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

More documents

Recommendations

Info

Weir et al.Fig. 36. Colletotrichum ti. A. ICMP 19444. B. ICMP 4832 – ex-holotype culture. C. ICMP 5285. Cultures on PDA, 10 d growth from single conidia, from above and below.Fig. 37. Colletotrichum tropicale. A. ICMP 18653 (ex CBS 124949 – ex-holotype culture). B. ICMP 18651 (ex CBS 124943). C. ICMP 18672 (ex MAFF 239933). Cultures onPDA, 10 d growth from single conidia, from above and below.172
The Colletotrichum gloeosporioides species complexSpecimens examined: Japan, Okinawa, on Litchi chinensis leaf (MAFF 239933 =ICMP 18672). Panama, Barro Colardo Monument, on Theobroma cacao leaf, coll.E.I. Rojas, L.C. Mejía, Z. Maynard 5101, 2008 (ex-holotype culture – CBS 124949= ICMP 18653); Escobal, Chiriqui, on Annona muricata fruit rot, coll. E.I. Rojas GJS08-42 (CBS 124943 = ICMP 18651).* Colletotrichum xanthorrhoeae R.G. Shivas, Bathgate &Podger, Mycol. Res. 102: 280. 1998. Fig. 38.Shivas et al. (1998) provide a description. One of the isolateswe examined (ICMP 17820) formed fertile perithecia in culture,a feature not mentioned in the original description. Peritheciaare dark-walled, globose with a prominent, narrow neck, wallcomprising several layers of pseudoparenchymatous cells 8–15µm diam, with several layers of densely packed hyphae outsidethis. Asci 75–100 × 10–12 µm, 8-spored. Ascospores (17–)18.5–20(–22) × (5–)5.5–6 µm (av. 19.4 × 5.6 µm, n = 24), more or lesselliptic, tapering to narrow, rounded ends, in side view flattened onone side, but generally not curved.Genetic identification: ITS sequences distinguish C. xanthorrhoeaefrom all other species.Notes: This pathogen of Xanthorrhoea has a distinctive morphology,with a very slow growth rate in culture and large conidia which tapertowards the basal end. The ascospore shape is distinct to that ofmost taxa within the C. gloeosporioides group, which typically havebent or curved ascospores.Specimens examined: Australia, Western Australia, Melville, on Xanthorrhoeapreissii leaf spots, coll. F.D. Podger, Jan. 1994 (ex-holotype culture − BRIP 45094= ICMP 17903 = CBS 127831); Queensland, Cunningham’s Gap, Main RangesNational Park, on Xanthorrhoea sp. leaf spot (IMI 350817a = ICMP 17820).DISCUSSIONThe species that we accept in the Colletotrichum gloeosporioidesspecies complex together form a strongly supported clade in theColletotrichum ITS gene tree (fig. 1 in Cannon et al. 2012, this issue).All species are micro-morphologically typical of C. gloeosporioidessensu von Arx (1970) and Sutton (1992). However, morphologyalone cannot unequivocally place an isolate in this complex,making the ITS particularly important for identification at thespecies complex level in Colletotrichum. For example, members ofthe C. boninense species complex (Damm et al. 2012b, this issue)and C. cliviae (Yang et al. 2009) are micro-morphologically similarto species in the C. gloeosporioides complex but genetically distinct(Cannon et al. 2012, this issue). The utility of ITS sequences isenhanced by their strong representation in GenBank, but this canalso be a problem. Nilsson et al. (2006) summarised the frequencyof inaccurately annotated data in GenBank. The diversity oftaxonomic concepts around the name C. gloeosporioides makesthis a particular problem. This is illustrated by the phylogenypresented by Hyde et al. (2010), based on GenBank accessionsof ITS sequences identified as C. gloeosporioides and Glomerellacingulata, that shows the taxa represented belong to many speciesin different Colletotrichum species complexes. See notes under C.boehmeriae, C. crassipes, and C. kahawae subsp. kahawae forspecific examples of misidentified GenBank accessions.The species we accept are based on a phylogenetic speciesconcept, all species forming strongly supported, monophyleticclades within our multigene phylogenies. However, not all terminalclades are recognised as named species. In most cases any wellsupported, within-species phylogenetic structure evident in themulti-gene phylogeny is not resolved consistently in all gene trees.This lack of congruence between gene trees is a signal that thediversity being sampled is below the species level, according tothe logic of the genealogical concordance phylogenetic speciesrecognition (GCPSR) concept (Taylor et al. 2000). Although theconcatenation of gene sequences is a convenient way to presentmultigene data, it masks discordance between individual genephylogenies. An alternative method, using a species-tree approach(Figs 3, 4B, 5B) combines multi-gene data from multiple isolateshypothesised to represent a single species, so that the evolutionaryhistory of the species rather than that of individual isolates isestimated. Fig. 3, shows the results of such an analysis for the C.gloeosporioides complex, Figs 4B and 5B show relationships withinthe Musae and Kahawae clades respectively, at an expandedscale. Posterior probabilities for some of the speciation eventsare low, particularly within the Musae and Kahawae clades. Thismay be because although the species-trees algorithms accountfor incomplete lineage sorting (Heled & Drummond 2010, Chung& Ané 2011), most do not compensate for horizontal gene transfer,reassortment, or introgression. Hybridisation could also resultin discordant gene phylogenies. Hybrids are known in the C.acutatum complex, e.g. Glomerella acutata, a hybrid formed bycrossing C. acutatum and C. fioriniae strains in the laboratory,and a putative hybrid strain between the same two species thathad been collected from terminal crook disease on Pinus in NewZealand, where both species occur in nature (Damm et al. 2012a,this issue). Hybrids also form in the C. gloeosporioides complex,e.g. the Carya and Aeschynomene populations discussed by Cisaret al. (1994), more or less genetically equivalent to our specieswithin the C. gloeosporioides complex.Our taxonomic conclusions are based, of necessity, on thelimited set of genes sampled. Potentially more powerful genes,such as ApMAT and Apn25L (Silva et al. 2012a) may providefiner resolution within the species-level clades that we recognise.However, even with these potentially more informative genes, thelow levels of genetic divergence across the C. gloeosporioidescomplex may always provide a technical challenge (Silva et al.2012a). The low level of diversity within this species complex isreflected by the branch lengths in fig. 2, Cannon et al. (2012, thisvolume), and is especially true across the Musae clade, whereaverage pairwise identity between all isolates treated in our 5gene alignment is 98.6 %. Pairwise identity between isolates ofC. siamense and C. theobromicola, two species showing strongwithin-species phylogenetic structure, are 99.4 % and 99.6%respectively. This suggests that the species recognised within theC. gloeosporioides complex are very recently evolved and Silva etal. (2012b) provide data supporting this. Their hypothesis of recentevolution of host-specialised Colletotrichum populations from moregeneralist fungi was also invoked in relation to the C. acutatumcomplex by Lardner et al. (1999) using the “episodic selection”framework of Brasier (1995).Several of the species we accept contain isolates with divergentlifestyles, for example C. aotearoa, C. clidemiae, C. kahawae, andC. theobromicola. Each of these species includes isolates capableof causing specific diseases. In the case of C. kahawae, recentpathogenicity tests have shown that only some isolates are ableto cause coffee berry disease (Silva et al. 2012a, Silva & Weir,unpubl. data) and that these isolates can be distinguished using GSsequences (this study), Apn25L and MAT1-2-1 (Silva et al. 2012b).Because of the well understood pathogenicity of isolates withinwww.studiesinmycology.org173
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 14 and 15:
Damm et al.combined sequence datase
Page 16 and 17:
Damm et al.Fig. 2. Colletotrichum a
Page 19 and 20:
The Colletotrichum boninense specie
Page 21 and 22:
Page 23 and 24:
Page 25 and 26:
Page 27 and 28:
Page 29 and 30:
Page 31 and 32:
Page 33 and 34:
Page 35 and 36:
Page 37 and 38:
Page 39 and 40:
Page 41 and 42:
Page 43 and 44:
Page 45 and 46:
available online at www.studiesinmy
Page 47 and 48:
The Colletotrichum acutatum species
Page 49 and 50:
Page 51 and 52:
Page 53 and 54:
Page 55 and 56:
Page 57 and 58:
Page 59 and 60:
Page 61 and 62:
Page 63 and 64:
Page 65 and 66:
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 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 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 170 and 171: Weir et al.(ex-epitype culture CBS
Page 172 and 173: Weir et al.of this species to C. ps
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 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

Create successful ePaper yourself

Delete template?

Save as template?