page 170 and 171:
Weir et al.(ex-epitype culture CBS
Page 172 and 173:
Weir et al.of this species to C. ps
Page 174 and 175:
Page 176 and 177:
Page 178 and 179:
Page 180 and 181:
Page 182 and 183:
Page 184 and 185:
Weir et al.Table 4. Performance of
Page 186 and 187:
Weir et al.Crous PW, Gams W, Stalpe
Page 188 and 189:
Weir et al.Simmonds JH (1968). Type
Page 190 and 191:
Cannon et al.182
Page 192 and 193:
Cannon et al.In rare instances, Col
Page 194 and 195:
Cannon et al.Table 1. Summary of pr
Page 196 and 197:
Cannon et al.Table 1. (Continued).P
Page 198 and 199:
Cannon et al.Table 2. Colletotrichu
Page 200 and 201:
Cannon et al.as did those for Colle
Page 202 and 203:
Cannon et al.Table 3. Authentic seq
Page 204 and 205:
Cannon et al.Table 3. (Continued).S
Page 206 and 207:
Page 208 and 209:
Page 210 and 211:
Cannon et al.110.74 C. cuscutae IMI
Page 212 and 213:
Cannon et al.Boninense cladeThe bon
Page 214 and 215:
Cannon et al.C. lindemuthianum AB08
Page 216 and 217:
Cannon et al.A further important ac
Page 218 and 219:
Cannon et al.Hawksworth DL (2011).
Page 220 and 221:
Cannon et al.Rodríguez-Guerra R, R
Page 223 and 224:
Studies in MycologyStudies in Mycol
Page 225 and 226:
CBS Biodiversity SeriesNo. 11:Taxon
Page 227:
Studies in Mycology (ISSN 0166-0616
show all

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

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?