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Cannon et al.C. lindemuthianum AB087222 (Phaseolus - Japan)C. lindemuthianum EU400130 (unknown host - Canada)C. lindemuthianum EU400131 (unknown host - Canada)C. lindemuthianum EU400132 (unknown host - Canada)C. lindemuthianum EU400133 (unknown host - Canada)C. lindemuthianum EU400134 (unknown host - Canada)C. lindemuthianum EU400135 (unknown host - Canada)89C. lindemuthianum AJ301958 (Phaseolus - unknown source)C. lindemuthianum AJ301947 (Phaseolus - USA)C. lindemuthianum (Phaseolus - UK)C. lindemuthianum EU400129 (unknown host - Canada)C. orbiculare AB042309 (Gerbera - Japan)C. orbiculare AB042308 (melon - Japan)C. orbiculare FJ459919 (unknown host - China)C. orbiculare EF570872 (unknown host - China)C. orbiculare AY376541 (Xanthium - Argentina)84C. orbiculare AY841133 (cherimoya - Mexico)85C. orbiculare HM989875 (watermelon - China)C. orbiculare HQ839785 (watermelon - China)C. trifolii AJ301941 (Trifolium - USA)83 C. trifolii EU400136 (unknown host and source)C. trifolii AB087223 (lucerne - Japan)C. trifolii AF451909 (lucerne - Australia)C. trifolii HQ148103 (Echinacea - USA)C. trifolii AJ301942 (Trifolium - Netherlands)61C. destructivum AJ558107 (unknown host and source)C. higginsianum AJ558109 (unknown host and source)71C. fuscum AJ301938 (Digitalis lanata - unknown source)Glomerella glycines AB057435 (unknown host - Japan)64C. paspali EU554100 (Paspalum notatum - unknown source)89C. circinans GU227855 ET99C. dematium GU227819 ET99 C. gloeosporioides EU371022 ET76Glomerella glycines EU520227 (unknown host - China)97 C. boninense JQ005153 HTC. lindemuthianum EF608059 (Phaseolus - Taiwan)Australiasca queenslandica HM2373270.03Fig. 4. Maximum likelihood phylogeny based on an ITS alignment of GenBank accessions of the C. lindemuthianum, C. orbiculare, C. trifolii and C. destructivum speciescomplexes (alignment with ClustalX, 1000 bootstrap replicates, PhyML package).that C. lindemuthianum is a separate lineage from C. orbiculareand C. trifolii, and that it might comprise more than one taxon.An analysis of C. lindemuthianum rDNA data by Balardin et al.(1999) showed that Phaseolus pathogens may occur in numeroussubordinate clades within the lindemuthianum subclade. Thenumber of sequences available is too small for confidence, butit does appear that C. lindemuthianum is specific to Phaseolus.However, none of the sequence data or strains used by Balardinet al. (1999) is available through public databases or collections;therefore these conclusions require further evaluation. There areno full ITS sequences from Colletotrichum malvarum available frompublic databanks, but a study using ITS2/LSU (Bailey et al. 1996)indicated that Colletotrichum species from Malvaceae occupy atleast three subclades within the overall orbiculare clade.Spaethianum cladeThe spaethianum clade receives strong support in both themultilocus and ITS-only analyses (Figs 2, 3). It contains only fivespecies as currently circumscribed, four of which are associatedwith petaloid monocot plants, and none appears to have economicimportance. Its phylogenetic significance is as a sister group tothe graminicola clade. The spaethianum clade was recognisedas a distinct assemblage by Damm et al. (2009) in their work onthe non-grass associated species of Colletotrichum with curvedconidia. Four of the five species in this assemblage have complexappressoria, but the clade does not otherwise have diagnosticcharacteristics in morphological terms.Truncatum cladeThe truncatum clade includes only one major species, C. truncatum(also frequently referred to as C. capsici; Damm et al. 2009), which isreported as an economically destructive pathogen of many tropicalcrops including legumes and solanaceous plants. The truncatumclade occupies a sister position to the combined C. gloeosporioidesand C. boninense clade according to our multilocus analysis (Fig.3), but to the boninense clade only in the ITS-only analysis (Fig.2). Conidial morphology in the truncatum group is quite differentto that found in the gloeosporioides and boninense clades (Dammet al. 2012b, Weir et al. 2012), providing evidence to support theold hypothesis (Sreenivasaprasad et al. 1996) that the evolution ofconidial form followed a complex pattern in Colletotrichum.Colletotrichum curcumae also belongs to this clade, a poorlyknownspecies considered to be the causal agent of turmericleaf spot disease (Curcuma longa, Zingiberaceae; Palarpawar &206
Colletotrichum – current status and future directionsGhurde 1988). The third member of the clade is C. jasminigenum,which was described as a new species causing leaf and blossomanthracnose disease on Jasminum sambac in Vietnam (Wikee etal. 2011).Other taxaOur multilocus tree (Fig. 3) includes various species that areisolated in phylogenetic terms, or form small clusters that do notjustify recognition as major clades.The most important of these species in economic termsis Colletotrichum coccodes. This is primarily a pathogen ofSolanaceae (potato and tomato), but also survives well in soiland is reported as an associate of a wide range of crops includingstrawberry (Buddie et al. 1999, Heilmann et al. 2006). Colletotrichumcoccodes was recently epitypified (Liu et al. 2011). The speciesis known to be variable in genetic terms (Ben-Daniel et al. 2010).It has been researched into as a potential biocontrol agent forAbutilon theophrasti (Dauch et al. 2006). Colletotrichum coccodeshas distinctive conidia that are straight, have acute ends and areoften slightly constricted in the mid portion. Our multilocus analysis(Fig. 3) places it as a sister taxon to the destructivum/spaethianum/graminicola clade. In our ITS-only tree (Fig. 2) it occupies the sameposition, although the posterior probability values are inadequate toconfirm its phylogeny from this gene fragment alone.Colletotrichum trichellum was placed into synonymy with C.dematium by von Arx (1957), though it was treated as a separate,apparently host-limited species by Sutton (1962, 1981) based onthe degree of curvature of the conidia. ITS-only and multilocusphylogenetic analyses (Figs 2, 3) indicate that this species doesnot belong to the dematium clade, but forms a sister clade (alongwith C. rusci) with the acutatum clade.Three poorly-known species occupy basal positions in the ITSonlyand multilocus phylogenetic trees (Figs 2, 3). Colletotrichumcliviae (from anthracnose of Clivia miniata, Amaryllidaceae; Yanget al. 2009) appears to constitute a monophyletic lineage that isa sister clade to the entire genus apart from the orbiculare clade.Colletotrichum yunnanense and C. dracaenophilum togetherform a small clade that is basal to the entire genus apart fromthe combined orbiculare and C. cliviae clade. Colletotrichumdracaenophilum is a stem pathogen of Dracaena species(Asparagaceae; Farr et al. 2006), while C. yunnanense wasisolated as an endophyte of Buxus (Buxaceae; Liu et al. 2007b).According to their publishing authors, all three species haveunusually large conidia. Colletotrichum yunnanense and C.cliviae have complex appressoria; those of C. dracaenophilumwere not recorded by the describing authors.WHERE DO WE GO FROM HERE?What more can we learn about Colletotrichum systematics?Several of the major clades have not yet been analysedcomprehensively using multilocus technologies. The phylogeneticposition of a large part of the species described is still unknown;these species would have to be recollected and epitypified.However, linking new strains to old species is difficult and thereare hundreds of “forgotten species” with little information amongthem. We should therefore focus on clarifying the identity of wellknownspecies that are commonly used and of Glomerella speciesin order to synonymise them in Colletotrichum. New species havebeen discovered regularly over the last five years (including somethat are highly distinct in phylogenetic terms) and novel taxa willdoubtless continue to appear. Studies of Colletotrichum from wildplants would be likely to be particularly fruitful, and provide insightsinto the taxa currently known from crops and ornamentals. It wouldbe presumptuous even to speculate that the overall systematicframework for the genus cannot be improved.Future innovations are likely to focus increasingly onunderstanding populations and host/parasite relationships, and onusing increasingly sophisticated analyses of whole genomes. It isonly then that we are likely to begin to understand Colletotrichumspecies in their evolutionary context, rather than as cultures incollections. The first major output in this new era of Colletotrichumresearch has now been published (O’Connell et al. 2012), devotedto a comparison of the genomes and transcriptomes of twoindividual strains of Colletotrichum, one each from C. graminicola(from Zea mays, Poaceae) and C. higginsianum (from Brassicacapestris, Brassicaceae). Overall genome size and chromosomenumber was found to be broadly similar, but substantial differenceswere noted between the two taxa in intrachromosomal organisationand in their suites of pathogenicity-related genes, These last wereshown to be a reflection of differing host cell wall characteristics;cell walls of Poaceae contain higher quantities of hemicelluloseand phenolic compounds, while those of Brassicaceae are richer inpectins. The two species were estimated as diverging aound 47 Myears ago, well after the divergence of their host clades.Recent changes to the newly renamed International Code ofNomenclature for Algae, Fungi and Plants (Hawksworth 2011),especially those Articles relating to registration of names and theabolition of the dual nomenclature system for Fungi, mark a furtherstep away from the inflexible application of the rules of date prioritytowards a consensus approach for choosing between competingnames. In response to these historic changes, the InternationalSubcommission on Colletotrichum Taxonomy has been set upwithin the framework of the International Commission on theTaxonomy of Fungi (http://www.fungaltaxonomy.org/). Its remitwill be to promote nomenclatural stability for the genus, developconsensus phylogenies, and develop a list of protected names forkey taxa that cannot be overturned by the rediscovery of obscureearlier names within the historical literature. An important partof this work is to ensure that all currently accepted species ofColletotrichum are adequately typified, with epitypes or neotypeslinked to cultures where original type material is lost or inadequatefor modern phylogenetic placement, or where no authentic originalcultures have been preserved.In the context of moving to a single name system for these fungi,probably few would argue for the retention of Glomerella (the later,sexual genus name with priority until the Melbourne nomenclaturalcongress in 2011) over Colletotrichum (the earlier, asexual name),but it will be the responsibility of the Subcommission to weighthe arguments for each and to recommend one or the other.Technically, we are aware that our publication prejudges this issue,but the transfer of such a large number of the names of multiplewell-known economically important species currently acceptedas Colletotrichum to Glomerella would cause chaos amongst theuser community. The issues of synonymy between anamorph andteleomorph at the species level are complex (as exemplified byour knowledge of the identities of Glomerella acutata (Damm etal. 2012a) and Ga. cingulata (Weir et al. 2012), and it will in mostcases be more practical to assign protected status to the asexualspecies names rather than go through the formal nomenclaturalconservation procedures.www.studiesinmycology.org207
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Colletotrichum: complex species or
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Damm et al.Table 1. Strains of Coll
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The Colletotrichum boninense specie
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available online at www.studiesinmy
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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.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.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.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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