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

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Cannon et al.Table 3. (Continued).Species Clade Source material [1] Status of source material GenBank accession number(s) ReferenceC. truncatum truncatum CBS 151.35 Culture from epitype ITS: GU227862; TUB2: GU228156; ACT: GU227960; CHS-1: GU228352; GAPDH:GU228254; HIS3: GU228058; LSU: JN940819C. verruculosum spaethianum IMI 45525 Culture from holotype ITS: GU227806; TUB2: GU228100; ACT: GU227904; CHS-1: GU228296; GAPDH:GU228198; HIS3: GU228002C. walleri acutatum CBS 125472 Culture from holotype ITS: JQ948275; TUB2: JQ949926; ACT: JQ949596; CHS-1: JQ948936; GAPDH:JQ948605; HIS3: JQ949266C. xanthorrhoeae gloeosporioides BRIP 45094, ICMP 17903,CBS127831C. yunnanense CGMCC AS3.9167, CBS132135ARSEF: ARS Collection of Entomopathogenic Fungal Cultures, Ithaca, NY, USA.Culture from holotype ITS: GU048667, GU174551, JX010261; TUB2: JX010448; ACT: JX009478; CHS-1:JX009823; GAPDH: GU174563, JX009927; CAL: JX009653; GS: JX010138; SOD2:JX010369; TEF1: GU174575Damm et al. (2009), Schoch et al.(2012)Damm et al. (2009)Damm et al. (2012a)Hyde et al. (2009), Weir & Johnston(2010), Weir et al. (2012)Culture from holotype ITS: EF369490 ; TUB2: JX519248; ACT: JX519239; CHS-1: JX519231 Liu et al. (2007b), this studyBBA: Culture collection of the Biologische Bundesanstalt für Land- und Forstwirtschaft, Berlin, Germany.BPI: Systematic Mycology and Microbiology Laboratory, USDA Agricultural Research Service, Beltsville, MD, USA.BRIP: Culture Collection of the DPI&F Plant Pathology Herbarium, Indooroopilly, Queensland, Australia.CBS: Culture collection of the Centraalbureau voor Schimmelcultures, Fungal Biodiversity Centre, Utrecht, The Netherlands.CGMCC: China General Microbiological Culture Collection Center, Beijing, China.ICMP: International Collection of Microorganisms from Plants, Landcare Research, Auckland, New Zealand.IMI: Culture collection of CABI Europe UK Centre, Egham, UK.M1.001: sourced from Lisa Vaillancourt, University of Kentucky.MAFF: NIAS Genebank, Microorganism Section, Tsukuba, Japan.MFU: fungarium of Mae Fah Luang University, Thailand (cultures in BCC (BIOTEC Culture Collection, Thailand).NBRC: NITE Biological Resource Center, Chiba, Japan.STE-U: Culture collection of the Department of Plant Pathology, University of Stellenbosch, South Africa.[1] Where possible, all taxa are represented by sequences from type or other authentic material. For some however, the necessary research to identify such cultures and/or to designate epitype material is not complete, especially for species within thedestructivum and orbiculare clades. To be able to generate robust phylogenetic trees for the entire genus (Figs 2, 3) that include all of the major clades, we have used sequences from some strains that have been used to represent the relevant species(mostly in recent literature) but which do not currently have any special nomenclatural status. Their details are included in Table 3 for reference, and can be recognised with ”none” in the type status column. It may be that some or all of these strains will bedesignated as epitypes in the future, but for the present it should not be assumed that they represent the species as originally circumscribed.[2] KS20BIG was one of four epitypes designated by Crouch et al. (2006) for C. cereale; the application of the name needs to be more precisely established.[3] Preliminary multilocus analysis suggests that C. chrysanthemi may not be a synonym of C. carthami as stated by Uematsu et al. (2012).[4] These sequences derive from one of two authentic but not genetically identical strains; the species was not epitypified as neither of them are now fertile.[5] A further collection from which a culture was obtained (CBS 131301) was designated as an epitype by Crouch et al. (2006) and recognised as representative of the species also by Du et al. (2005) and Crouch et al. (2009d). It was subsequently confirmedas closely similar to the lectotype based on multilocus DNA sequence analysis (Crouch & Tomaso-Peterson 2012).200
Colletotrichum – current status and future directionsMultilocus phylogenies are now typically used as the primarybasis on which to describe new species of Colletotrichum (seeTable 1) and the trend is to include more and more sequencesinto the analyses. One might conclude that phylogenetic signal isstrongly correlated with the number of characters (in this case basepairs) included in the analysis, a position first advanced nearly 250years ago (Adanson 1763), but genes are differential at varyingpositions in the hierachy of taxa. Inclusion of multiple genes thatresolve at similar positions in the hierarchy can therefore increasethe size (not to mention the cost) of the data set without clarifyingthe phylogenetic signal. This is highly relevant to species diagnosis,as was observed by Min & Hickey (2007) in a study of mitochondrialgenes from 31 fungi of widely varying taxonomic position todetermine the optimum sequence length for robust identification.Research by Dentinger et al. (2010a) showed that both bootstrapsupport and Bayesian posterior probability values were eroded in amultilocus ATP6/LSU/RPB1 analysis of Boletus species comparedwith an analysis based on RPB1 alone. Similar results wereobtained by Walker et al. (2012) in a study on two genera of theDiaporthales. They found in an analysis of Ophiognomonia speciesthat adding TEF1 sequence data to any combination of three ofthe other loci used (ITS, Tub2, FG1093 and MS204) decreasedsupport and increased the number of tree topologies recovered.Our own preliminary studies on Colletotrichum (data not shown)also indicate that in some circumstances, increasing the number ofloci may decrease phylogenetic performance, although the effectis minor. Taken together, these data suggest that the recent fungalphylogenetic “arms race”, whereby a steadily increasing number ofloci are analysed in concert, may add complexity but not improveinsight.MAJOR CLADESPhylogenetic analysis of the genus Colletotrichum reveals that itcomprises nine major clades, as well as a number of small clustersand isolated species (Figs 2, 3).There is currently no universally accepted process for namingclades and reconciling them with the traditional taxonomiccategories of the International Code of Nomenclature for Algae,Fungi and Plants (ICNAFP), although the draft PhyloCode(http://www.ohio.edu/phylocode/) represents a major step inthis direction. Formal recognition of infrageneric categorieswithin Colletotrichum is highly desirable. This is for phylogeneticreasons, in that the genus contains many monophyletic subunitswith common characteristics (not least in spore morphology).There are also pragmatic reasons for defining such categories,for example to allow linkage to the immense historical bodyof pathological literature in which the fungal subjects are notassignable to currently accepted species.Use of the strictly hierarchical infrageneric nomenclaturesystem in the ICNAFP is a possible way to assign formal names tospecies groups within Colletotrichum. However, although the Codeallows for extra categories to be interspersed between the threeformal ranks (subgenus, section and series), their adoption impliesan equality of taxa at the same rank that is not reconcilable withevolutionary processes. We therefore favour a formal (or at leastsemi-formal) clade-based nomenclature system.In this paper, we refer to 119 Colletotrichum species (Table 3)that collectively encompass almost all of the known phylogeneticvariety within the genus, most of them belonging to one of thenine major clades. Additionally, there is a number of small clustersand isolated species, which we believe to represent independentevolutionary units, but which are insufficiently well known to justifyformal nomenclatural recognition. Throughout this paper, we referto these clades using the specific epithet of the first-recognised(or historically most prominent) of their constituent species – forexample the acutatum clade is the monophyletic unit containingC. acutatum and its close relatives (see Fig. 3). An obviousshortcoming of this system is that there is no objective methodof deciding which is the basal node of the named clade. In thecase of the acutatum clade, we have decided that the clade hasC. orchidophilum as its sister taxon, because the ingroup taxa aremuch more closely related to each other than to C. orchidophilumor C. pseudoacutatum, but there are arguments for extending theclade to include this species, and indeed also C. pseudoacutatum.The species in the graminicola clade are much less closely relatedthan those of the C. acutatum clade; the decision for combiningthem was made rather on the basis of common morphology andhost family. The process is to some extent subjective, so while wecommend adoption of the nine clades detailed below as formalentities, we hope that clade definition and recognition will be takenon as a task by the new ICTF Subcommission on Colletotrichum.In this paper, reference to the term clade indicates that weare confident that the associated information can be referred toour formal clades (or to species within the clades). We also referon occasion to informal groupings of taxa, generally as speciesclusters. In these circumstances, we may know that the knowledgeis associated with a particular species group, but are unsure asto its constituent taxa, or to the phylogenetic extent it represents.This frequently occurs when attempting to relate information frompathology papers to our new phylogeny.Several of the clades indicated in Fig. 3 represent the speciescomplexes as defined by Crouch et al. (2009c, d), Damm et al.(2012a, b, this issue), and Weir et al. (2012, this issue). While thesefour complexes can be confirmed as monophyletic, the assemblageof curved-spored species from herbaceous hosts studied by Dammet al. (2009) can be seen to be polyphyletic; the species included inthat research are placed in three of the formal clades we recognisehere, with additional outliers.In this section, we provide an overview of the nine Colletotrichumclades that we recognise. Several additional individual speciesand small clusters are recognised that do not fall into clear clades(see Fig. 3). The phylogenetic tree presented as Fig. 3 providesa comprehensive visual overview of phylogenetic diversity withinColletotrichum as treated in the current literature, but it seems likelythat there are further outlying taxa that have not yet been sampled,or for which phylogenetic positions have not been fixed effectively.For example, the tea pathogen C. theae-sinensis (Moriwaki et al.2002, Yoshida & Takeda 2006) has unusually small conidia andmay well fall outside of Colletotrichum as outlined in Fig. 3. AlthoughMoriwaki et al. (2002) included a strain of C. theae-sinensis inphylogenies derived from rDNA datasets, the relevant sequencedata from that study are not found in public sequence repositories.Based on these rDNA sequence data, Moriwaki and colleaguessuggested that C. theae-sinensis might constitute a sister group tothe genus, a prediction that needs to be tested further.Acutatum cladeThe acutatum clade is defined as a collective of Colletotrichumacutatum and 29 closely related species (see Fig. 3), with C.www.studiesinmycology.org201
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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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