The Colletotrichum gloeosporioides species complex - CBS - KNAW

Studies in Mycology 

available online at www.studiesinmycology.org 

The Colletotrichum gloeosporioides species complex 

B.S. Weir 1* , P.R. Johnston 1 , and U. Damm 2 

1 Landcare Research, Private Bag 92170 Auckland, New Zealand; 2 CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands 

*Correspondence: Bevan Weir, WeirB@LandcareResearch.co.nz 

Abstract: The limit of the Colletotrichum gloeosporioides species complex is defined genetically, based on a strongly supported clade within the Colletotrichum ITS gene tree. 

All taxa accepted within this clade are morphologically more or less typical of the broadly defined C. gloeosporioides, as it has been applied in the literature for the past 50 years. 

We accept 22 species plus one subspecies within the C. gloeosporioides complex. These include C. asianum, C. cordylinicola, C. fructicola, C. gloeosporioides, C. horii, C. 

kahawae subsp. kahawae, C. musae, C. nupharicola, C. psidii, C. siamense, C. theobromicola, C. tropicale, and C. xanthorrhoeae, along with the taxa described here as new, 

C. aenigma, C. aeschynomenes, C. alatae, C. alienum, C. aotearoa, C. clidemiae, C. kahawae subsp. ciggaro, C. salsolae, and C. ti, plus the nom. nov. C. queenslandicum 

(for C. gloeosporioides var. minus). All of the taxa are defined genetically on the basis of multi-gene phylogenies. Brief morphological descriptions are provided for species 

where no modern description is available. Many of the species are unable to be reliably distinguished using ITS, the official barcoding gene for fungi. Particularly problematic 

are a set of species genetically close to C. musae and another set of species genetically close to C. kahawae, referred to here as the Musae clade and the Kahawae clade, 

respectively. Each clade contains several species that are phylogenetically well supported in multi-gene analyses, but within the clades branch lengths are short because of 

the small number of phylogenetically informative characters, and in a few cases individual gene trees are incongruent. Some single genes or combinations of genes, such as 

glyceraldehyde-3-phosphate dehydrogenase and glutamine synthetase, can be used to reliably distinguish most taxa and will need to be developed as secondary barcodes for 

species level identification, which is important because many of these fungi are of biosecurity significance. In addition to the accepted species, notes are provided for names 

where a possible close relationship with C. gloeosporioides sensu lato has been suggested in the recent literature, along with all subspecific taxa and formae speciales within 

C. gloeosporioides and its putative teleomorph Glomerella cingulata. 

Key words: anthracnose, Ascomycota, barcoding, Colletotrichum gloeosporioides, Glomerella cingulata, phylogeny, systematics. 

Taxonomic novelties: Name replacement - C. queenslandicum B. Weir & P.R. Johnst. New species - C. aenigma B. Weir & P.R. Johnst., C. aeschynomenes B. Weir & P.R. 

Johnst., C. alatae B. Weir & P.R. Johnst., C. alienum B. Weir & P.R. Johnst, C. aotearoa B. Weir & P.R. Johnst., C. clidemiae B. Weir & P.R. Johnst., C. salsolae B. Weir & P.R. 

Johnst., C. ti B. Weir & P.R. Johnst. New subspecies - C. kahawae subsp. ciggaro B. Weir & P.R. Johnst. Typification: Epitypification - C. queenslandicum B. Weir & P.R. 

Johnst. 

Published online: 21 August 2012; doi:10.3114/sim0011. Hard copy: September 2012. 

INTRODUCTION 

The name Colletotrichum gloeosporioides was first proposed 

in Penzig (1882), based on Vermicularia gloeosporioides, the 

type specimen of which was collected from Citrus in Italy. Much 

of the early literature used this name to refer to fungi associated 

with various diseases of Citrus, with other species established for 

morphologically similar fungi from other hosts. However, several 

early papers discussed the morphological similarity between many 

of the Colletotrichum spp. that had been described on the basis of 

host preference, and used inoculation tests to question whether or 

not the species were distinct. Some of these papers investigated 

in culture the link between the various Colletotrichum species and 

their sexual Glomerella state (e.g. Shear & Wood 1907, Ocfemia 

& Agati 1925). Authors such as Shear & Wood (1907, 1913) and 

Small (1926) concluded that many of the species described on the 

basis of host preference were in fact the same, rejecting apparent 

differences in host preference as a basis for taxonomic segregation. 

Small (1926) concluded that the names Glomerella cingulata and 

Colletotrichum gloeosporioides should be used for the sexual and 

asexual morphs, respectively, of the many Colletotrichum spp. 

they regarded as conspecific. Colletotrichum gloeosporioides 

was stated to be the earliest name with a proven link to what they 

Copyright CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands. 

StudieS in Mycology 73: 115–180. 

regarded as a biologically diverse G. cingulata. The studies of 

von Arx & Müller (1954) and von Arx (1957, 1970) taxonomically 

formalised this concept. 

The “von Arxian” taxonomic concept for Colletotrichum 

saw large numbers of species synonymised with the names C. 

graminicola (for grass-inhabiting species) and C. gloeosporioides 

(for non-grass inhabiting species with straight conidia). The 

genetic and biological diversity encompassed by these names 

was so broad that they became of little practical use to plant 

pathologists, conveying no information about pathogenicity, host 

range, or other attributes. The von Arx & Müller (1954) and von 

Arx (1957) studies were not based on direct examination of type 

material of all species and some of the synonymy proposed 

in these papers has subsequently been found to be incorrect. 

Examples include the segregation of C. acutatum (Simmonds 

1965) and C. boninense (Moriwaki et al. 2003) from C. 

gloeosporioides sensu von Arx (1957). Other studies published 

elsewhere in this volume (Damm et al. 2012a, b) show that 

several species regarded as synonyms of C. gloeosporioides 

by von Arx (1957) are members of the C. acutatum complex 

(e.g. C. godetiae, Gloeosporium limetticola, G. lycopersici, and 

G. phormii) or the C. boninense complex (e.g. C. dracaenae). 

Recent molecular studies have resulted in a much better 

understanding of phylogenetic relationships amongst the 

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Weir et al. 

grass-inhabiting species of the C. graminicola group and the 

development of a more useful taxonomy for this group of fungi 

(e.g. Hsiang & Goodwin 2001, Du et al. 2005, and Crouch et 

al. 2006). This group is now recognised as comprising several 

host-specialised, genetically well characterised species, but a 

modern taxonomy for C. gloeosporioides has yet to be resolved. 

Von Arx (1970) and Sutton (1980) distinguished the C. 

gloeosporioides group using conidial shape and size. A few apparently 

host-specialised, C. gloeosporioides-like taxa were retained by these 

authors, but the basis of their identification was often difficult to 

understand. Prior to the availability of DNA sequence data, taxonomic 

concepts within Colletotrichum were based on features such as host 

species, substrate, conidial size and shape, shape of appressoria, 

growth rate in culture, colour of cultures, presence or absence of 

setae, whether or not the teleomorph develops, etc. Some studies 

have found characters such as these useful for distinguishing 

groups within C. gloeosporioides (e.g. Higgins 1926, Gorter 1956, 

Hindorf 1973, and Johnston & Jones 1997). However, problems 

arise because many of these morphological features change under 

different conditions of growth (dependent upon growth media, 

temperature, light regime, etc.), or can be lost or change with repeated 

subculturing. Host preference is poorly controlled — even good, welldefined 

pathogens causing a specific disease can be isolated by 

chance from other substrates (e.g. Johnston 2000). Colletotrichum 

conidia will germinate on most surfaces, form an appressorium, 

remain attached to that surface as a viable propagule or perhaps as 

a minor, endophytic or latent infection, and grow out from there into 

senescing plant tissue or onto agar plates if given the opportunity. 

In addition, the same disease can be caused by genetically distinct 

sets of isolates, the shared pathogenicity presumably independently 

evolved, e.g. the bitter rot disease of apple is caused by members 

of both the C. acutatum and C. gloeosporioides species complexes 

(Johnston et al. 2005). 

Sutton (1992) commented on C. gloeosporioides that “No 

progress in the systematics and identification of isolates belonging 

to this complex is likely to be made based on morphology alone”. 

A start was made towards a modern understanding of this name 

with the designation of an epitype specimen with a culture derived 

from it to stabilise the application of the name (Cannon et al. 2008). 

Based on ITS sequences, the ex-epitype isolate belongs in a 

strongly supported clade, distinct from other taxa that have been 

confused with C. gloeosporioides in the past, such as C. acutatum 

and C. boninense (e.g. Abang et al. 2002, Martinez-Culebras et 

al. 2003, Johnston et al. 2005, Chung et al. 2006, Farr et al. 2006, 

Than et al. 2008). However, biological and genetic relationships 

within the broad C. gloeosporioides clade remain confused and ITS 

sequences alone are insufficient to resolve them. 

In this study we define the limits of the C. gloeosporioides 

species complex on the basis of ITS sequences, the species we 

accept within the complex forming a strongly supported clade 

in the ITS gene tree (fig. 1 in Cannon et al. 2012, this issue). In 

all cases the taxa we include in the C. gloeosporioides complex 

would fit within the traditional morphological concept of the C. 

gloeosporioides group (e.g. von Arx 1970, Mordue 1971, and 

Sutton 1980). Commonly used species names within the C. 

gloeosporioides complex include C. fragariae, C. musae, and C. 

kahawae. Since the epitype paper (Cannon et al. 2008), several 

new C. gloeosporioides-like species have been described in 

regional studies, where multi-gene analyses have shown the new 

species to be phylogenetically distinct from the ex-epitype strain of 

C. gloeosporioides (e.g. Rojas et al. 2010, Phoulivong et al. 2011, 

and Wikee et al. 2011). 

116 

The regional nature of most of these studies, the often restricted 

genetic sampling across the diversity of C. gloeosporioides globally, 

and the minimal overlap between isolates treated and gene regions 

targeted in the various studies, means that the relationship between 

the newly described species is often poorly understood. 

While some authors have embraced a genetically highly 

restricted concept for C. gloeosporioides, many applied researchers 

continue to use the name in a broad, group-species concept (e.g. 

Bogo et al. 2012, Deng et al. 2012, Kenny et al. 2012, Parvin et 

al. 2012, and Zhang et al. 2012). In this paper we accept both 

concepts as useful and valid. When used in a broad sense, we 

refer to the taxon as the C. gloeosporioides species complex or C. 

gloeosporioides s. lat. 

This paper aims to clarify the genetic and taxonomic 

relationships within the C. gloeosporioides species complex using 

a set of isolates that widely samples its genetic, biological and 

geographic diversity. Type specimens, or cultures derived from 

type specimens, have been examined wherever possible. Although 

we do not treat all of the names placed in synonymy with C. 

gloeosporioides or Glomerella cingulata by von Arx & Müller (1954) 

and von Arx (1957, 1970), we treat all names for which a possible 

close relationship with C. gloeosporioides has been suggested in 

the recent literature, along with all subspecific taxa and formae 

speciales within C. gloeosporioides and G. cingulata. 

ITS sequences, the official barcoding gene for fungi (Seifert 

2009, Schoch et al. 2012), do not reliably resolve relationships within 

the C. gloeosporioides complex. We define species in the complex 

genetically rather than morphologically, on the basis of phylogenetic 

analyses of up to eight genes. Following Cannon et al. (2012, this 

issue) the generic name Colletotrichum is used as the preferred 

generic name for all species wherever possible throughout this 

paper, whether or not a Glomerella state has been observed for that 

fungus, and whether or not the Glomerella state has a formal name. 

MATERIALS AND METHODS 

Specimen isolation and selection 

An attempt was made to sample the genetic diversity across C. 

gloeosporioides as widely as possible, with isolates from diverse 

hosts from around the world selected for more intensive study. A 

BLAST search of GenBank using the ITS sequence of the epitype 

culture of C. gloeosporioides (Cannon et al. 2008) provided a 

coarse estimate for the genetic limit of the C. gloeosporioides 

complex and ITS diversity across the complex was used to 

select a genetically diverse set of isolates. Voucher cultures were 

obtained from the research groups who deposited the GenBank 

records. To these were added isolates representing the known 

genetic and morphological diversity of C. gloeosporioides from 

New Zealand, isolated from rots of native and introduced fruits, 

from diseased exotic weeds, and as endophytes from leaves of 

native podocarps. Additional isolates representing ex-type and 

authentic cultures of as many named taxa and formae speciales 

within the C. gloeosporioides complex as possible were obtained 

from international culture collections. Approximately 400 isolates 

belonging to the C. gloeosporioides complex were obtained. 

GAPDH gene sequences were generated for all isolates as an initial 

measure of genetic diversity. A subset of 156 isolates, selected to 

represent the range of genetic, geographic, and host plant diversity, 

was used in this research (Table 1).

Most of the New Zealand isolates had been stored as conidial 

suspensions made from single conidium or ascospore cultures and 

then stored at -80 °C in a 5 % glycerol/water suspension. Additional 

isolates from New Zealand were obtained from the ICMP culture 

collection, where isolates are stored as lyophilised (freeze-dried) 

ampoules or in a metabolically inactive state in liquid nitrogen 

at -196 °C. The storage history of most of the isolates received 

from other research groups is not known. Table 1 lists the isolates 

studied. All those supplying cultures are acknowledged at the 

end of this manuscript, and additional details on each culture are 

available on the ICMP website (http://www.landcareresearch.co.nz/ 

resources/collections/icmp). 

Culture collection and fungal herbarium (fungarium) 

abbreviations used herein are: CBS = Centraalbureau voor 

Schimmelcultures (Netherlands), ICMP = International Collection 

of Microorganisms from Plants, MFLU = Mae Fah Luang University 

Herbarium (Thailand) MFLUCC = Mae Fah Luang University 

Culture Collection (Thailand), GCREC = University of Florida, 

Gulf Coast Research and Education Centre (USA), HKUCC = The 

University of Hong Kong Culture Collection (China), IMI = CABI 

Genetic Resource Collection (UK), MAFF = Ministry of Agriculture, 

Forestry and Fisheries (Japan), DAR = Plant Pathology Herbarium 

(Australia), NBRC = Biological Resource Center, National Institute 

of Technology and Evaluation (Japan), BCC = BIOTEC Culture 

Collection (Thailand), GZAAS = Guizhou Academy of Agricultural 

Sciences herbarium (China), MUCL = Belgian Co-ordinated 

Collections of Micro-organisms, (agro)industrial fungi & yeasts 

(Belgium), BRIP = Queensland Plant Pathology Herbarium 

(Australia), PDD = New Zealand Fungal and Plant Disease 

Collection (New Zealand), BPI = U.S. National Fungus Collections 

(USA), STE-U = Culture collection of the Department of Plant 

Pathology, University of Stellenbosch (South Africa), and MCA = 

M. Catherine Aime’s collection series, Louisiana State University 

(USA). 

DNA extraction, amplification, and sequencing 

Mycelium was collected from isolates grown on PDA agar, and 

manually comminuted with a micropestle in 420 μL of Quiagen 

DXT tissue digest buffer; 4.2 μL of proteinase K was added and 

incubated at 55 °C for 1 h. After a brief centrifugation 220 μL of 

the supernatant was placed in a Corbett X-tractorGene automated 

nucleic acid extraction robot. The resulting 100 μL of pure DNA in 

TE buffer was stored at -30 °C in 1.5 mL tubes until use. 

Gene sequences were obtained from eight nuclear gene regions, 

actin (ACT) [316 bp], calmodulin (CAL) [756 bp], chitin synthase 

(CHS-1) [229 bp], glyceraldehyde-3-phosphate dehydrogenase 

(GAPDH) [308 bp], the ribosomal internal transcribed spacer 

(ITS) [615 bp], glutamine synthetase (GS) [907 bp], manganesesuperoxide 

dismutase (SOD2) [376 bp], and β-tubulin 2 (TUB2) 

[716 bp]. 

PCR Primers used during this study are shown in Table 2. 

The standard CAL primers (O’Donnell et al. 2000) gave poor or 

non-specific amplification for most isolates, thus new primers 

(CL1C, CL2C) were designed for Colletotrichum based on the C. 

graminicola M1.001 genome sequence. The standard GS primers 

(Stephenson et al. 1997) sequenced poorly for some isolates due 

to an approx. 9 bp homopolymer T run 71 bp in from the end of 

the GSF1 primer binding site. A new primer, GSF3, was designed 

41 bp downstream of this region to eliminate the homopolymer 

slippage error from sequencing. The reverse primer GSR2 was 

www.studiesinmycology.org 

The ColletotriChum gloeosporioides species complex 

designed in the same location as GSR1 with one nucleotide 

change. Both new GS primers were based on similarity with a 

C. theobromicola UQ62 sequence (GenBank L78067, as C. 

gloeosporioides). 

The PCRs were performed in an Applied Biosystems Veriti 

Thermal Cycler in a total volume of 25 μL. The PCR mixtures 

contained 15.8 μL of UV-sterilised ultra-filtered water, 2.5 μL of 10× 

PCR buffer (with 20 mM MgCl 2 ), 2.5 μL of dNTPs (each 20 μM), 1 

μL of each primer (10 μM), 1 μL of BSA, 1 μL of genomic DNA, and 

0.2 μL (1 U) of Roche FastStart Taq DNA Polymerase. 

The PCR conditions for ITS were 4 min at 95 °C, then 35 

cycles of 95 °C for 30 s, 52 °C for 30 s, 72 °C for 45 s, and then 

7 min at 72 °C. The annealing temperatures differed for the other 

genes, with the optimum for each; ACT: 58 °C, CAL: 59 °C, CHS- 

1: 58 °C, GAPDH: 60 °C, GS: 54 °C, SOD2: 54 °C, TUB2: 55 

°C. Some isolates required altered temperatures and occasionally 

gave multiple bands, which were excised separately from an 

electrophoresis gel and purified. PCR Products were purified on a 

Qiagen MinElute 96 UF PCR Purification Plate. 

DNA sequences were obtained in both directions on an Applied 

Biosystems 3130xl Avant Genetic analyzer using BigDye v. 3.1 

chemistry, electropherograms were analysed and assembled in 

Sequencher v. 4.10.1 (Gene Codes Corp.). 

Phylogenetic analyses 

Multiple sequence alignments of each gene were made with 

ClustalX v. 2.1 (Larkin et al. 2007), and manually adjusted where 

necessary with Geneious Pro v. 5.5.6 (Drummond et al. 2011). 

Bayesian inference (BI) was used to reconstruct most of 

the phylogenies using MrBayes v. 3.2.1 (Ronquist et al. 2012). 

Bayesian inference has significant advantages over other methods 

of analysis such as maximum likelihood and maximum parsimony 

(Archibald et al. 2003) and provides measures of clade support as 

posterior probabilities rather than random resampling bootstraps. 

jModelTest v. 0.1.1 (Posada 2008) was used to carry out statistical 

selection of best-fit models of nucleotide substitution using the 

corrected Akaike information criteria (AICc) (Table 3). Initial 

analyses showed that individual genes were broadly congruent, 

thus nucleotide alignments of all genes were concatenated using 

Geneious, and separate partitions created for each gene with 

their own model of nucleotide substitution. Analyses on the full 

data set were run twice for 5 x 10 7 generations, and twice for 2 x 

10 7 generations for the clade trees. Samples were taken from the 

posterior every 1000 generations. Convergence of all parameters 

was checked using the internal diagnostics of the standard 

deviation of split frequencies and performance scale reduction 

factors (PSRF), and then externally with Tracer v. 1.5 (Rambaut 

& Drummond 2007). On this basis the first 25 % of generations 

were discarded as burn-in. 

An initial BI analysis treated all 158 isolates using a concatenated 

alignment for five of the genes, ACT, CAL, CHS-1, GAPDH, and ITS. 

Colletotrichum boninense and C. hippeastri were used as outgroups. 

A second BI analysis, restricted to ex-type or authentic isolates 

of each of the accepted species, was based on a concatenated 

alignment of all eight genes. A third set of BI analyses treated 

focussed on taxa within the Musae clade and the Kahawae clade. 

For each clade, the ex-type or authentic isolates, together with 2–3 

additional selected isolates of each accepted taxon where available, 

were analysed using a concatenated alignment of all eight genes, 

with C. gloeosporioides used as the outgroup for both analyses. 

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Weir et al. 

Table 1. A list of strains used in this study. 

Species Culture* Host Country GenBank accession number 

118 

ITS GAPDH CAL ACT CHS-1 GS SOD2 TUB2 

C. aenigma ICMP 18608* Persea americana Israel JX010244 JX010044 JX009683 JX009443 JX009774 JX010078 JX010311 JX010389 

ICMP 18686 Pyrus pyrifolia Japan JX010243 JX009913 JX009684 JX009519 JX009789 JX010079 JX010312 JX010390 

C. aeschynomenes ICMP 17673*, ATCC 201874 Aeschynomene virginica USA JX010176 JX009930 JX009721 JX009483 JX009799 JX010081 JX010314 JX010392 

C. alatae CBS 304.67*, ICMP 17919 Dioscorea alata India JX010190 JX009990 JX009738 JX009471 JX009837 JX010065 JX010305 JX010383 

ICMP 18122 Dioscorea alata Nigeria JX010191 JX010011 JX009739 JX009470 JX009846 JX010136 JX010371 JX010449 

C. alienum IMI 313842, ICMP 18691 Persea americana Australia JX010217 JX010018 JX009664 JX009580 JX009754 JX010074 JX010307 JX010385 

ICMP 18703 Persea americana New Zealand JX010252 JX010030 JX009656 JX009528 JX009885 

ICMP 12071* Malus domestica New Zealand JX010251 JX010028 JX009654 JX009572 JX009882 JX010101 JX010333 JX010411 

ICMP 17972 Diospyros kaki New Zealand JX010247 JX009944 JX009655 JX009497 JX009750 


ICMP 18621 Persea americana New Zealand JX010246 JX009959 JX009657 JX009552 JX009755 JX010075 JX010308 JX010386 

ICMP 12068 Malus domestica New Zealand JX010255 JX009925 JX009660 JX009492 JX009889 

ICMP 18725 Malus domestica New Zealand JX010254 JX009943 JX009659 JX009530 JX009887 

C. aotearoa ICMP 18532 Vitex lucens New Zealand JX010220 JX009906 JX009614 JX009544 JX009764 JX010108 JX010338 JX010421 

ICMP 18734 Agathis australis New Zealand JX010211 JX010004 JX009627 JX009569 JX009878 

ICMP 18528 Berberis glaucocarpa New Zealand JX010199 JX009977 JX009615 JX009527 JX009879 

ICMP 17324 Kunzea ericoides New Zealand JX010198 JX009991 JX009619 JX009538 JX009770 JX010109 JX010344 JX010418 

ICMP 18533 Prumnopitys ferruginea New Zealand JX010197 JX010026 JX009624 JX009522 JX009769 JX010110 JX010340 JX010416 

ICMP 18535 Dacrycarpus dacrydioides New Zealand JX010201 JX009968 JX009617 JX009545 JX009766 JX010107 JX010364 JX010423 

ICMP 18577 Coprosma sp. New Zealand JX010203 JX009978 JX009612 JX009567 JX009851 JX010111 JX010360 JX010417 

ICMP 18529 Acmena smithii New Zealand JX010222 JX009956 JX009618 JX009539 JX009883 

ICMP 18537* Coprosma sp. New Zealand JX010205 JX010005 JX009611 JX009564 JX009853 JX010113 JX010345 JX010420 

ICMP 18536 Coprosma sp. New Zealand JX010204 JX009907 JX009610 JX009577 JX009852 

ICMP 18748 Ligustrum lucidum New Zealand JX010209 JX009918 JX009613 JX009453 JX009858 

ICMP 17326 Podocarpus totara New Zealand JX010202 JX010049 JX009616 JX009578 JX009768 JX010106 JX010341 JX010422 

ICMP 18540 Geniostoma ligustrifolium New Zealand JX010207 JX010043 JX009622 JX009514 JX009855 

ICMP 18541 Coprosma sp. New Zealand JX010208 JX009960 JX009607 JX009513 JX009856 

ICMP 18742 Meryta sinclairii New Zealand JX010210 JX010025 JX009626 JX009477 JX009862 

ICMP 18740 Dysoxylum spectabile New Zealand JX010218 JX009988 JX009625 JX009517 JX009763 JX010135 JX010368 JX010446 

ICMP 18530 Vitex lucens New Zealand JX010268 JX009911 JX009623 JX009521 JX009884 JX010112 JX010339 JX010419 

ICMP 18735 Hedychium gardnerianum New Zealand JX010221 JX010023 JX009620 JX009500 JX009880 JX010115 JX010343 JX010424

Table 1. (Continued). 



ICMP 18736 Lonicera japonica New Zealand JX010200 JX009912 JX009608 JX009454 JX009894 

ICMP 18548 Coprosma sp. New Zealand JX010206 JX009961 JX009609 JX009854 JX009445 JX010114 JX010342 JX010425 

ICMP 18543 Melicytus ramiflorus New Zealand JX010156 JX009983 JX009621 JX009524 JX009859 

C. asianum IMI 313839, ICMP 18696 Mangifera indica Australia JX010192 JX009915 JX009723 JX009576 JX009753 JX010073 JX010306 JX010384 


MAFF 306627, ICMP 18603 Mangifera indica Philippines JX010195 JX009938 JX009725 JX009579 JX009825 

HKUCC 10862, ICMP 18605 Mangifera indica Thailand JX010194 JX010021 JX009726 JX009465 JX009787 

ICMP 18580*, CBS 130418 Coffea arabica Thailand FJ972612 JX010053 FJ917506 JX009584 JX009867 JX010096 JX010328 JX010406 

CBS 124960, ICMP 18648 Mangifera indica Panama JX010193 JX010017 JX009724 JX009546 JX009871 

Japan JX010292 JX009905 JX009583 JX009827 

Crinum asiaticum var. 

sinicum 

C. boninense MAFF 305972*, ICMP 17904, 

CBS 123755 

C. clidemiae ICMP 18706 Vitis sp. USA JX010274 JX009909 JX009639 JX009476 JX009777 JX010128 JX010353 JX010439 

ICMP 18658* Clidemia hirta USA, Hawaii JX010265 JX009989 JX009645 JX009537 JX009877 JX010129 JX010356 JX010438 

C. cordylinicola MFLUCC 090551*, ICMP 18579 Cordyline fruticosa Thailand JX010226 JX009975 HM470238 HM470235 JX009864 JX010122 JX010361 JX010440 

C. fructicola ICMP 12568 Persea americana Australia JX010166 JX009946 JX009680 JX009529 JX009762 

ICMP 17787 Malus domestica Brazil JX010164 JX009958 JX009667 JX009439 JX009807 

ICMP 17788 Malus domestica Brazil JX010177 JX009949 JX009672 JX009458 JX009808 

IMI 345051, ICMP 17819 Fragaria × ananassa Canada JX010180 JX009997 JX009668 JX009469 JX009820 

ICMP 18613 Limonium sinuatum Israel JX010167 JX009998 JX009675 JX009491 JX009772 JX010077 JX010310 JX010388 

ICMP 18698 Limonium sp. Israel JX010168 JX010052 JX009677 JX009585 JX009773 




ICMP 18610 Pyrus pyrifolia Japan JX010174 JX010034 JX009681 JX009526 JX009788 

ICMP 18120 Dioscorea alata Nigeria JX010182 JX010041 JX009670 JX009436 JX009844 JX010091 JX010323 JX010401 

CBS 125395, ICMP 18645 Theobroma cacao Panama JX010172 JX009992 JX009666 JX009543 JX009873 JX010098 JX010330 JX010408 

ICMP 18581*, CBS 130416 Coffea arabica Thailand JX010165 JX010033 FJ917508 FJ907426 JX009866 JX010095 JX010327 JX010405 

ICMP 18727 Fragaria × ananassa USA JX010179 JX010035 JX009682 JX009565 JX009812 JX010083 JX010316 JX010394 

CBS 120005, ICMP 18609 Fragaria × ananassa USA JX010175 JX009926 JX009673 JX009534 JX009792 

ICMP 17789 Malus domestica USA JX010178 JX009914 JX009665 JX009451 JX009809 

ICMP 18125 Dioscorea alata Nigeria JX010183 JX010009 JX009669 JX009468 JX009847 

C. fructicola (syn. C. ignotum) CBS 125397(*), ICMP 18646 Tetragastris panamensis Panama JX010173 JX010032 JX009674 JX009581 JX009874 JX010099 JX010331 JX010409 

C. fructicola (syn. Glomerella cingulata var. CBS 238.49(*), ICMP 17921 Ficus edulis Germany JX010181 JX009923 JX009671 JX009495 JX009839 JX010090 JX010322 JX010400 

minor) 

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C. gloeosporioides DAR 76936, ICMP 18738 Carya illinoinensis Australia JX010151 JX009976 JX009730 JX009542 JX009797 

IMI 356878*, ICMP 17821, 

Citrus sinensis Italy JX010152 JX010056 JX009731 JX009531 JX009818 JX010085 JX010365 JX010445 


ICMP 12939 Citrus sp. New Zealand JX010149 JX009931 JX009728 JX009462 JX009747 

ICMP 12066 Ficus sp. New Zealand JX010158 JX009955 JX009734 JX009550 JX009888 

ICMP 18730 Citrus sp. New Zealand JX010157 JX009981 JX009737 JX009548 JX009861 

ICMP 12938 Citrus sinensis New Zealand JX010147 JX009935 JX009732 JX009560 JX009746 

ICMP 18694 Mangifera indica South Africa JX010155 JX009980 JX009729 JX009481 JX009796 

CBS 119204, ICMP 18678 Pueraria lobata USA JX010150 JX010013 JX009733 JX009502 JX009790 

ICMP 18695 Citrus sp. USA JX010153 JX009979 JX009735 JX009494 JX009779 

ICMP 18697 Vitis vinifera USA JX010154 JX009987 JX009736 JX009557 JX009780 

C. gloeosporioides (syn. Gloeosporium CBS 273.51(*), ICMP 19121 Citrus limon Italy JX010148 JX010054 JX009745 JX009558 JX009903 

pedemontanum) 

C. hippeastri CBS 241.78, ICMP 17920 Hippeastrum sp. Netherlands JX010293 JX009932 JX009740 JX009485 JX009838 

C. horii ICMP 12942 Diospyros kaki New Zealand GQ329687 GQ329685 JX009603 JX009533 JX009748 JX010072 JX010296 JX010375 

ICMP 12951 Diospyros kaki New Zealand GQ329689 GQ329683 JX009602 JX009466 JX009751 

NBRC 7478*, ICMP 10492 Diospyros kaki Japan GQ329690 GQ329681 JX009604 JX009438 JX009752 JX010137 JX010370 JX010450 

ICMP 17968 Diospyros kaki China JX010212 GQ329682 JX009605 JX009547 JX009811 JX010068 JX010300 JX010378 

MAFF 306429, ICMP 17970 Diospyros kaki Japan JX010213 GQ329686 JX009606 JX009467 JX009824 

C. kahawae subsp. ciggaro ICMP 18539* Olea europaea Australia JX010230 JX009966 JX009635 JX009523 JX009800 JX010132 JX010346 JX010434 

ICMP 18728 Miconia sp. Brazil JX010239 JX010048 JX009643 JX009525 JX009850 

ICMP 18741 Kunzea ericoides New Zealand JX010229 JX010039 JX009631 JX009472 JX009767 

ICMP 18534 Kunzea ericoides New Zealand JX010227 JX009904 JX009634 JX009473 JX009765 JX010116 JX010351 JX010427 

ICMP 18544 Toronia toru New Zealand JX010240 JX009920 JX009632 JX009430 JX009860 


ICMP 12952 Persea americana New Zealand JX010214 JX009971 JX009648 JX009431 JX009757 JX010126 JX010348 JX010426 


CBS 112984, ICMP 17932 Dryandra sp. South Africa JX010237 JX009973 JX009633 JX009434 JX009833 

IMI 359911, ICMP 17931, 

Dryas octopetala Switzerland JX010236 JX009965 JX009637 JX009475 JX009832 JX010121 JX010354 JX010428 


CBS 237.49(*), ICMP 17922 Hypericum perforatum Germany JX010238 JX010042 JX009636 JX009450 JX009840 JX010120 JX010355 JX010432 

C. kahawae subsp. ciggaro (syn. Glomerella 

cingulata var. migrans)




C. kahawae subsp. ciggaro (syn. Glomerella CBS 124.22(*), ICMP 19122 Vaccinium sp. USA JX010228 JX009950 JX009744 JX009536 JX009902 JX010134 JX010367 JX010433 

rufomaculans var. vaccinii) 

C. kahawae subsp. kahawae CBS 982.69, ICMP 17915 Coffea arabica Angola JX010234 JX010040 JX009638 JX009474 JX009829 JX010125 JX010352 JX010435 

IMI 361501, ICMP 17905 Coffea arabica Cameroon JX010232 JX010046 JX009644 JX009561 JX009816 JX010127 JX010349 JX010431 


IMI 319418*, ICMP 17816 Coffea arabica Kenya JX010231 JX010012 JX009642 JX009452 JX009813 JX010130 JX010350 JX010444 

CBS 135.30, ICMP 17928 Coffea sp. Kenya JX010235 JX010037 JX009640 JX009554 JX009831 

IMI 301220, ICMP 17811 Coffea arabica Malawi JX010233 JX009970 JX009641 JX009555 JX009817 JX010131 JX010347 JX010430 

C. musae CBS 192.31, ICMP 17923 Musa sp. Indonesia JX010143 JX009929 JX009690 JX009587 JX009841 

IMI 52264, ICMP 17817 Musa sapientum Kenya JX010142 JX010015 JX009689 JX009432 JX009815 JX010084 JX010317 JX010395 

ICMP 12931 Musa sp. New Zealand JX010140 JX009995 JX009688 JX009442 JX009756 

(imported) 

ICMP 18600 Musa sp. Philippines JX010144 JX010038 JX009686 JX009556 JX009848 

ICMP 12930 Musa sp. New Zealand JX010141 JX009986 JX009685 JX009566 JX009881 

ICMP 18701 Musa sp. Philippines JX010145 JX010047 JX009687 JX009551 JX009849 

CBS 116870*, ICMP 19119 Musa sp. USA JX010146 JX010050 JX009742 JX009433 JX009896 JX010103 JX010335 HQ596280 

USA JX010189 JX009936 JX009661 JX009486 JX009834 JX010087 JX010319 JX010397 

C. nupharicola CBS 469.96, ICMP 17938 Nuphar lutea subsp. 

polysepala 

USA JX010187 JX009972 JX009663 JX009437 JX009835 JX010088 JX010320 JX010398 

CBS 470.96*, ICMP 18187 Nuphar lutea subsp. 

polysepala 

CBS 472.96, ICMP 17940 Nymphaea ordorata USA JX010188 JX010031 JX009662 JX009582 JX009836 JX010089 JX010321 JX010399 


C. psidii CBS 145.29*, ICMP 19120 Psidium sp. Italy JX010219 JX009967 JX009743 JX009515 JX009901 JX010133 JX010366 JX010443 

C. queenslandicum ICMP 1778* Carica papaya Australia JX010276 JX009934 JX009691 JX009447 JX009899 JX010104 JX010336 JX010414 

ICMP 1780 Carica sp. Australia JX010186 JX010010 JX009693 JX009504 JX009900 

ICMP 12564 Persea americana Australia JX010184 JX009919 JX009692 JX009573 JX009759 

ICMP 18705 Coffea sp. Fiji JX010185 JX010036 JX009694 JX009490 JX009890 JX010102 JX010334 JX010412 

C. salsolae ICMP 19051* Salsola tragus Hungary JX010242 JX009916 JX009696 JX009562 JX009863 JX010093 JX010325 JX010403 

CBS 119296, ICMP 18693 Glycine max (inoculated) Hungary JX010241 JX009917 JX009695 JX009559 JX009791 

C. siamense ICMP 12567 Persea americana Australia JX010250 JX009940 JX009697 JX009541 JX009761 JX010076 JX010309 JX010387 

DAR 76934, ICMP 18574 Pistacia vera Australia JX010270 JX010002 JX009707 JX009535 JX009798 JX010080 JX010313 JX010391 

ICMP 12565 Persea americana Australia JX010249 JX009937 JX009698 JX009571 JX009760 

CBS 125379, ICMP 18643 Hymenocallis americana China JX010258 JX010060 GQ849451 GQ856776 GQ856729 

ICMP 18121 Dioscorea rotundata Nigeria JX010245 JX009942 JX009715 JX009460 JX009845 JX010092 JX010324 JX010402 

ICMP 18118 Commelina sp. Nigeria JX010163 JX009941 JX009701 JX009505 JX009843 

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122 


ICMP 18117 Dioscorea rotundata Nigeria JX010266 JX009954 JX009700 JX009574 JX009842 

ICMP 18739 Carica papaya South Africa JX010161 JX009921 JX009716 JX009484 JX009794 

ICMP 18570 Persea americana South Africa JX010248 JX009969 JX009699 JX009510 JX009793 

ICMP 18569 Persea americana South Africa JX010262 JX009963 JX009711 JX009459 JX009795 

ICMP 18578*, CBS 130417 Coffea arabica Thailand JX010171 JX009924 FJ917505 FJ907423 JX009865 JX010094 JX010326 JX010404 

HKUCC 10884, ICMP 18575 Capsicum annuum Thailand JX010256 JX010059 JX009717 JX009455 JX009785 

HKUCC 10881, ICMP 18618 Capsicum annuum Thailand JX010257 JX009945 JX009718 JX009512 JX009786 


ICMP 18571 Fragaria × ananassa USA JX010159 JX009922 JX009710 JX009482 JX009782 


ICMP 17795 Malus domestica USA JX010162 JX010051 JX009703 JX009506 JX009805 JX010082 JX010315 JX010393 




C. siamense (syn. C. hymenocallidis) CBS 125378(*), ICMP 18642 Hymenocallis americana China JX010278 JX010019 JX009709 GQ856775 GQ856730 JX010100 JX010332 JX010410 

C. siamense (syn. C. jasmini-sambac) CBS 130420(*), ICMP 19118 Jasminum sambac Vietnam HM131511 HM131497 JX009713 HM131507 JX009895 JX010105 JX010337 JX010415 

Stylosanthes guianensis Australia JX010291 JX009948 JX009598 JX009498 JX009822 JX010067 JX010303 JX010381 

C. theobromicola MUCL 42295, ICMP 17958, 


ICMP 18566 Olea europaea Australia JX010282 JX009953 JX009593 JX009496 JX009801 JX010071 JX010297 JX010376 




ICMP 17895 Annona diversifolia Mexico JX010284 JX010057 JX009600 JX009568 JX009828 JX010066 JX010304 JX010382 

ICMP 15445 Acca sellowiana New Zealand JX010290 JX010027 JX009601 JX009509 JX009893 

CBS 125393, ICMP 18650 Theobroma cacao Panama JX010280 JX009982 JX009590 JX009503 JX009872 

CBS 124945*, ICMP 18649 Theobroma cacao Panama JX010294 JX010006 JX009591 JX009444 JX009869 JX010139 JX010372 JX010447 

ICMP 17099 Fragaria × ananassa USA JX010285 JX009957 JX009588 JX009493 JX009778 

ICMP 17100 Quercus sp. USA JX010281 JX009947 JX009596 JX009507 JX009781 

IMI 348152, ICMP 17814 Fragaria vesca USA JX010288 JX010003 JX009589 JX009448 JX009819 JX010062 JX010301 JX010379 

C. theobromicola (syn. C. fragariae) CBS 142.31(*), ICMP 17927 Fragaria × ananassa USA JX010286 JX010024 JX009592 JX009516 JX009830 JX010064 JX010295 JX010373 

C. theobromicola (syn. C. gloeosporioides f. MUCL 42294(*), ICMP 17957, Stylosanthes viscosa Australia JX010289 JX009962 JX009597 JX009575 JX009821 JX010063 JX010302 JX010380 

stylosanthis) 

CBS 124251




C. ti ICMP 5285 Cordyline australis New Zealand JX010267 JX009910 JX009650 JX009553 JX009897 JX010124 JX010363 JX010441 

ICMP 4832* Cordyline sp. New Zealand JX010269 JX009952 JX009649 JX009520 JX009898 JX010123 JX010362 JX010442 

C. tropicale MAFF 239933, ICMP 18672 Litchi chinensis Japan JX010275 JX010020 JX009722 JX009480 JX009826 JX010086 JX010318 JX010396 

CBS 124949*, ICMP 18653 Theobroma cacao Panama JX010264 JX010007 JX009719 JX009489 JX009870 JX010097 JX010329 JX010407 


CBS 124943, ICMP 18651 Annona muricata Panama JX010277 JX010014 JX009720 JX009570 JX009868 

Xanthorrhoea preissii Australia JX010261 JX009927 JX009653 JX009478 JX009823 JX010138 JX010369 JX010448 

C. xanthorrhoeae BRIP 45094*, ICMP 17903, 


IMI 350817a, ICMP 17820 Xanthorrhoea sp. Australia JX010260 JX010008 JX009652 JX009479 JX009814 

Glomerella cingulata “f.sp. camelliae” ICMP 10643 Camellia × williamsii UK JX010224 JX009908 JX009630 JX009540 JX009891 JX010119 JX010358 JX010436 

ICMP 18542 Camellia sasanqua USA JX010223 JX009994 JX009628 JX009488 JX009857 JX010118 JX010357 JX010429 

ICMP 10646 Camellia sasanqua USA JX010225 JX009993 JX009629 JX009563 JX009892 JX010117 JX010359 JX010437 

* = ex-type or authentic culture, (*) = ex-type or authentic culture of synonymised taxon. Sequences downloaded from GenBank, not generated as part of this project are in bold font. Collection abbreviations are listed in the methods. 


Several species-trees analyses were conducted using BEAST 

v. 1.7.1 (Drummond et al. 2012). Species-trees combine multi-gene 

and multiple isolate data to reconstruct the evolutionary history 

of hypothesised species, rather than individual isolates. BEAST 

does not use concatenation, but rather co-estimates the individual 

gene trees embedded inside the summary species tree. It also 

estimates the time since each species shared a common ancestor 

(divergence times). For these analyses the species tree ancestral 

reconstruction option was selected (Heled & Drummond 2010), the 

gene data partitioned as for BI and the substitution model for each 

gene was selected based on the models selected using jModelTest. 

The individual isolates were grouped into sets of species by setting 

species names as trait values. A strict clock was used for the 

GAPDH gene (as an all intronic sequence it was assumed to be 

accumulating mutations at a steady rate) and the other gene clock 

rates were estimated relative to GAPDH, using an uncorrelated 

lognormal relaxed clock. The species tree prior used for all genes 

was the Yule process, with the ploidy type set to nuclear autosomal. 

Uninformative priors were used for all parameters, and were 

allowed to auto optimise. 

The first species-tree analysis was conducted using the 158 

isolate, five gene dataset, with C. boninense and C. hippeastri as 

the outgroups. The MCMC chain was set to 1 × 10 8 generations 

for the species complex tree and samples were taken from the 

posterior every 1000 generations. The analysis was run twice 

independently. The effective sample size (ESS) and traces of 

all parameters and convergence of the two runs was checked 

with Tracer and a summary maximum clade credibility species 

tree was built with TreeAnnotator v. 1.7.1 (Drummond et al. 

2012) using a 10 % burn-in and a posterior probability limit of 

0.5, setting the heights of each node in the tree to the mean 

height across the entire sample of trees for that clade. Separate 

analyses were conducted using all eight genes and the same 

restricted set of isolates chosen to represent taxa within the 

Musae clade and the Kahawae clade as were used for the BI 

analyses of the eight gene concatenated analyses outlined 

above. For each of the Musae and Kahawae clade analyses, 

the MCMC chain was set to 5 × 10 7 generations, but otherwise 

run as for the five gene dataset. 

To illustrate the potential limitations of ITS to discriminate species 

within the C. gloeosporioides complex, an UPGMA tree was built 

of all 158 ITS sequences, using the Geneious tree builder tool. A 

UPGMA tree visually approximates a BLAST search, which is based 

on distances (and sequence length) rather than corrected nucleotide 

substitutions of more sophisticated, model-based analyses. 

Sequences derived in this study were lodged in GenBank (Table 

1), the concatenated alignment and trees in TreeBASE (www. 

treebase.org) study number S12535, and taxonomic novelties in 

MycoBank (Crous et al. 2004). 

Morphology 

Detailed morphological descriptions are provided only for those 

species with no recently published description. Few specimens 

were examined from infected host material; the descriptions 

provided are mostly from agar cultures. Cultures were grown on 

Difco PDA from single conidia, or from single hyphal tips for the few 

specimens where no conidia were formed, with culture diameter 

measured and appearance described after 10 d growth at 18–20 o C 

under mixed white and UV fluorescent tubes, 12 h light/12 h dark. 

Colour codes follow Kornerup & Wanscher (1963). 

123

Weir et al. 

Table 2. Primers used in this study, with sequences and sources. 

Gene Product name Primer Direction Sequence (5’–3’) Reference 

ACT Actin ACT-512F Foward ATG TGC AAG GCC GGT TTC GC Carbone & Kohn 1999 

ACT-783R Reverse TAC GAG TCC TTC TGG CCC AT Carbone & Kohn 1999 

CAL Calmodulin CL1 Foward GAR TWC AAG GAG GCC TTC TC O’Donnell et al. 2000 

CL2A Reverse TTT TTG CAT CAT GAG TTG GAC O’Donnell et al. 2000 

CL1C Foward GAA TTC AAG GAG GCC TTC TC This study 

CL2C Reverse CTT CTG CAT CAT GAG CTG GAC This study 

CHS-1 Chitin synthase CHS-79F Foward TGG GGC AAG GAT GCT TGG AAG AAG Carbone & Kohn 1999 

CHS-345R Reverse TGG AAG AAC CAT CTG TGA GAG TTG Carbone & Kohn 1999 

GAPDH Glyceraldehyde-3-phosphate dehydrogenase GDF Foward GCC GTC AAC GAC CCC TTC ATT GA Templeton et al. 1992 

GDR Reverse GGG TGG AGT CGT ACT TGA GCA TGT Templeton et al. 1992 

GS Glutamine synthetase GSF1 Foward ATG GCC GAG TAC ATC TGG Stephenson et al. 1997 

GSF3 Foward GCC GGT GGA GGA ACC GTC G This study 

GSR1 Reverse GAA CCG TCG AAG TTC CAG Stephenson et al. 1997 

GSR2 Reverse GAA CCG TCG AAG TTC CAC This study 

ITS Internal transcribed spacer ITS-1F Foward CTT GGT CAT TTA GAG GAA GTA A Gardes & Bruns 1993 

ITS-4 Reverse TCC TCC GCT TAT TGA TAT GC White et al. 1990 

SOD2 Manganese-superoxide dismutase SODglo2-F Foward CAG ATC ATG GAG CTG CAC CA Moriwaki & Tsukiboshi 2009 

SODglo2-R Reverse TAG TAC GCG TGC TCG GAC AT Moriwaki & Tsukiboshi 2009 

TUB2 β-Tubulin 2 T1 Foward AAC ATG CGT GAG ATT GTA AGT O’Donnell & Cigelnik 1997 

T2 Reverse TAG TGA CCC TTG GCC CAGT TG O’Donnell & Cigelnik 1997 

Bt2b Reverse ACC CTC AGT GTA GTG ACC CTT GGC Glass & Donaldson 1995 

Table 3. Nucleotide substitution models used in phylogenetic 

analyses. 

Gene All taxa Musae clade Kahawae clade 

ITS TrNef+G TrNef+G TrNef 

GAPDH HKY+G TPM1uf+G TrN 

CAL TIM1+G TIM1+G TrN+G 

ACT HKY+G TrN JC 

CHS-1 TrNef+G TrNef+G K80 

GS TIM2+G TIM3+G 

SOD2 HKY+G GTR+I+G 

TUB2 TrN+G HKY+G 

Conidia were measured and described using conidia taken from 

the conidial ooze on acervuli and mounted in lactic acid, at least 

24 conidia were measured for each isolate, range measurements 

are provided in the form (lower extreme–) 25 % quartile – 75 % 

quartile (–upper extreme), all ranges were rounded to the nearest 

0.5 µm. Cultures were examined periodically for the development 

of perithecia. Ascospores were measured and described from 

perithecia crushed in lactic acid. 

Appressoria were producing using a slide culture technique. A 

small square of agar was inoculated on one side with conidia and 

immediately covered with a sterile cover slip. After 14 d the cover 

slip was removed and placed in a drop of lactic acid on a glass 

slide. 

All morphological character measurements were analysed 

with the statistical programme “R” v. 2.14.0 (R Development Core 

Team 2011). The R package ggplot2 (Wickham 2009) was used for 

graphical plots. The box plots show the median, upper and lower 

124 

quartiles, and the ‘whisker’ extends to the outlying data, or to a 

maximum of 1.5× the interquartile range, individual outliers outside 

this range are shown as dots. 

Taxa treated in the taxonomic section 

Species, subspecific taxa, and formae speciales within the C. 

gloeosporioides species complex are treated alphabetically by 

epithet. The names of formae speciales are not governed by the 

International Code of Botanical Nomenclature (ICBN) (McNeill 

et al. 2006, Art. 4, Note 4), and are hence enclosed in quotation 

marks to indicate their invalid status. Other invalid names that 

are governed by the ICBN are also enclosed in quotation marks. 

Accepted names are marked with an asterisk (*). The breadth of 

the taxonomic names treated includes: 

all taxonomic names with DNA sequence data in GenBank 

that place them in the C. gloeosporioides complex as it has been 

defined here on the basis of the ITS gene tree. The sense that the 

names were used in GenBank may have been misapplied; 

names that have been used in the literature in recent years 

for which a possible relationship to C. gloeosporioides has been 

suggested; 

all subspecific taxa and formae speciales within C. 

gloeosporioides and Glomerella cingulata. 

We have not considered the full set of species in Colletotrichum, 

Gloeosporium and Glomerella that were placed in synonymy with 

C. gloeosporioides or Glomerella cingulata by von Arx & Müller 

(1954) or von Arx (1957, 1970). 

For each accepted species, comments are provided regarding 

the limitations of ITS, the official barcoding gene for fungi, to 

distinguish that species from others within the C. gloeosporioides 

complex.

RESULTS 

Phylogenetics 

DNA sequences of five genes were obtained from all 158 isolates 

included in the study and concatenated to form a supermatrix of 

2294 bp. The gene boundaries in the alignment were: ACT: 1–316, 

CAL: 317–1072, CHS-1: 1073–1371, GAPDH: 1372–1679, ITS: 

1680–2294. A BI analysis of the concatenated dataset is presented 

in Fig.1. This tree is annotated with the species boundaries of the 

taxa that we accept in the C. gloeosporioides complex, and the 

clades representing these taxa formed the basis for investigating 

the morphological and biological diversity of our species. Ex-type 

and authentic isolates are highlighted in bold and labelled with the 

names under which they were originally described. The posterior 

probability (PP) support for the grouping of most species ranges 

from 1 to 0.96, however support for deeper nodes is often lower, 

e.g. 0.53 for the root of C. ti and C. aotearoa, indicating that the 

branching may be uncertain for the root of these species. Branch 

lengths and node PP are typically lower within a species than 

between species. 

The large number of taxa in Fig. 1 makes it difficult to visualise 

the interspecific genetic distance between the recognised species. 

The unrooted tree in Fig. 2 represents the results of a BI analysis 

based on a concatenation of all eight genes, but restricted to the 

ex-type or authentic cultures from each of the accepted taxa. The 

analysis was done without out-group taxa and clearly shows two 

clusters of closely related species that we informally label the 

Musae clade, and the Kahawae clade. 

To better resolve relationships within the Musae and Kahawae 

clades a further set of BI analyses included eight genes and, 

wherever possible, several representative isolates of each of the 

accepted species. All eight gene sequences were concatenated 

to form a supermatrix for each clade. For the Musae clade of 

32 isolates the alignment was 4199 bp and the gene boundaries 

were: ACT: 1–292, TUB2: 293–1008, CAL: 1009–1746, CHS-1: 

1747–2045, GAPDH: 2046–2331, GS: 2332–3238, ITS: 3239– 

3823, SOD2: 3824–4199. For the Kahawae clade of 30 isolates 

the alignment was 4107 bp and the gene boundaries were: ACT: 

1–281, TUB2: 282–988, CAL: 989–1728, CHS-1: 1729–2027, 

GAPDH: 2028–2311, GS: 2312–3179, ITS: 3198–3733, SOD2: 

3734–4107. The additional genes sequenced provided additional 

support for our initial species delimitations with better resolution 

for some closely related species. For example, the highly 

pathogenic coffee berry isolates (referred to here as C. kahawae 

subsp. kahawae) were distinguished from other C. kahawae 

isolates. 

Analyses based on concatenated data sets can mask 

incongruence between individual gene trees. The low levels of 

support within some parts of the species-tree analysis (Fig. 3), 

in part reflects incongruence between gene trees. The levels of 

support for the Kahawae clade and for the Musae clade are strong 

(PP=1) but the species that we accept within these clades have 

lower levels of support than is shown between the other species 

outside of the clades. The scale bar in Fig. 3 represents a time scale, 

calibrated at zero for the present day, and at 1 for the last common 

ancestor (LCA) of the C. gloeosporioides and C. boninense species 

complexes. The separate species-tree analyses for the Musae and 

Kahawae clades provide a finer resolution of evolutionary history 

within each clade, the time scale based on the same calibration 

as Fig. 3. 



The UPGMA-based ITS gene tree (Fig 6). shows that C. 

theobromicola, C. horii, C. gloeosporioides, G. cingulata “f. sp. 

camelliae”, C. asianum, C. musae, C. alatae, C. xanthorrhoeae all 

form monophyletic clades and may be distinguished with ITS, but 

many species are unable to be discriminated using this gene alone. 

Note that C. cordylinicola and C. psidii are represented by a single 

isolate, meaning that variation within ITS sequences across these 

species has not been tested. 

Morphology and biology 

Brief morphological descriptions, based on all specimens examined, 

are provided for only those species with no recently published 

description. Conidial sizes for all accepted species are summarised 

in Fig. 7. Within a species, conidial sizes are reasonably consistent 

across isolates, independent of geographic origin or host. However, 

differences between species are often slight and size ranges often 

overlap (Fig. 7). The shape of appressoria is generally consistent 

within a species, some being simple in outline, others complex and 

highly lobed. 

Several species are characterised in part by the development 

of perithecia in culture. These include four species in the Musae 

clade (C. alienum, C. fructicola, C. queenslandicum, and C. 

salsolae) and three in the Kahawae clade (C. clidemiae, C. 

kahawae subsp. ciggaro, and C. ti). Ascospore size and shape 

can be a useful species-level diagnostic feature (Fig. 8). In most 

species the ascospores are strongly curved and typically tapering 

towards the ends, but in C. clidemiae and C. ti, they are more or 

less elliptic with broadly rounded ends and not, or only slightly, 

curved. Individual isolates within any of these species may lose the 

ability to form perithecia, perhaps associated with cultural changes 

during storage. 

Large, dark-walled stromatic structures are present in the 

cultures of some species not known to form perithecia. Often 

embedded in agar, less commonly on the surface or amongst 

the aerial mycelium, these structures differ from perithecia in 

comprising a compact tissue of tightly tangled hyphae rather than 

the pseudoparenchymatous, angular cells typical of perithecial 

walls. They have a soft, leathery texture compared to the more 

brittle perithecia. These stromatic structures sometimes develop 

a conidiogenous layer internally, and following the production 

of conidia they may split open irregularly, folding back to form a 

stromatic, acervulus-like structure. These kind of structures are 

also formed by some species in the C. boninense species complex 

(Damm et al. 2012b, this issue). 

The macroscopic appearance of the cultures is often highly 

divergent within a species (e.g. C. fructicola and C. theobromicola), 

in most cases probably reflecting different storage histories of the 

isolates examined. Prolonged storage, especially with repeated 

subculturing, results in staling of the cultures, the aerial mycelium 

often becoming dense and uniform in appearance and colour, and 

a loss of conidial and perithecial production, and variable in growth 

rate (Fig. 9). In some species, individual single ascospore or single 

conidial isolates show two markedly different cultural types, see 

notes under C. kahawae subsp. ciggaro. 

Some species appear to be host specialised, e.g. C. horii, 

C. kahawae subsp. kahawae, C. nupharicola, C. salsolae, C. ti, 

and C. xanthorrhoeae, but those most commonly isolated have 

broad host and geographic ranges, e.g. C. fructicola, C. kahawae 

subsp. ciggaro, C. siamense, and C. theobromicola. Colletotrichum 

gloeosporioides s. str. is commonly isolated from Citrus in many 

125

Weir et al. 

126 

1 

1 

ICMP 17789 Malus USA 

ICMP 17819 Fragaria Canada 

ICMP 18609 Fragaria USA 

ICMP 18120 Dioscorea Nigeria 

1 

ICMP 17787 Malus Brazil 

ICMP 17788 Malus Brazil 


ICMP 17921 Glomerella cingulata var. minor Ficus Germany 

ICMP 18645 Theobroma Panama 

0.96 ICMP 18667 Limonium Israel 

ICMP 18613 Limonium Israel 

0.98 


0.97 ICMP 18610 Pyrus Japan 


1 1 ICMP 18727 Fragaria USA 

ICMP 18581 C. fructicola Coffea Thailand 

0.99 ICMP 12568 Persea Australia 

ICMP 18646 C. ignotum Tetragastris Panama 

1 ICMP 18187 C. nupharicola Nuphar USA 

1 

1 ICMP 17940 Nuphar USA 

ICMP 17938 Nuphar USA 

0.92 ICMP 12071 C. alienum Malus New Zealand 

ICMP 18691 Persea Australia 

ICMP 18704 Persea New Zealand 

ICMP 12068 Malus New Zealand 

1 

ICMP 17972 Diospyros New Zealand 


ICMP 18725 Malus New Zealand 


1 0.99 

1 

ICMP 17817 Musa Kenya 

ICMP 12931 Musa New Zealand (imported) 

ICMP 17923 Musa Indonesia 

0.95 

ICMP 18600 Musa Philippines 

1 

ICMP 12930 Musa New Zealand 

98 

ICMP 19119 C. musae Musa USA 

ICMP 18701 Musa Philippines 

1 ICMP 18608 C. aenigma Persea Israel 

ICMP 18686 Pyrus Japan 

1 ICMP 18739 Carica South Africa 

0.92 ICMP 18572 Vitis USA 

0.51 ICMP 18571 Fragaria USA 

1 ICMP 18118 Commelina Nigeria 

0.74 ICMP 18117 Dioscorea Nigeria 

0.68 

ICMP 18578 C. siamense Coffea Thailand 

0.98 


1 ICMP 18570 Persea South Africa 

1 ICMP 12567 Persea Australia 


0.68 

0.53 

1 ICMP 18573 Vitis USA 


ICMP 18643 Hymenocallis China 

ICMP 18642 C. hymenocallidis Hymenocallis China 

1 ICMP 17797 Malus USA 


0.83 

1 

ICMP 18569 Persea South Africa 

ICMP 18574 Pistacia Australia 

1 ICMP 18575 Capsicum Thailand 

0.99 0.99ICMP 

18618 Capsicum Thailand 

ICMP 19118 C. jasmini-sambac Jasminum Vietnam 

1 


ICMP 17673 C. gloeosporioides “f. sp. aeschynomenes” Aeschynomene USA 

1 ICMP 18653 C. tropicale Theobroma Panama 

1 ICMP 18651 Annona Panama 

1 

ICMP 18672 Litchi Japan 

1 ICMP 1780 Carica Australia 

1 

1 ICMP 12564 Persea Australia 

ICMP 1778 C. gloeosporioides var. minus Carica Australia 

1 ICMP 18705 Coffea Fiji 

1 ICMP 18693 Glycine (inoculated) Hungary 

ICMP 19051 C. gloeosporioides “f. sp. salsolae” Salsola Hungary 

1 

1 

ICMP 18605 Mangifera Thailand 

ICMP 18648 Mangifera Panama 

ICMP 18696 Mangifera Australia 

ICMP 18603 Mangifera Philippines 

ICMP 18580 C. asianum Coffea Thailand 

0.88 ICMP 12939 Citrus New Zealand 

ICMP 18678 Pueraria USA 

0.76 ICMP 17821 C. gloeosporioides Citrus Italy 

0.78 ICMP 18738 Carya Australia 

ICMP 12938 Citrus New Zealand 

1 

ICMP 18694 Mangifera South Africa 

ICMP 18695 Citrus USA 

ICMP 18730 Citrus New Zealand 

0.99 

ICMP 12066 Ficus New Zealand 

ICMP 18697 Vitis USA 

ICMP 19121 Gloeosporium pedemontanum lemon drink Italy 

1 ICMP 18122 Dioscorea Nigeria 

ICMP 17919 C. gloeosporioides “f. alatae” Dioscorea India 

C. fructicola 

C. nupharicola 

C. alienum 

C. musae 

C. aenigma 

C. siamense 

C. aeschynomenes 

C. tropicale 

C. queenslandicum 

C. salsolae 

C. asianum 

C. gloeosporioides 

(sensu stricto) 

C. alatae 

Fig. 1. A Bayesian inference phylogenetic tree of 156 isolates in the Colletotrichum gloeosporioides species complex. The tree was built using concatenated sequences of the 

ACT, CAL, CHS-1, GAPDH, and ITS genes each with a separate model of DNA evolution. Bayesian posterior probability values ≥ 0.5 are shown above nodes. Culture accession 

numbers are listed along with host plant genus and country of origin. Ex-type and authentic cultures are emphasised in bold font, and include the taxonomic name as originally 

described. Species delimitations are indicated with grey boxes. Colletotrichum boninense and C. hippeastri isolates are used as outgroups. The scale bar indicates the number 

of expected changes per site.

Fig. 1. (Continued). 

parts of the world, but has been isolated from other hosts as well, 

such as Ficus, Mangifera, Pueraria, and Vitis. Not all of the species 

with a broad host range are found everywhere, for example in New 

Zealand C. alienum is commonly associated with cultivated fruits, 

whereas species such as C. siamense and C. fructicola, common 

on these same cultivated fruits in other parts of the world, have not 

been reported from New Zealand. 

Taxonomy 

Based on results of the multigene concatenated BI phylogenies, 

we accept 22 species plus one subspecies within the C. 


1.0 

1 


0.99 



ICMP 17927 C. fragariae Fragaria USA 

1 

1 ICMP 18649 C. theobromicola Theobroma Panama 


0.72 ICMP 17100 Quercus USA 

ICMP 18567 Olea Australia 

0.99 

0.61 

0.64 

ICMP 17958 Stylosanthes Australia 

ICMP 15445 Acca New Zealand 

ICMP 17895 Annona Mexico 

0.88 

1 ICMP 17957 C. gloeosporioides f. stylosanthis 

Stylosanthes Australia 

1 ICMP 18565 Olea Australia 

ICMP 18566 Olea Australia 


1 ICMP 17903 C. xanthorrhoeae Xanthorrhoea Australia 

ICMP 17820 Xanthorrhoea Australia 

ICMP 10492 C. horii Diospryos Japan 

1 

ICMP 17970 Diospryos Japan 

0.85 

ICMP 17968 Diospryos China 

1 

ICMP 12951 Diospryos New Zealand 

ICMP 12942 Diospryos New Zealand 

C. horii 

1 ICMP 18543 Melicytus New Zealand 

0.93 ICMP 17324 Kunzea New Zealand 

ICMP 18533 Prumnopitys New Zealand 

ICMP 18528 Berberis New Zealand 

0.97 ICMP 18535 Dacrycarpus New Zealand 

0.68 ICMP 18734 Berberis New Zealand 

ICMP 18540 Geniostoma New Zealand 

0.99 ICMP 18532 Vitex New Zealand 

ICMP 17326 Podocarpus New Zealand 

0.54 ICMP 18577 Coprosma New Zealand 



ICMP 18537 C. aotearoa Coprosma New Zealand 

0.66 

ICMP 18530 Vitex New Zealand 

ICMP 18735 Hedychium New Zealand 


ICMP 18736 Lonicera New Zealand 

1 0.69 

ICMP 18748 Ligustrum New Zealand 

0.83 

0.69 ICMP 18742 Meryta New Zealand 

C. aotearoa 

0.53 ICMP 18740 Dysoxylum New Zealand 

ICMP 18529 Acmena New Zealand 

1 ICMP 4832 C. ti Cordyline New Zealand 

ICMP 5285 Cordyline New Zealand 


1 



C. ti 

0.96 

ICMP 17915 Coffea Angola 

ICMP 17905 Coffea Cameroon 

ICMP 18544 Toronia New Zealand 

ICMP 17932 Dryandra South Africa 

ICMP 17922 Glomerella cingulata var. migrans Hypericum Germany 

1 

ICMP 17816 C. kahawae subsp. kahawae Coffea Kenya 

ICMP 18741 Kunzea New Zealand 

C. kahawae 

0.75 


ICMP 17931 Dryas Switzerland 

ICMP 18539 C. kahawae subsp. ciggaro Olea Australia 

ICMP 18728 Miconia Brazil 

0.99 ICMP 19122 Glomerella rufomaculans var. vaccinii Vaccinium USA 

ICMP 17928 Coffea Kenya 

1 

ICMP 17811 Coffea Malawi 

0.97 ICMP 10643 Glomerella cingulata “f. sp. camelliae” Camellia UK 

1 ICMP 18542 Camellia USA 

0.99 ICMP 10646 Camellia USA 

1 ICMP 18706 Vitis USA 

ICMP 18658 C. gloeosporioides “f. sp. clidemiae”Clidemia USA 

ICMP 19120 C. psidii Psidium Italy 

ICMP 18579 C. cordylinicola Cordyline Thailand 

1 

ICMP 17904 C. boninense Crinum Japan 

ICMP 17920 C. hippeastri Hippeastrum Netherlands 

C. theobromicola 

C. xanthorrhoeae 

Glomerella cingulata “f. sp.camelliae” 

C. clidemiae 

C. psidii 

C. cordylinicola 

gloeosporioides complex. Isolates authentic for G. cingulata “f. 

sp. camelliae” form a genetically distinct group, but this is not 

formally named because of doubts over its relationship to C. 

camelliae. Based on DNA sequence comparisons, a few other 

isolates almost certainly represent additional unnamed species. 

We do not formally describe them because most are known from 

a single isolate, often stale, with little understanding of either their 

morphological or biological diversity. In the Musae clade these 

include ICMP 18614 and ICMP 18616, both from grape from 

Japan, and ICMP 18726 from pawpaw from the Cook Islands, 

and in the Kahawae clade ICMP 18699 from chestnut from Japan. 

These isolates are not included in the phylogenies in this study, 

127

Weir et al. 

128 

C. alatae 

C. asianum 

C. fructicola 


C. alienum 

C. horii 

C. aenigma 

C. musae 


C. siamense 

Musae clade 

C. tropicale 

C. ti 


C. aotearoa 

C. salsolae 


C psidii 

C. clidemia 


Kahawae clade 

G. cingulata “f.sp. camelliae” 

C. kahawae subsp. ciggaro 

C. kahawae subsp. kahawae 


0.0060 


1.0 0.8 

0.6 

0.4 

0.2 

0.0 

1 

1 

0.30 

0.73 

0.97 

0.99 

0.30 

Fig. 2. An unrooted Bayesian inference phylogenetic tree 

of ex-type and authentic cultures of the 24 taxa within 

the Colletotrichum gloeosporioides species complex, 

illustrating their relative genetic distances, as indicated by 

branch lengths. There are two clusters within the species 

complex, the ‘Musae clade’ and the ‘Kahawae clade’. The 

tree was build using concatenated sequences of the ACT, 

TUB2, CAL, CHS-1, GAPDH, GS, ITS, and SOD2 genes 

each with a separate model of DNA evolution. 

0.91 

0.41 

0.37 

0.57 

0.95 

1 

0.37 

0.47 

0.45 

0.64 

0.98 

1 

0.53 

0.46 

0.45 

0.47 

C. fructicola 


C. alienum 


C. siamense 

C. aenigma 

C. tropicale 

C. musae 

C. salsolae 


C. asianum 


C. alatae 

G.c. “f. sp. camelliae” 

C. kahawae 

C. clidemia 

C. ti 


C. psidii 

C. aotearoa 

C. horii 



C. boninense 

C. hippeastri 

Fig. 3. A Bayesian inference species-tree of the C. gloeosporioides species complex. The tree was built by grouping all 158 isolates into species and simultaneously estimating 

the individual five gene trees (ACT, CAL, CHS-1, GAPDH, and ITS) and the summary species tree using BEAST. The scale is an uncalibrated clock set relative to the last 

common ancestor of the C. gloeosporioides and C. boninense species complexes.

1 

0.13 

A 

0.87 

B 

1 

0.94 


1 

1 

1 

0.117 

0.99 

1 

1 

1 

1 

1 

0.104 

0.82 

1 

1 

1 

1 

1 

1 

1 

1 

ICMP 18574 Pistacia Australia 

0.0030 

0.97 

1 



ICMP 18581 C. fructicola Coffea Thailand 

ICMP 17921 Glomerella cingulata var. minor Ficus Germany 





ICMP 19118 C. jasmini-sambac Jasminum Vietnam 


ICMP 18121 Dioscoria Nigeria 

ICMP 18653 C. tropicale Theobroma Panama 

ICMP 18705 Coffea Fiji 

ICMP 19051 C.g. “f. sp. salsolae” Salsola Hungary 

ICMP 18696 Mangifera Australia 

ICMP 18187 C. nupharicola Nuphar USA 


ICMP 12071 C. alienum Malus New Zealand 

ICMP 18686 Pyrus Japan 

ICMP 18646 C. ignotum Tetragastris Panama 


0.69 


ICMP 18608 C. aenigma Persea Israel 

1 

0.091 

1 

0.95 

1 

0.99 

1 

ICMP 17817 Musa Kenya 


ICMP 19119 C. musae Musa USA 

ICMP 18642 C. hymenocallidis Hymenocallis China 

ICMP 18578 C. siamense Coffee Thailand 

ICMP 17673 C.g. “f. sp. aeschynomenes”Aeschynomene USA 

ICMP 18672 Litchi Japan 

1 

ICMP 1778 C. gloeosporioides var. minus Carica Australia 

ICMP 18580 C. asianum Coffea Thailand 

1 

0.078 

0.44 

0.55 

0.065 

0.33 

0.47 

0.75 

0.052 

ICMP 17821 C. gloeosporioides Citrus Italy 

0.90 

0.039 

0.97 

0.97 

0.60 

0.026 

0.013 

C. fructicola 


C. alienum 

C. aenigma 

C. musae 

C. siamense 


C. tropicale 


C. salsolae 

C. asianum 

0.0 

C. fructicola 

C. alienum 


C. aenigma 

C. musae 


C. siamense 

C. tropicale 

C. salsolae 


C. asianum 


Fig. 4. A Bayesian inference phylogenetic tree of 32 selected isolates in the Musae clade of the Colletotrichum gloeosporioides species complex. The tree was build using 

concatenated sequences of the ACT, TUB2, CAL, CHS-1, GAPDH, GS, ITS, and SOD2 genes each with a separate model of DNA evolution. Other details as per Fig.1. B. A 

species-tree constructed from the same data, the scale is an clock set relative to the last common ancestor of the Musae clade and C. gloeosporioides s. str., as calibrated in 

Fig. 3. 

but DNA sequences from these isolates have been accessioned 

into GenBank (ITS: JX009423–JX009428, GAPDH: JX009416– 

JX009422, ACT: JX009404–JX009407, CAL: JX009408– 

JX009411, CHS-1: JX009412–JX009415). 

Many of the species that we recognise fall into one of two 

clades, the informally named Musae clade and Kahawae clade (Fig. 

2). Each clade contains several species that are phylogenetically 

well supported in multi-gene analyses, but within the clades branch 

lengths are short because of the small number of phylogenetically 

informative characters. This is reflected in the low support values in 

the gene tree analyses for the species we accept within that clade 

(Figs 3, 4). Both the Musae and Kahawae clades contain ex-type 

or authentic cultures from several long accepted species. In this 

work we have made a pragmatic decision to minimise taxonomic 

disruption, so that monophyletic subclades within the Kahawae 

and Musae clades are accepted as species where they include 

129

Weir et al. 

ex-type or authentic cultures. The Musae clade thus includes C. 

fructicola, C. musae, C. nupharicola, C. siamense, and C. tropicale; 

and the Kahawae clade includes C. cordylinicola, C. psidii, and C. 

kahawae. Also belonging in the latter is Glomerella cingulata “f. 

sp. camelliae”. To provide a consistent taxonomic treatment of the 

subclades resolved within the Musae and Kahawae clades, several 

new species and one new subspecies are proposed. In the Musae 

130 

1 

A 

B 

0.62 

0.94 

0.0040 

0.58 

1 

1 

0.99 ICMP 17905 Coffea Cameroon 

1 ICMP 17915 Coffea Angola 

ICMP 17811 Coffea Malawi 

1 

ICMP 17816 C. kahawae Coffea Kenya 

0.89 


0.95 ICMP 17931 Dryas Switzerland 

C. kahawae 

subsp. 

1 ICMP 17922 G. c. var. migrans Hypericum Germany 

1 0.89 ICMP 19122 G. rufomaculans var. vaccinii Vaccinium USA 

0.98 

ICMP 18539 C. kahawae subsp. ciggaro Olea Australia 


ICMP 10643 Glomerella cingulata “f. sp. camelliae” Camellia UK 

1 ICMP 18542 Camellia USA 

1 

ICMP 10646 Camellia USA 

ICMP 18706 Vitis USA 

ICMP 18658 C. gloeosporioides “f. sp.clidemia” Clidemia USA 

ICMP 19120 C. psidii Psidium Italy 

C. psidii 


0.99 ICMP 18537 C. aotearoa Coprosma New Zealand 

1 

1 ICMP 18735 Hedychium New Zealand 

ICMP 18740 Dysoxylum New Zealand 

0.98 

0.56 




1 

ICMP 18533 Prumnopitys New Zealand 

1 

ICMP 18577 Coprosma New Zealand 

1 ICMP 17326 Podocarpus New Zealand 

ICMP 18535 Dacrycarpus New Zealand 

1 ICMP 4832 C. ti Cordyline New Zealand 

ICMP 5285 Cordyline New Zealand 

ICMP 18579 C. cordylinicola Cordyline Thailand 

C. ti 

ICMP 17821 C. gloeosporioides Citrus Italy 

0.2 0.18 0.16 0.14 0.12 0.1 

0.08 0.06 0.04 0.02 

1 

0.17 

0.32 

0.39 

1 

0.91 

1 

C. kahawae 

subsp. kahawae 

ciggaro 

G. cingulata “f. sp. camelliae” 

C. clidemia 

C. aotearoa 


C. kahawae subsp. ciggaro 

C. kahawae subsp. kahawae 

G. c. “f. sp. camelliae” 

C. clidemia 

C. ti 

C. psidii 


C. aotearoa 


Fig. 5. A Bayesian inference phylogenetic tree of 30 selected isolates in the Kahawae clade of the Colletotrichum gloeosporioides species complex. The tree was build using 

concatenated sequences of the ACT, TUB2, CAL, CHS-1, GAPDH, GS, ITS, and SOD2 genes each with a separate model of DNA evolution. Other details as per Fig.1. B. A 

species-tree constructed from the same data, the scale is a clock set relative to the last common ancestor of the Kahawae clade and C. gloeosporioides s. str., as calibrated 

in Fig. 3. 

clade these are C. aenigma, C. aeschynomenes, C. alienum, 

C. queenslandicum, and C. salsolae; in the Kahawae clade C. 

aotearoa, C. clidemiae, C. kahawae subsp. ciggaro, and C. ti. The 

other accepted species, well resolved in all of the gene trees, are C. 

alatae, C. asianum, C. gloeosporioides, C. horii, C. theobromicola, 

and C. xanthorrhoeae. 

0.0

B 

A 


0.3 

1bp 


C.queenslandicum 

C.tropicale 

C.ti 

C.clidemiae 

C.siamense 

C.aotearoa 

C.siamense 

C.ti 

C.aotearoa 

C.aotearoa 

C.alienum 

C.siamense 

C.aenigma 

C.salsolae 

C.siamense 

C.kahawae 

C.alienum 

C.theobromicola 



C.horii 

C.aotearoa 

C.fructicola 

C.aeschynomenes 

C.fructicola 




C.siamense 

C.siamense 

C.gloeosporioides 

C.gloeosporioides 

C.aotearoa 

C.nupharicola 

C.kahawae 

C.aotearoa 

C.kahawae 

C.aotearoa 

C.psidii 

G. c. “f. sp. camelliae” 

C.cordylinicola 

C.asianum 

C.musae 

C.musae 

C.alatae 

C.xanthorrhoeae 

C.hippeastri 

C.boninense 

Fig. 6. An UPGMA tree of ITS sequences from 156 isolates in the Colletotrichum gloeosporioides species complex. Isolate names have been replaced with species present 

in each clade. Species that are in monophyletic clades are emphasised in bold font to indicate those for which ITS barcoding is likely to work well. B: A 50 % majority-rule 

consensus Bayesian inference tree of the same data, showing the collapse of structure when analysed with a more robust method. 

131

Weir et al. 

Conidial width variation 

Conidial length variation 

132 

8 

35 

7 

30 

6 

25 

20 

5 

width 

15 

4 

(µm) 

length (µm) 

10 

G. c.“f.sp. camelliae” 


C. tropicale 

C. ti 


C. siamense 

C. salsaloe 



C. musae 

C. kahawae ssp. kahawae 

C. kahawae ssp. ciggaro 

C. horii 

C. gloeosporiodes 

C. fructicola 

C. clidemiae 

C. asianum 

C. aotearoa 

C. alienum 

C. alatae 


C. aenigma 



C. tropicale 

C. ti 


C. siamense 

C. salsaloe 



C. musae 



C. horii 


C. fructicola 

C. clidemiae 

C. asianum 

C. aotearoa 

C. alienum 

C. alatae 


C. aenigma 

Fig. 7. Box plots showing the variation 

in length and width of conidia produced 

by the cultures examined in this study. 

The dashed lines show the mean length 

(16.74 µm) and width (5.1 µm) across the 

species complex (n = 1958).

Ascospore width variation 

Ascospore length variation 

6.5 

24 

6.0 

22 


5.5 

20 

5.0 

18 

4.5 

16 

4.0 

width (µm) 

length (µm) 

14 

3.5 

C. ti 

C. fructicola 

C. clidemiae 

C. alienum 

C. aenigma 



C. ti 


C. fructicola 

C. clidemiae 

C. alienum 

C. aenigma 



Fig. 8. Box plots showing the variation in 

length and width of ascospores produced 

by the cultures examined in this study. The 

dashed lines show the mean length (17.46 

µm) and width (4.8 µm) across the species 

complex (n = 452). 

133

Weir et al. 

134 

Culture size at10days 

80 

60 

40 

diameter (mm) 

20 



C. tropicale 

C. ti 


C. siamense 

C. salsaloe 



C. musae 




C. fructicola 


C. clidemiae 

C. asianum 

C. aotearoa 

C. alienum 

C. alatae 

C. aeschynomene 

C. aenigma 

Fig. 9. A box plot of the diameter of cultures grown on PDA agar at 18 °C for 10 d. The dashed line shows the mean culture size (61.56 mm) across the species complex (n = 

719). Note that the data is skewed by some fast growing cultures that reached the agar plate diam (85 mm) in under 10 d.

* Colletotrichum aenigma B. Weir & P.R. Johnst., sp. nov. 

MycoBank MB563759. Fig. 10. 

Etymology: from the Latin aenigma, based on the enigmatic 

biological and geographic distribution of this species. 

Holotype: Israel, on Persea americana, coll. S. Freeman Avo-37- 

4B, PDD 102233; ex-holotype culture ICMP 18608. 

Colonies grown from single conidia on Difco PDA 30–35 mm 

diam after 10 d. Aerial mycelium sparse, cottony, white, surface 

of agar uniformly pale orange (7A5) towards centre, more 

or less colourless towards edge, conidia not associated with 

well differentiated acervuli and no masses of conidial ooze. In 

reverse pale orange towards centre. Conidiogenous cells arising 

haphazardly from dense, tangled hyphae across agar surface, 

short-cylindric with a poorly differentiated conidiogenous locus. 

Conidia often germinating soon after release, sometimes forming 

appressoria, so forming a thin, compact, layer of germinated, 

septate conidia, germ tubes, and appressoria across the central 

part of the colony surface. Conidia (12–)14–15(–16.5) × (5–)6– 

6.5(–7.5) µm (av. 14.5 × 6.1 µm, n = 53), cylindric with broadly 

rounded ends. Appressoria 6–10 µm diam, subglobose or with a 

few broad lobes. 

Geographic distribution and host range: known from only two 

collections, one from Pyrus pyrifolia from Japan, the other from 

Persea americana from Israel. 

Genetic identification: ITS sequences are insufficient to separate C. 

aenigma from C. alienum and some C. siamense isolates. These 

taxa are best distinguished using TUB2 or GS. 

Notes: Although the biology of this species is more or less unknown, 

it has been found in two widely separate regions and is, therefore, 

likely to be found to be geographically widespread in the future. 

Genetically distinct within the Musae clade, this species has a 

distinctive appearance in culture with sparse, pale aerial mycelium 

and lacking differentiated acervuli. 

Other specimen examined: Japan, on Pyrus pyrifolia, coll. H. Ishii Nashi-10 (ICMP 

18686). 

* Colletotrichum aeschynomenes B. Weir & P.R. Johnst., 

sp. nov. MycoBank MB563590. Fig. 11. 

= C. gloeosporioides “f. sp. aeschynomenes” (Daniel et al. 1973, as 

aeschynomene). 

Etymology: Based on C. gloeosporioides “f. sp. aeschynomenes”, 

referring to the host from which this species was originally 

described. 

Holotype: USA, Arkansas, on Aeschynomene virginica stem lesion, 

coll. D. TeBeest 3-1-3, PDD 101995; ex-type culture ICMP 17673 

= ATCC 201874. 

Colonies grown from single conidia on Difco PDA 25–35 mm diam 

after 10 d, aerial mycelium sparse, cottony, white, surface of colony 

with numerous acervuli, some with dark bases, with orange conidial 

ooze; in reverse more or less colourless apart from the dark 

acervuli and orange conidial masses showing through the agar. 

Conidia (14–)17–18.5(–20) × 4(–5) µm (av. 17.6 × 4.1 µm, n = 



30), cylindric, straight, tapering slightly near both ends. Appressoria 

mostly elliptic to subfusoid, deeply lobed. Perithecia not seen. 

Geographic distribution and host range: Reported only from USA, 

pathogenic to Aeschynomeme. 

Genetic identification: ITS sequences do not distinguish 

C. aeschynomenes from C. fructicola. These taxa are best 

distinguished using TUB2, GAPDH, or GS. 

Notes: Colletotrichum gloeosporioides “f. sp. aeschynomenes” 

has been used to refer to isolates pathogenic to Aeschynomene 

virginica, later developed as the weed biocontrol agent Collego 

(references in Ditmore et al. 2008). It has also been reported from 

a range of other hosts (TeBeest 1988). Our analyses, based on a 

single, authentic strain of C. gloeosporioides “f. sp. aeschynomenes” 

(TeBeest 3.1.3, apparently the source of the single spore isolate 

originally used in the development of Collego, Ditmore et al. (2008)) 

show it to be genetically distinct within the Musae clade of the C. 

gloeosporioides complex. Genetically close to the geographically 

and biologically diverse C. siamense, it differs morphologically from 

this species in having slightly longer and narrower conidia which 

taper slightly toward the ends, and in having larger, strongly lobed 

appressoria. 

An isolate deposited as C. gloeosporioides f. sp. 

aeschynomenes in CBS (CBS 796.72) by G.E. Templeton, one of 

the early C. gloeosporioides f. sp. aeschynomenes researchers 

(Daniel et al. 1973), is genetically distinct to TeBeest 3.1.3 and has 

been identified by Damm et al. (2012a, this issue) as C. godetiae, a 

member of the C. acutatum complex. The strain that we examined 

(Te Beest 3.1.3) matches genetically another strain often cited 

in the C. gloeosporioides f. sp. aeschynomenes literature (Clar- 

5a = ATCC 96723) (GenBank JX131331). It is possible that two 

distinct species, both highly pathogenic to Aeschynomene in 

Arkansas, have been confused. A survey of additional isolates of 

Colletotrichum highly virulent to Aeschynomene in Arkansas would 

clarify the interpretation of the past literature on this pathogen. For 

example, C. gloeosporioides “f. sp. aeschynomenes” was initially 

reported as specific to Aeschynomene virginica (Daniel et al. 

1973), while later studies reported isolates putatively of the same 

taxon, to have a wider host range (TeBeest 1988). 

Cisar et al. (1994) reported fertile ascospores from 

crosses between isolates identified as C. gloeosporioides “f. 

sp. aeschynomenes” and isolates of C. gloeosporioides “f. sp. 

jussiaeae”, a pathogen of Jussiaea decurrens. The position of 

C. gloeosporioides “f. sp. jussiaeae” within our phylogeny is not 

known, but these taxa could prove useful for better understanding 

of the biological differences between phylogenetically defined 

species of Colletotrichum. 

Specimen examined: USA, Arkansas, on Aeschynomene virginica stem lesion, coll. 

D. TeBeest 3.1.3 (ICMP 17673 = ATCC 201874). 

* Colletotrichum alatae B. Weir & P.R. Johnst., sp. nov. 


= Colletotrichum gloeosporioides “f. alatae” R.D. Singh, Prasad & R.L. Mathur, 

Indian Phytopathol. 19: 69. 1966. [nom. inval., no Latin description, no type 

designated]. 

Etymology: Based on the invalid name C. gloeosporioides “f. alatae” 

(Singh et al. 1966), referring to Dioscorea alata, the scientific name 

for yam. 

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Weir et al. 

Fig. 10. Colletotrichum aenigma. A, C, D, E, F. ICMP 18608 – ex-holotype culture. B. ICMP 18616. A–B. Cultures on PDA, 10 d growth from single conidia, from above and 

below. C–D. Conidia. E–F. Appressoria. Scale bar C = 20 µm. Scale bar of C applies to C–F. 

Holotype: India, Rajasthan, Udaipur, on Dioscorea alata leaves and 

stems, coll. K.L. Kothari & J. Abramham, 1959, CBS H-6939; extype 

culture and putatively authentic isolate of C. gloeosporioides f. 

alatae CBS 304.67 = ICMP 17919. 

136 


after 10 d. Ex-holotype culture looks “stale”, with low, felted, dense, 

pale grey aerial mycelium, orange agar surface showing through 

near the margin, scattered dark based acervuli with orange conidial



Fig. 11. Colletotrichum aeschynomenes. ICMP 17673 – ex-holotype culture. A–C. Appressoria. D. Conidiogenous cells. E. Conidia. F. Cultures on PDA, 10 d growth from single 

conidia, from above and below. Scale bar of A = 20 µm. Scale bar of A applies to A–E. 

masses near centre; in reverse deep pinkish orange with patches of 

grey pigment near centre. ICMP 18122 with aerial mycelium sparse, 

colony surface with numerous discrete, dark-based acervuli with 

bright orange conidial ooze, margin of colony feathery; in reverse 

irregular sectors with pale grey pigment within the grey, otherwise 

colourless apart from the colour of the acervuli and conidial 

masses. Conidia (14.5−)18–19.5(−23.5) × (4.5−)5−5.5(−6.5) µm 

(av. 18.9 × 5.2 µm, n = 40), cylindric, straight, ends rounded, a few 

tapering towards the basal end. Appressoria mostly simple, elliptic 

to fusoid in shape, sometime developing broad, irregular lobes, 

about 7–13.5 × 5–10.5 µm. Perithecia not seen. 

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Weir et al. 

Fig. 12. Colletotrichum alatae. ICMP 18122. A. Cultures on PDA, 10 d growth from single conidia, from above and below. B–C. Appressoria. D. Conidiogenous cells and conidia. 

E. Conidia. F. Setae. Scale bars B, F = 20 µm. Scale bar of B applies to B–E. 

138

Geographic distribution and host range: Known only from yam 

(Dioscorea alata), from Nigeria, Barbardos, India, Guadeloupe. 

Genetic identification: ITS sequences distinguish C. alatae from all 

other taxa. 

Notes: Anthracnose diseases of yam are found throughout the 

regions where the host is grown (e.g. Winch et al. 1984, Prasad & 

Singh 1960, Singh et al. 1966, Abang et al. 2002, 2003). Isolates 

from diseased yam leaves are morphologically (Winch et al. 1984) 

and genetically (Abang et al. 2002) diverse. Both of these authors 

used a broad species concept, grouping all isolates sourced from 

yam under the single name C. gloeosporioides. In this paper we 

accept part of that diversity to represent a distinct species, newly 

described here as C. alatae. The type specimen of C. alatae 

matches the SGG (slow growing grey) group of Abang et al. (2002), 

the group that these authors found to be more pathogenic to yam 

than the other morphological and genetic groups they recognised 

within C. gloeosporioides. In addition to the Nigerian isolates of 

Abang et al. (2002), isolates from yam from Barbados (isolates 

SAS8 and SAS9 from Sreenivasaprasad et al. 1996), Guadeloupe 

(GenBank accession GQ495617) and India (CBS 304.67 and 

GenBank accession FJ940734) belong in this clade, while no 

isolates from other hosts have been found. 

Other isolates from yam that we sequenced included some 

representing the Abang et al. (2002) FGS group (Abang Cg22 = 

ICMP 18120, Abang Cg13 = ICMP 18125, Abang CgS6 = ICMP 

18117, Abang CgS2 = ICMP 18121), a group distinguished from 

the highly pathogenic SGG isolates by faster growth in culture and 

shorter conidia (Abang et al. 2002). Two of these isolates (ICMP 

18120, 18125) genetically match C. fructicola, the others match C. 

siamense. 

Several names have been applied to Colletotrichum 

specimens from anthracnose of yam stems and leaves, including 

Gloeosporium pestis Massee, G. “dioscoreae” Sawada (nom. 

inval.; no Latin diagnosis), Colletotrichum dioscoreae Av.-Saccá 

1917, and C. dioscoreae Tehon 1933. In addition, Gloeosporium 

bomplandii Speg. was described from a host doubtfully 

identified as Dioscorea. Because of the broad genetic diversity 

of Colletotrichum spp. associated with diseased yam, the lack 

of cultures from any of these early type specimens, and the 

uncertainty to which part of the yam-associated diversity they 

correspond, we have chosen not to use these names for our 

newly recognised, yam-specialised pathogen. Whether the postharvest 

tuber rot referred to as dead skin disease of yam (Abang 

et al. 2003, Green & Simmons 1994) is caused by the same 

Colletotrichum population as associated with diseased foliage is 

not known. 

Other specimen examined: Nigeria, Kpite, on Dioscorea alata leaf, coll. M.M. Abang 

Cg25, 2001 (ICMP 18122). 

* Colletotrichum alienum B. Weir & P.R. Johnst., sp. nov. 

MycoBank MB563591. Figs 13, 14. 

Etymology: Based on the biology of this species, confined to exotic 

hosts and presumed to be a recent introduction to Australasia. 

Holotype: New Zealand, Auckland, Kumeu research orchard, 

Malus domestica fruit rot, coll. P.R. Johnston C824, 14 Aug. 1987, 

PDD 101996; ex-type culture ICMP 12071. 



Colonies grown from single conidia on Difco PDA 85 mm diam after 

10 d. Colonies often with distinct sectors; some with cottony, grey 

aerial mycelium with numerous dark-based acervuli and orange 

conidial ooze visible through the mycelium; others with dense, 

cottony to felted mycelium, fewer acervuli and these hidden by 

the dense mycelium. In reverse, irregular dark grey patches and 

sectors masking the pale orange coloured pigmentation. ICMP 

18691 looks “stale” with slow growth, dense, pale aerial mycelium 

and sparse conidial production and no perithecia. Conidia (12.5–) 

15.5–17.5(–22) × (3–)5–5.5(–6) µm (av. 16.5 × 5.0 µm, n = 70), 

cylindric with broadly rounded ends. Appressoria mostly simple, 

globose to short-cylindric, a few with broad, irregular lobes; ICMP 

18691 has mostly lobed appressoria. Perithecia forming in most 

cultures after about 10 d, dark-walled, globose with short, narrow 

ostiolar neck. Ascospores (14.5–)17–19.5(–22) × 4–5(–6) µm (av. 

18.1 × 4.6 µm, n = 55), cylindric, curved, tapering slightly to each 

end. 

Geographic distribution and host range: Known only from Australia 

and New Zealand, common on a wide range of introduced fruit 

crops. 

Genetic identification: ITS sequences do not separate C. alienum 

from some C. siamense isolates. These taxa are best distinguished 

using CAL or GS. 

Notes: Common on commercial fruit crops, this fungus was referred 

to as C. gloeosporioides Group A by Johnston & Jones (1997) and 

Johnston et al. (2005). 

Other specimens examined: Australia, New South Wales, Murwillumbah, on Persea 

americana (DAR 37820 = IMI 313842 = ICMP 18691). New Zealand, Auckland, 

Oratia, Shaw Rd, on Malus domestica fruit rot, coll. P.R. Johnston C938.5, 14 Apr. 

1988 (ICMP 18725); Bay of Plenty, Katikati, on Diospyros kaki ripe fruit rot, coll. M.A. 

Manning, Jun. 1989 (ICMP 17972); Bay of Plenty, Te Puke, on Persea americana 

ripe fruit rot, coll. W.F.T. Hartill, 2 Feb. 1988 (ICMP 18704); Bay of Plenty, Te Puna, 

on Persea americana ripe fruit rot, coll. W.F.T. Hartill, 25 Jan. 1988 (ICMP 18703); 

Bay of Plenty, on Persea americana ripe fruit rot, coll. W.F.T. Hartill, Feb. 1991 

(ICMP 18621); Waikato, Hamilton, on Malus domestica fruit rot, coll. G.I. Robertson, 

May 1988 (ICMP 12068). 

* Colletotrichum aotearoa B. Weir & P.R. Johnst., sp. nov. 


Etymology: Based on the Maori name for New Zealand; most 

isolates from native New Zealand plants belong here. 

Holotype: New Zealand, Auckland, Glen Innes, Auckland University 

campus, on Coprosma sp. incubated berries, coll. B. Weir C1282.4, 

30 Apr 2009, PDD 101076; ex-type culture ICMP 18537. 


after 10 d, several isolates with restricted growth, 50–55 mm diam 

with an irregularly scalloped margin. Aerial mycelium cottony to 

dense cottony, tufted near centre, grey to dark grey, scattered, 

small, dark-based acervuli and large, globose, stromatic structures 

partially embedded in agar, these sometimes splitting apart and 

forming conidia. In reverse typically with pinkish-orange pigments, 

variable in intensity, in some isolates this colour partially hidden 

by more or less concentric bands of dark grey pigment. Conidia 

(12–)16–17.5(–21.5) × (4.5–)5–5.5(–6.5) µm (av. 16.9 × 5.2 µm, 

n = 216), cylindric, straight, apex broadly rounded, often tapering 

slightly towards subtruncate base, 0-septate, hyaline. Appressoria 

139

Weir et al. 

Fig. 13. Colletotrichum alienum. A, E, F. ICMP 12071 – ex-holotype culture. B. ICMP 18703. C–D. ICMP 12068. G–I. ICMP 18691 (ex DAR 37820). A–B. Appressoria. C–D. Asci 

and ascospores. E. Conidia. F. Conidiogenous cells. G. Appressoria. H. Conidia. I. Conidiogenous cells. Scale bar D = 20 µm. Scale bar of D applies to A–I. 

140



Fig. 14. Colletotrichum alienum. A. ICMP 12071 – ex-holotype culture. B. ICMP 12068. C. ICMP 18691 (ex DAR 37820). A–C. Cultures on PDA, 10 days growth from single 

conidia, from above and below. 

variable in shape, simple to broadly lobed, sometimes in groups, 

sometimes intercalary, about 7–17 × 4–9.5 µm. Perithecia not seen 

in culture. 

Geographic distribution and host range: Confirmed only from New 

Zealand, but GenBank records suggest C. aotearoa also occurs in 

China (see below). In New Zealand this species is common on a 

taxonomically diverse set of native plants, as both a fruit rot and a 

leaf endophyte, and has also been isolated from leaves of several 

species of naturalised weeds. 

Genetic identification: ITS sequences do not separate C. aotearoa 

from several taxa in the Kahawae and Musae clades. This species 

can be distinguished using several other genes, including TUB2, 

CAL, GS, and GAPDH. 

Notes: All isolates in the C. gloeosporioides complex from New 

Zealand native plants studied here belong in the Kahawae 

clade, and most of these are C. aotearoa; a small number of leaf 

endophyte isolates from New Zealand native trees are C. kahawae 

subsp. ciggaro. The C. aotearoa isolates have been isolated as 

endophytes from symptomless leaves as well as from rotting fruit 

from native trees. Morphologically indistinguishable from isolates 

of C. kahawae subsp. ciggaro, this species is distinguished 

genetically with all genes sampled, except ITS. The GAPDH gene 

tree splits C. aotearoa into two well supported clades, but these do 

not correlate to any other features, either geographic or biological. 

Isolates associated with distinctive and common leaf spots on 

Meryta sinclairii, first recorded by Beever (1984), belong in this 

species. Whether isolates of C. aotearoa from other hosts are able 

to cause the same disease on Meryta is not known. 

Also in C. aotearoa are a range of isolates from weeds that 

have become naturalised in New Zealand. We assume that C. 

aotearoa is a New Zealand native species. It has a broad host 

range amongst native plants and has apparently jumped host to 

some weeds. It has never been found associated with cultivated 

plants or as a rot of cultivated fruit. 

Colletotrichum aotearoa may also occur in China. ITS 

sequences from isolates from Boehmeria from China (GenBank 

records GQ120479 and GQ120480) from Wang et al. (2010) 

match exactly a set of C. aotearoa isolates. ITS between-species 

differences within the C. gloeosporioides complex are very small, 

so this match needs confirming with additional genes. C. aotearoa 

was referred to as Undescribed Group 2 by Silva et al. (2012b). 

Other specimens examined: New Zealand, Auckland, Freemans Bay, on Vitex 

lucens fruit, coll. P.R. Johnston C1252.1, 26 Aug. 2007 (ICMP 18532; PDD 92930). 

on Berberis sp. leaf spot, coll. N. Waipara C69 (ICMP 18734); Auckland, Mangere, 

on Berberis glaucocarpa leaf spot, coll. N. Waipara C7, Jun. 2007 (ICMP 18528); 

Auckland, Waitakere Ranges, on Kunzea ericoides leaf endophyte, coll. S. Joshee 

7Kun3.5, Jan. 2004 (ICMP 17324); Auckland, Waitakere Ranges, on Prumnopitys 

ferruginea leaf endophyte, coll. S. Joshee 8Mb5.1, Jan. 2004 (ICMP 18533); Auckland, 

Waitakere Ranges, on Dacrycarpus dacrydioides leaf endophyte, coll. S. Joshee 

5K5.9, Jan. 2004 (ICMP 18535); Auckland, St Johns, Auckland University campus, 

on Coprosma sp. incubated berries, coll. B. Weir C1282.1, 30 Apr. 2009 (ICMP 

18577); Auckland, Mt Albert, on Acmena smithii lesions fruit, coll. P.R. Johnston C847, 

9 Sep. 1987 (ICMP 18529); Auckland, Glen Innes, Auckland University campus, on 

Coprosma sp. incubated berries, coll. B. Weir C1282.3, 30 Apr. 2009 (ICMP 18536); 

Auckland, Orakei, on Ligustrum lucidum leaf spot, coll. C. Winks & D. Than M136.3 

(ICMP 18748); Auckland, Waitakere Ranges, on Podocarpus totara leaf endophyte, 

coll. S. Joshee 3T5.6, Jan. 2004 (ICMP 17326); Auckland, Waitakere Ranges, Huia, 

on Geniostoma ligustrifolium leaf endophyte, coll. S. Bellgard M128, 8 Jul. 2010 (ICMP 

18540); Auckland, Waitakere Ranges, Huia, on Coprosma sp. rotten berry, coll. S. 

Bellgard M130-2, 8 Jul. 2010 (ICMP 18541); Auckland, Waiheke Island, Palm Beach, 

on Meryta sinclairii leaf spot, coll. P.R. Johnston C1310.1, 21 Mar. 2010 (PDD 99186; 

ICMP 18742); Auckland, Tiritiri Island, on Dysoxylum spectabile fruit rot, coll. P.R. 

141

Weir et al. 

Fig. 15. Colletotrichum aotearoa. A. ICMP 17324. B. ICMP 18529. C. ICMP 18548. D. 18532. E. ICMP 18540. A–C. Appressoria. D. Conidiogenous cells. E. Conidia. Scale bar 

A = 20 µm. Scale bar of A applies to A–E. 

Johnston C1220, 12 Feb. 1997 (PDD 67042; ICMP 18740); Northland, Whangaruru, 

on Vitex lucens fruit rot, coll. P.R. Johnston C880.1, L. Brako, P. Berry, 28 Jan. 1988 

(PDD 48408; ICMP 18530); on Berberis sp. leaf spot, coll. N. Waipara C77 (ICMP 

18735), on Lonicera japonica leaf spot, coll. N. Waipara J3 (ICMP 18736); Wellington, 

Waikanae, on Coprosma sp. leaf, coll. B. Weir C1285, 14 May 2009 (ICMP 18548); 

Auckland, Wenderholm Regional Park, on Melicytus ramiflorus leaf endophyte, coll. 

G.C. Carroll MELRA, 16 Sep. 2009 (ICMP 18543). 

* Colletotrichum asianum Prihastuti, L. Cai & K.D. Hyde, 

Fungal Diversity 39: 96. 2009. Fig. 17. 

Prihastuti et al. (2009) provide a description of this species. 

Geographic distribution and host range: Known on Mangifera 

indica from Australia, Colombia, Japan, Panama, Philippines, and 

Thailand; also reported on Coffea arabica from Thailand. 

142 

Genetic identification: Colletotrichum asianum is distinguished from 

all other taxa using any of the genes tested, including ITS. 

Notes: Although the type specimen is from coffee, this fungus is isolated 

commonly from mango (Mangifera indica) (e.g. Morphological Group 

1 from Than et al. 2008; IMI 313839 from Australia; MAFF 306627 

from Japan). Isolates referred to Colletotrichum indet. sp. 1 by Rojas 

et al. (2010), also associated with mango fruit rots, again match C. 

asianum. Based on ITS sequences, isolates Man-63 and Man-69 

cited by Afanador-Kafuri et al. (2003) from mango from Colombia, are 

probably also C. asianum. Several papers have reported genetically 

uniform populations of C. gloeosporioides associated with M. indica 

around the world (e.g. Hodson et al. 1993, Alahakoon et al. 1994, 

Sanders & Korsten 2003) and these perhaps also represent C. 

asianum, although DNA sequences are not available to confirm this.



Fig. 16. Colletotrichum aotearoa. A. ICMP 18537 – ex-holotype culture. B. ICMP 18548. C. ICMP 18532. D. ICMP 18740. E. ICMP 18533. F. ICMP 18530. A–F. Cultures on 

PDA, 10 d growth from single conidia, from above and below. 

Three earlier species, originally described from leaves rather 

than fruit of Mangifera, may provide earlier names for C. asianum 

but type material for these species has not been examined in this 

study; C. mangiferae Kelkar, Gloeosporium mangiferae Henn. 1898, 

and G. mangiferae Racib. 1900. As with most substrates, several 

different species of Colletotrichum often occur on the same host. 

143

Weir et al. 

For example, Damm et al. (2012a, b, this issue) report members 

of the C. acutatum and C. boninense species complexes, C. 

simmondsii, C. fioriniae, and C. karstii, from mango from Australia. 

Isolates from Capsicum reported by Than et al. (2008) as C. 

gloeosporioides Morphological Group 2 (e.g. isolates Ku4 = ICMP 

144 

Fig. 17. Colletotrichum asianum. A. ICMP 18648 (ex 

CBS 124960). B. ICMP 18580 (ex MFLU 090234). C. 

ICMP 18603 (ex MAFF 306627). D. ICMP 18604 (ex 

HKUCC 18602). E. ICMP 18696 (ex IMI 313839). A–E. 

Cultures on PDA, 10 d growth from single conidia, from 

above and below. 

18575 and Ku8 = ICMP 18618), were referred to as C. asianum by 

Hyde et al. (2009), however they are genetically distinct from C. 

asianum and belong to C. siamense based on our analyses. 

The C. asianum protologue designates the holotype as MFLU 

090234, and the culture derived from the holotype as “BCC” with

no strain number. The ex-holotype culture is listed as BDP-I4 in the 

Prihastuti et al. (2009) Table 1, but this number is not mentioned 

in the description. Culture BDP-I4 was obtained from the authors 

(Prihastuti et al. 2009) for this study. 

Specimens examined: Australia, New South Wales, Sextonville, on Mangifera 

indica, 1987 (IMI 313839 = ICMP 18696). Philippines, on Mangifera indica (MAFF 

306627 = ICMP 18603). Thailand, Chiang Mai, on Mangifera indica fruit, coll. P.P. 

Than M3 (HKUCC 10862 = ICMP 18605); Chiang Mai, on Mangifera indica fruit, 

coll. P.P. Than M4 (HKUCC 10863 = ICMP 18604); Mae Lod Village, Mae Taeng 

District, Chiang Mai, on Coffea arabica berries, coll. H. Prihastuti BPD-I4, 16 Jan. 

2008 (ex-holotype culture of C. asianum from specimen MFLU 090234 = ICMP 

18580 = CBS 130418). Panama, Gamboa, on Mangifera indica fruit rot, coll. S. Van 

Bael GJS 08-144, Jul 2008 (CBS 124960 = ICMP 18648). 

Colletotrichum boehmeriae Sawada, Hakubutsu Gakkwai 

Kwaihô (Trans. Nat. Hist. Soc. Formosa) 17: 2. 1914. 

Notes: Sawada (1922) provided an English translation of his original 

description. This species was described as a stem pathogen of 

Boehmeria nivea, and remains in use in this sense (e.g. Li & Ma 

1993). Wang et al. (2010) cite several GenBank accessions from 

isolates they identify as C. gloeosporioides that cause severe 

disease of Boehmeria. Based on a comparison of the GenBank data 

with our ITS gene tree, these and other isolates from the same host 

deposited by the same authors (GQ120479–GQ120499), appear 

to represent three different taxa within the C. gloeosporioides 

complex — C. gloeosporioides s. str., C. aotearoa, and C. fructicola. 

Isolates representative of all three taxa are reportedly pathogenic 

on Boehmeria (Wang et al. 2010). The genetic relationship of these 

fungi needs to be confirmed using additional genes. 

Colletotrichum camelliae Massee, Bull. Misc. Inform. Kew. 

1899: 91. 1899. 

Notes: Colletotrichum camelliae was described by Massee (in 

Willis 1899) from the living leaves of tea (Camellia sinensis) from 

Sri Lanka. It was placed in synonymy with C. gloeosporioides by 

von Arx (1957). Although not listed by Hyde et al. (2009), the name 

is widely used in the trade and semi-popular literature as the causal 

agent of the brown blight disease of tea (e.g. Sosa de Castro et al. 

2001, Muraleedharan & Baby 2007). 

We have been unable to sample Colletotrichum isolates 

from tea with typical brown blight symptoms. There are four 

GenBank accessions of Colletotrichum from tea, two from China 

(EU732732, FJ515007), one from Japan (AB218993), and 

another from Iran (AB548281), referred variously to C. camelliae, 

C. crassipes and C. gloeosporioides. Although ITS sequences 

only are available for these geographically widespread isolates, 

the DNA sequence of the Iranian isolate appears to match C. 

gloeosporioides s. str., while those from the other three isolates 

are all very similar to each other. The ITS sequence from these 

isolates matches that of CBS 232.79, from tea shoots from Java 

(GenBank JX009429). GAPDH and ITS sequences from CBS 

232.79 (GenBank JX009417, JX009429) place this isolate in C. 

fructicola. Note that CBS 571.88, isolated from tea from China 

and deposited as Glomerella cingulata, is a Colletotrichum sp. 

outside C. gloeosporioides s. lat., based on ITS sequences 

(GenBank JX009424). 

We tested the pathogenicity of CBS 232.79 and isolates of G. 

cingulata “f. sp. camelliae” (see below) using detached tea leaves 

and found that only the G. cingulata “f. sp. camelliae” isolates were 

strong pathogens (unpubl. data). 



The genetic relationship between the pathogen of ornamental 

Camellia (here referred to G. cingulata “f. sp. camelliae”), isolates 

from tea with DNA sequence data in GenBank, and isolates 

associated with brown blight symptoms of tea remain unresolved. 

Additional isolates with known pathogenicity, collected from typical 

brown blight symptoms from the field, are required to determine 

whether or not there are two distinct pathogens of Camellia, one of 

tea, the other of ornamental varieties. 

Other Colletotrichum species reported from tea include C. 

“theae-sinensis”, an invalid recombination of Gloeosporium theaesinensis 

I. Miyake, proposed by Yamamoto (1960). Moriwaki and 

Sato (2009) summarised the taxonomic history of this name and 

transferred G. theae-sinensis to Discula on the basis of DNA 

sequences. Sphaerella camelliae Cooke and its recombination 

Laestadia camelliae (Cooke) Berl. & Voglino were listed by von Arx 

& Müller (1954) as synonyms of Glomerella cingulata. This species 

is now accepted as Guignardia camelliae (Cooke) E.J. Butler ex 

Petch and is regarded as the causal agent of copper blight disease 

of tea (Spaulding 1958). 

Thang (2008) placed C. camelliae in synonymy with C. 

coccodes, presumably on the basis of the Species Fungorum 

synonymy (www.speciesfungorum.org, website viewed 6 Oct 

2010). Thang (2008) questioned the synonymy, noting differences 

between the descriptions of the two species provided by Massee 

(in Willis 1899) and Sutton (1980) respectively. 

Colletotrichum caricae F. Stevens & J.G. Hall, Z. 

Pflanzenkrankh., 19: 68. 1909. 

Notes: Placed in synonymy with C. gloeosporioides by von Arx 

(1957), C. caricae was listed as a separate species by Sutton (1992). 

It was described from fruits and leaves of Ficus carica from the USA 

(Stevens & Hall 1909) but is poorly understood both morphologically 

and biologically. Its genetic relationship to and within the C. 

gloeosporioides species complex, and to other Ficus-associated 

species such as Colletotrichum ficus Koord. and Glomerella cingulata 

var. minor (here placed in synonymy with C. fructicola) is unknown. 

Glomerella cingulata (Stonem.) Spauld. & H. Schrenk, 

Science, n.s. 17: 751. 1903. 

Basionym: Gnomoniopsis cingulata Stonem., Bot. Gaz. 26: 101. 

1898. 

= Gloeosporium cingulatum G.F. Atk., Bull. Cornell Univ. Agric. Exp. Sta. 49: 

306. 1892. [fide Stoneman 1898] 

Notes: Stoneman (1898) described Glomerella cingulata from 

diseased stems of Ligustrum vulgare from the USA and reported the 

development of perithecia in cultures initiated from conidia of what 

she considered its asexual morph, Gloeosporium cingulatum. There 

are recent reports of anthracnose diseases of Ligustrum (e.g. Alfieri 

et al. 1984, Vajna & Bagyinka 2002) but the relationship of isolates 

causing this disease to the C. gloeosporioides complex is not known. 

Glomerella cingulata is often linked taxonomically to the 

anamorph Colletotrichum gloeosporioides, and the name has in the 

past been applied in an equally broad sense to C. gloeosporioides 

s. lat. (e.g. Small 1926, von Arx & Müller 1954). However, it is 

unlikely that the type specimen of G. cingulata represents the 

same species as C. gloeosporioides s. str. (see notes under C. 

gloeosporioides). Colletotrichum gloeosporioides s. str. is not 

known to form perithecia in culture, and there are no isolates of 

C. gloeosporioides s. str. known to us that are associated with a 

Glomerella state on diseased stems of Ligustrum, An isolate of C. 

145

Weir et al. 

Fig. 18. Glomerella cingulata “f. sp. camelliae”. A, C, D. ICMP 10643. B, E. ICMP 10646. A–B. Appressoria. C. Conidiogenous cells. D–E. Conidia. Scale bar A = 20 µm. Scale 

bar of A applies to A–E. 

aotearoa (ICMP 18748) was isolated from Ligustrum lucidum in 

New Zealand, but it was not associated with a stem lesion and no 

C. aotearoa isolates were observed forming perithecia. 

Glomerella cingulata var. brevispora Wollenw., Z. 

Parasitenk. (Berlin) 14: 260. 1949. 

Notes: Described from fruit rots from Germany, this name has not 

been used since. No cultures are available and its relationship to 

and within the C. gloeosporioides complex is not known. 

146 

* Glomerella cingulata “f. sp. camelliae” (Dickens & Cook 

1989). Figs 18, 19. 

Notes: Dickens & Cook (1989) proposed the name Glomerella 

cingulata “f. sp. camelliae” for isolates morphologically typical of 

C. gloeosporioides s. lat. that were highly pathogenic to leaves and 

shoots of ornamental Camellia saluenensis hybrids, causing the 

disease Camellia twig blight. These authors reported the fungus 

from plants imported into the UK from New Zealand and noted that 

a similar disease had been reported from plants grown in the UK,



Fig. 19. Glomerella cingulata “f. sp. camelliae”. A. ICMP 18542. B. ICMP 10643. C. ICMP 10646. A–C. Cultures on PDA, 10 d growth from single conidia, from above and below. 

USA, Australia, France, and Italy. The disease has been reported 

from Camellia japonica, C. reticulata, and C. sasanqua. Although 

isolated in the UK from plants imported from New Zealand, this 

pathogen has not yet been found on Camellia plants growing in 

New Zealand. 

We have sequenced authentic isolates cited by Dickens & 

Cook (1989) as well as isolates pathogenic to Camellia saluenensis 

collected from the USA. They are similar to each other genetically 

as well as biologically and morphologically. ITS sequences alone 

distinguish G. cingulata “f. sp. camelliae” from all other taxa in the 

C. gloeosporioides complex, and there is good genetic evidence to 

consider these isolates to be representative of a distinct species 

within the C. kahawae clade. A new species is not proposed here 

because the relationship between the G. cingulata “f. sp. camelliae” 

isolates and C. camelliae, the fungus causing brown blight of tea, 

remains uncertain. 

Dickens & Cook (1989) also reported two C. acutatum strains 

from ornamental Camellia species that were avirulent in tests 

with detached Camellia cv. Donation leaves. Strain IMI 351261, 

deposited 1992 in IMI by R. Cook, is likely to be one of them. This 

strain was confirmed as belonging to the C. acutatum species 

complex and identified as C. lupini, which causes lupin anthracnose 

and is occasionally found on other hosts (Damm et al. 2012a, this 

issue). Another strain from Camellia reticulata from China belongs 

to C. fioriniae, also a species in the C. acutatum complex, while 

a strain from New Zealand (ICMP 10338) is C. boninense s. str. 

(Damm et al. 2012a, b, this issue). 

See notes under C. camelliae. 

Specimens examined: UK, plants imported from New Zealand, on Camellia × 

williamsii, coll. Dickens & Cook 82/437, 1982 (authentic culture of Glomerella 

cingulata “f. sp. camelliae” – ICMP 10643; dried culture PDD 56488). USA, 

Mississippi, on Camellia sasanqua twig blight, coll. W.E. Copes CG02g, May 2002 

(ICMP 18542); South Carolina, on Camellia sp., coll. G. Laundon 20369, 1 Jan. 

1982 (ICMP 10646). 

Glomerella cingulata var. crassispora Wollenw., Z. 

Parasitenk. (Berlin) 14: 260. 1949. 

Notes: Described from Coffea arabica from a glasshouse in 

Germany, this name has not been used since. No cultures are 

available and its relationship to and within the C. gloeosporioides 

complex is not known. 

Glomerella cingulata “f. sp. manihotis” (Chevaugeon 

1956) 

Notes: See notes under Colletotrichum manihotis. 

Glomerella cingulata var. minor Wollenw., Z. Parasitenk. 

(Berlin) 14: 261. 1949. 

= Gloeosporium elasticae Cooke & Massee, Grevillea 18: 74. 1890. [fide 

Wollenweber & Hochapfel 1949] 

Notes: Placed here in synonymy with C. fructicola. 

Glomerella cingulata var. minor was described from Ficus from 

Germany, but Wollenweber & Hochapfel (1949) noted that the 

same fungus occurred also on other hosts in Europe, Africa, and 

America, including Malus and Coffea. Genetically the ex-holotype 

culture of G. cingulata var. minor (CBS 238.49) matches the type 

specimen of C. fructicola, although the culture itself appears to be 

stale, with slow growth and an irregularly scalloped margin (see 

147

Weir et al. 

images under C. fructicola). Wollenweber & Hochapfel (1949) used 

the name Gloeosporium elasticae Cooke & Massee for the conidial 

state of G. cingulata var. minor, the type specimens for both names 

being from Ficus. 

See also notes under C. queenslandicum. 

Specimen examined: Germany, Berlin-Dahlem, from Ficus edulis leaf spot, May 

1936 (ex-holotype culture of G. cingulata var. minor – CBS 238.49 = ICMP 17921). 

Glomerella cingulata var. migrans Wollenw., Z. Parasitenk. 

(Berlin) 14: 262. 1949. 

Notes: Placed here in synonymy with C. kahawae subsp. ciggaro, 

see notes under this species. 

Specimen examined: Germany, Berlin-Dahlem, on stem of Hypericum perforatum, 

Jun. 1937 (ex-holotype culture of Glomerella cingulata var. migrans – CBS 237.49 

= ICMP 17922). 

Glomerella cingulata “var. orbiculare” Jenkins & Winstead, 

Phytopathology 52: 15. 1962. 

Notes: Listed in Index Fungorum, this name was mentioned 

in an abstract, but is invalid (no Latin description) and never 

formally published. It was being used to refer to the teleomorph of 

Colletotrichum orbiculare, not part of the C. gloeosporioides complex 

(Cannon et al. 2012, this issue). Glomerella lagenaria (Pass.) 

F. Stevens, a recombination of the anamorphic name Fusarium 

lagenarium Pass., has also been used to refer to this teleomorph. 

Correll et al. (1993) comment on the pathogenicity of cucurbitassociated 

strains that form a Glomerella state in culture, suggesting 

a degree of confusion around the application of these names. 

Glomerella cingulata “f. sp. phaseoli” (Kimati & Galli 1970). 

Notes: Both G. cingulata “f. sp. phaseoli” (e.g. Castro et al. 2006) 

and Glomerella lindemuthiana (e.g. Rodríguez-Guerra et al. 2005, 

as G. lindemuthianum) have been used for the teleomorph of 

Colletotrichum lindemuthianum in the recent literature, the two 

names placed in synonymy by Sutton (1992). This fungus is not part 

of the C. gloeosporioides complex (Cannon et al. 2012, this issue). 

Glomerella cingulata var. sorghicola Saccas, Agron. Trop. 

(Maracay). 9: 171. 1954. 

Notes: Not a member of the C. gloeosporioides complex. Sutton 

(1992) suggested using this name to refer to the teleomorph of 

Colletotrichum sublineola, although Crouch et al. (2006) note that 

C. sublineola has no known teleomorph. 

* Colletotrichum clidemiae B. Weir & P.R. Johnst. sp. nov. 


= Colletotrichum gloeosporioides “f. sp. clidemiae” (Trujillo et al. 1986). 

Etymology: Based on the host reportedly susceptible to this species. 

Holotype: USA, Hawai’i, Aiea, on Clidemia hirta leaf spot, coll. S.A. 

Ferreira & K. Pitz, 14 May 2010, PDD 101997; ex-type culture 

ICMP 18658. 

Colonies grown from single conidia on Difco PDA 25 mm diam after 

10 d, aerial mycelium grey, cottony, sparse, surface of colony with 

148 

numerous small, dark-based acervuli with deep orange conidial 

ooze and scattered setae, in reverse more or less colourless except 

for the acervuli and masses of conidial ooze showing through. After 

18 d numerous globose, pale walled protoperithecia developing 

near centre of colony. Conidia (16−)18−20(−26.5) × (4.5−)5.5−6 

µm (av. 19.3 × 5.5 µm, n = 48), broad-cylindric, ends broadly 

rounded, longer conidia sometimes tapering slightly towards the 

base. Appressoria variable in shape, some simple, subglobose, 

but often with a small number of broad, irregular lobes. Perithecia 

mature after about 21 d, dark-walled, about 200–250 µm diam with 

short ostiolar neck, perithecial wall of 3–4 layers of angular cells 

10–15 µm diam with walls thin, pale brown to brown. Asci 8-spored 

60–67 × 10–14 µm. Ascospores (14–)15.5–19(–21.5) × 4.5–5.5(– 

6.5) µm (av. 17.2 × 5.0 µm, n = 46), oblong-elliptic, tapering to 

rounded ends, widest point toward one end, in side view flat on one 

side, rarely curved and if so, then slightly. 

Geographic distribution and host range: First reported from 

Clidemia, native to Panama, and subsequently introduced to 

Hawai’i as a pathogen of that host. Genetically matching isolates 

occur on native Vitis and Quercus spp. in Florida (see notes below). 

Genetic identification: ITS sequences do not separate C. clidemiae 

from C. aotearoa. The two species are best distinguished using 

ACT, GAPDH, or GS. 

Notes: Isolates referred to C. gloeosporioides “f. sp. clidemiae” by 

Trujillo et al. (1986) were highly pathogenic to Clidemia, but not to 

the other species of Melastomataceae tested. No voucher cultures 

of the original isolates collected from Panama were kept, but 

recent specimens isolated from naturalised Clidemia hirta plants in 

Hawai’i with typical disease symptoms are genetically uniform and 

distinct within the Kahawae clade. Phylogenetic, biological, and 

morphological evidence support this fungus being described as a 

new species within the C. gloeosporioides complex. 

A fungus isolated from a Vitis sp. in Florida and referred to as 

“Glomerella cingulata native host” by MacKenzie et al. (2007), is 

genetically close to our isolates from Clidemia and is here referred 

to the same species. Data in MacKenzie et al. (2007) shows the 

same fungus occurs on both Vitis and Quercus in Florida. Micromorphologically 

the isolates from Clidemia and from Vitis that 

we examined are similar with respect to the size and shape of 

appressoria, conidia, and ascospores. They are distinct in cultural 

appearance, the cultures of the Vitis-associated fungus having 

aerial mycelium darker and more dense, and a faster growth rate. 

Similar variation in cultural appearance is present in several of the 

phylogenetically defined species that we recognise. Whether or 

not the Clidemia-associated isolates are biologically distinct from 

the Vitis- and Quercus-associated isolates from Florida requires 

pathogenicity tests to determine. 

Other specimens examined: USA, Florida, Sarasota, on Vitis sp. leaf, coll. S. 

MacKenzie SS-Grape-12, 2002 (ICMP 18706); Hawai’i, Aiea, on Clidemia hirta leaf 

spot, coll. S.A. Ferreira & K. Pitz, 14 May 2010 (ICMP 18659, ICMP 18660, ICMP 

18661, ICMP 18662, ICMP 18663). 

Colletotrichum coffeanum F. Noak, Z. Pflanzenkrankh. 11: 

202. 1901. 

Notes: Waller et al. (1993) discussed the use of the names 

Colletotrichum coffeanum and Gloeosporium coffeanum Delacr. 

and the geographic and biological differences between these



Fig. 20. Colletotrichum clidemiae. A, B, E. ICMP 18658 – ex-holotype culture. C, D. ICMP 18706. A, D. Appressoria. B, C. Asci and ascospores. E. Conidia. Scale bar C = 20 

µm. Scale bar of C applies to A–E. 

species and the pathogen of coffee berries, C. kahawae. Both C. 

coffeanum and G. coffeanum were described from leaves of coffee, 

the two species distinguished by Noak (1901) by the presence 

or absence of setae in the acervuli. There is a wide range of C. 

gloeosporioides-like species on coffee plants (see Waller et al. 

1993 and notes under C. kahawae) and the relationships of C. 

coffeanum and G. coffeanum within the C. gloeosporioides species 

complex remain uncertain. 

149

Weir et al. 

Fig. 21. Colletotrichum clidemiae. A. ICMP 18658 – ex-holotype culture. ICMP 

18706. Cultures on PDA, 10 d growth from single conidia, from above and below. 

Colletotrichum cordylines Pollacci, Atti Ist. Bot. Univ. 

Pavia, Serie 2, 5: 44. 1899. 

Notes: Described from leaves of Cordyline indivisa from a botanical 

garden in Italy, the genetic and biological status of this species is not 

known. Two Cordyline-associated species are accepted in this study, 

C. cordylinicola from Thailand and the newly described C. ti from New 

Zealand. The original description of C. cordylines is brief (Pollacci 

1899) but it specifically mentions setae more than 100 µm long. 

Colletotrichum cordylinicola is described as lacking setae (Phoulivong 

et al. 2011) and in C. ti they are rare and when present much less than 

100 µm long. The phylogenetic significance of this apparent difference 

and confirmation that these names represent different fungi requires 

DNA sequences to be generated from type material of C. cordylines. 

* Colletotrichum cordylinicola Phoulivong, L. Cai & K.D. 

Hyde, Mycotaxon 114: 251. 2011 [“2010”]. Fig. 22. 

Phoulivong et al. (2011) provide a description. 

Geographic distribution and host range: Known only from Cordyline 

from Thailand and Eugenia from Laos. 

Genetic identification: ITS sequences separate C. cordylinicola 

from all other species. 

Notes: Phoulivong et al. (2011) report C. cordylinicola from 

Cordyline (Agavaceae) and Eugenia (Myrtaceae). They noted 

that the isolate from Eugenia was not pathogenic to Cordyline and 

vice versa, and they also showed that the specimens from the 

two hosts are genetically somewhat distinct, although forming a 

sister relationship amongst the taxa included in their analysis. The 

calmodulin gene tree generated from our sequence data together 

with the sequences provided by Phoulivong et al. (2011) (GenBank 

accession HM470236) supports placing the isolates from Eugenia 

and from Cordyline in the same species (unpubl. data). 

Colletotrichum cordylinicola is genetically distinct from a 

species associated with Cordyline leaf spots from New Zealand, 

described here as C. ti. See also notes under C. cordylines. 

150 

Specimen examined: Thailand, Chiang Mai, Sam Sai District, Maejo Village, on 

Cordyline fruticosa, coll. S. Phoulivong, 15 Mar. 2009 (ex-holotype culture – 

MFLUCC 090551 = ICMP 18579). Note that the ex-holotype culture was mistakenly 

cited as MFUCC 090551 by Phoulivong et al. (2011). 

Colletotrichum crassipes (Speg.) Arx, Verh. Kon. Ned. 

Akad. Wetensch., Afd. Natuurk., Sect. 2, 51(3): 77. 1957. 

Basionym: Gloeosporium crassipes Speg., Rivista Vitic. Enol. 2: 

405. 1878. 

Notes: Several isolates identified as Colletotrichum crassipes 

that have sequences accessioned to GenBank belong in C. 

gloeosporioides s. lat. GenBank accessions identified as C. 

crassipes that have a publically available culture include C. 

kahawae subsp. ciggaro (STE-U 5302 = CBS 112988 – AY376529, 

AY376577, FN557348, FN557538, and FN599821; STE-U 4445 

= CBS 112984 – AY376530, AY376578, – FN557347, FN557537, 

and FN599820), along with several other species outside of 

the C. gloeosporioides complex (CBS 169.59 = IMI 309371 – 

AJ536230, FN557344, and FN599817; CBS 159.75 – FN557345 

and FN599818; CBS 109355 – FN557346 and FN599819). 

Those with no isolates in a public collection include C. kahawae 

subsp. ciggaro (CORCS3 cited in Yang et al. (2011), HM584410, 

HM582002, HM585412), C. fructicola (strain 080912009 Jining, 

unpubl. data, FJ515007), and a possibly undescribed species 

within the Kahawae clade (strain SYJM02, unpubl. data, 

JF923835). Originally described from the berries of Vitis vinifera 

from Italy (Spegazzini 1878), the identity of C. crassipes remains 

unresolved. There is confusion regarding its morphology. Von Arx 

(1970) uses the name C. crassipes for fungi in which setae are 

rare, conidia are 22–34 × 6–8 µm (more or less matching the 

original description), and the lobed appressoria are distinctively 

globose in shape. Sutton (1980) uses a different morphological 

concept – setae common (according to Sutton these are rare in the 

otherwise morphologically similar C. musae), conidia 10–15 × 4.5– 

6.5 µm (Sutton’s concept of C. gloeosporioides is characterised by 

narrower conidia), and the appressoria deeply lobed. The conidial 

width cited for C. gloeosporioides by Sutton (1980), 3–4.5 µm, is 

narrower than we have found for all the taxa we accept within C. 

gloeosporioides s. lat., whereas his C. crassipes measurement of 

4.5–6.5 µm matches many of the taxa we recognise. Several of 

these taxa also have deeply lobed appressoria. 

Colletotrichum dracaenae Allesch., Rabenhorst’s 

Kryptogamen-Flora von Deutschland, Oesterreich und der 

Schweiz, Ed. 2, 1(7): 560. 1902. 

Notes: Farr et al. (2006) examined the type specimen of this 

species and concluded it was a member of C. gloeosporioides s. 

lat., based on conidial size and shape. Genetic data is not available 

to confirm this. See also discussion under C. petchii in Damm et al. 

(2012b, this issue) 

Colletotrichum fragariae A.N. Brooks, Phytopathology 21: 

113. 1931. 

Notes: Placed here in synonymy with C. theobromicola. See notes 

and additional specimens examined under C. theobromicola. 

The name C. fragariae was originally applied to isolates 

associated with a disease of strawberry (Fragaria × ananassa) 

runners (stolons) and petioles in Florida (Brooks 1931). Although 

the name was placed in synonymy with C. gloeosporioides by

von Arx (1957), it has continued to be used in the literature for 

strawberry-associated Colletotrichum isolates. It was accepted as 

distinct by Sutton (1992), although he noted confusion surrounding 

application of the name. Designation of one of Brook’s cultures 

(CBS 142.31 = IMI 346325) as the epitype of C. fragariae by Buddie 

et al. (1999) has allowed a modern, genetic basis for this name to 

be fixed. The ex-epitype culture of C. fragariae sits in a strongly 

supported clade containing isolates from a wide range of hosts 

from many parts of the world, including the ex-epitype culture of C. 

theobromicola, an earlier name for C. fragariae in the sense that we 

accept these species in this paper. 

There are several species from the C. gloeosporioides 

complex which inhabit diseased strawberry plants, and as shown 

by MacKenzie et al. (2007, 2008) isolates that genetically match 

the epitype of C. fragariae have a wide host range. Despite its 

name MacKenzie et al. (2007, 2008) regarded this fungus as 

simply one of a group of several species sometimes found on 

strawberry. Our study confirms that members of the C. fragariae/ 

theobromicola clade occur throughout the world on a wide range of 

hosts. Within the diversity of the C. fragariae/theobromicola clade, 

there is a subclade consisting of the C. fragariae epitype and two 

contemporary ex-strawberry isolates from the USA (Fig. 1), further 

work will be needed to establish if the strawberry stolon disease is 

restricted to this subclade. Despite regular surveys this disease has 

not been found on strawberries in New Zealand. 

Xie et al. (2010b) provides a good example of the confusion 

that continues to surround the application of Colletotrichum names 

to isolates from strawberry. These authors noted that putative C. 

gloeosporioides and C. fragariae isolates were difficult to distinguish 

using ITS sequences, the only sequences that they generated. 

Xie et al. (2010b) found 4 groups of isolates, each with a slightly 

different ITS sequence, two of those groups they considered to 

be C. fragariae and two to be C. gloeosporioides. To classify their 

isolates as either C. fragariae of C. gloeosporioides they used a 

restriction enzyme method based on Martinez-Culebras et al. 

(2000). Incorporating their ITS sequences into our ITS alignment, 

one of their groups genetically matches C. tropicale, one matches 

C. gloeosporioides s. str., one matches C. fructicola, and one 

matches C. siamense. These relationships are based on ITS 

sequences only — the genetic differences between some of these 

species are small and are indicative only of possible relationships. 

However, it is clear that none of the Xie et al. (2010b) sequences 

match those of the epitype of C. fragariae. There are also several 

species within the C. acutatum species complex associated with 

Fragaria (Damm et al. 2012, this issue). 



Fig. 22. Colletotrichum cordylinicola. ICMP 18579 (ex 

MFLUCC 090551 – ex-holotype culture). A. Cultures on 

PDA, 10 d growth from single conidia, from above and 

below. 

Specimen examined: USA, Florida, on Fragaria × ananassa, coll. A.N. Brooks, 1931 

(ex-epitype culture – CBS 142.31 = ICMP 17927). 

* Colletotrichum fructicola Prihastuti, L. Cai & K.D. Hyde, 


= Colletotrichum ignotum E.I. Rojas, S. A. Rehner & Samuels, Mycologia 102: 

1331. 2010. 

= Glomerella cingulata var. minor Wollenw., Z. Parasitenk. (Berlin) 14: 261. 

1949. 

Prihastuti et al. (2009) and Rojas et al. (2010) provide descriptions. 

Geographic distribution and host range: Originally reported 

from coffee berries from Thailand (as C. fructicola) and as a 

leaf endophyte from several plants in Central America (as C. 

ignotum), isolates that we accept as C. fructicola are biologically 

and geographically diverse. Known from Coffea from Thailand, 

Pyrus pyrifolia from Japan, Limonium from Israel, Malus domestica 

and Fragaria × ananassa from the USA, Persea americana from 

Australia, Ficus from Germany, Malus domestica from Brazil, 

Dioscorea from Nigeria, and Theobroma and Tetragastris from 

Panama. 

Genetic identification: ITS sequences do not separate C. fructicola 

from C. aeschynomenes and some C. siamense isolates. These 

taxa are best distinguished using GS or SOD2. 

Notes: Rojas et al. (2010) noted the occurrence of two distinct 

haplotype subgroups (A4-3 and A5-4) within their concept of C. 

ignotum. Our genetic analyses resolve the two clades representative 

of these two subgroups. However, together they are monophyletic 

within the Musae clade of the C. gloeosporioides complex, and we 

retain them here as a single species. Both clades include isolates 

from a wide range of hosts from many countries, and both are 

similar in morphology and cultural appearance. The types of both 

C. fructicola and C. ignotum are in the same haplotype subgroup. 

The C. fructicola protologue designates the holotype as MFLU 

090228, but the culture derived from holotype as “BCC” with no 

specimen number. The ex-holotype culture is listed as BDP-I16 in 

Table 1 of Prihastuti et al. (2009) but this number is not mentioned 

in the description. Culture BDP-I16 was obtained from the authors 

(Prihastuti et al. 2009) for this study and deposited as ICMP 18581. 

See also notes under G. cingulata var. minor. 

Specimens examined: Australia, Queensland, Bli-Bli, on Persea americana fruit 

rot, coll. L. Coates 24154 (ICMP 12568). Brazil, Rio Grande do Sul State, on Malus 

domestica leaf, coll. T. Sutton BR 8 2001, Jan. 2001 (ICMP 17787); Santa Catarina 

State, on Malus domestica leaf, coll. T. Sutton BR 21 2001, Jan. 2001 (ICMP 17788). 

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Fig. 23. Colletotrichum fructicola. A. ICMP 12568. B. ICMP 18615. C. ICMP 18581 (ex MFLU 090228 – ex-holotype culture of C. fructicola). D. ICMP 18610. E. ICMP 18646 

(ex CBS 125379 – ex-holotype culture of C. ignotum). F. ICMP 17921 (ex CBS 238.49 – ex-holotype culture of G. cingulata var. minor). A–F. Cultures on PDA, 10 d growth from 

single conidia, from above and below. 

Canada, Ontario, on Fragaria × ananassa, Jan. 1991 (IMI 345051 = ICMP 17819). 

Germany, Berlin-Dahlem Botanical Garden, on Ficus edulis leaf spot, (ex-holotype 

culture of Glomerella cingulata var. minor – CBS 238.49 = ICMP 17921). Indonesia, 

152 

Java, Bandung, Pangheotan Estate, on Camellia sinensis shoots, coll. H. Semangun, 

Apr. 1979 (CBS 232.79 = ICMP 18656). Israel, on Limonium sinuatum leaf lesion, coll. 

S. Freeman L32 (cited in Moriwaki et al. 2006) (ICMP 18613); on Limonium sp. leaf

lesion, coll. S. Freeman L50 (cited in Maymon et al. 2006) (ICMP 18698); on Limonium 

sp. leaf lesion, coll. S. Freeman Cg2 (cited in Maymon et al. 2006) (ICMP 18667); 

on Limonium sinuatum, coll. S. Freeman L11 (cited in Maymon et al. 2006) (ICMP 

18615). Japan, Saga, on Pyrus pyrifolia, coll. H. Ishii sA02-5-1 (cited in Chung et al. 

2006) (ICMP 18610). Nigeria, Ibadan, on Dioscorea alata leaf spot, M. Abang Cg13 

(cited in Abang et al. 2002) (ICMP 18125); Ilesha, Dioscorea rotundata leaf spots, coll. 

M. Abang Cg22 (cited in Abang et al. 2002) (ICMP 18120). Panama, Barro Colorado 

Monument, Tetragastris panamensis leaf endophyte, coll. E.I. Rojas E886, 1 Jun. 2004 

(ex-holotype culture of C. ignotum − CBS 125397 = ICMP 18646); Theobroma cacao 

leaf endophyte, coll. E. Rojas E183 (CBS 125395 = ICMP 18645). Thailand, Chiang 

Mai, Pa Daeng Village, on Coffea arabica berry, coll. H. Prihastuti BPD-I16, 12 Dec. 

2007 (ex-holotype culture of C. fructicola, from specimen MFLU 090228 – ICMP 

18581 = CBS 130416). USA, on Fragaria × ananassa crown, F. Louws 9, (ICMP 

18727); Florida, on Fragaria × ananassa, coll. F.A. Ueckes FAU552 (CBS 120005 = 

BPI 747977 = ICMP 18609); North Carolina, Lincoln County, on Malus domestica fruit, 

coll. T. Sutton CROTTS 13 2001, Jan. 2001 (ICMP 17789). 

* Colletotrichum gloeosporioides (Penz.) Penz. & Sacc., 

Atti Reale Ist. Veneto Sci. Lett. Arti., Serie 6, 2: 670. 1884. 

Fig. 24. 

Basionym: Vermicularia gloeosporioides Penz., Michelia 2: 450. 

1882. 

= Gloeosporium pedemontanum Pupillo, Ann. Sperim. Agrar. n.s. 6: 57. 1952. 

Cannon et al. (2008) provide a description of the species. 

Geographic distribution and host range: Most isolates of C. 

gloeosporioides are associated with Citrus, and in many parts of 

the world this fungus is common on Citrus, but it also occurs on 

other hosts including Ficus, Mangifera, Pueraria, and Vitis. The 

isolate reported as a pathogen of paper mulberry (Broussonetia 

papyrifera) by Yan et al. (2011) matches C. gloeosporioides s. str. 

genetically. 

Genetic identification: ITS separates C. gloeosporioides from all 

other species. 

Notes: The name Colletotrichum gloeosporioides is currently in 

common use in two senses, one a genetically and biologically 

broad sense more or less following von Arx (1957, 1970) and 

Sutton (1992), including the whole species complex, the other a 

strict sense, encompassing only those specimens genetically 

matching the epitype selected for this name by Cannon et al. 

(2008). Depending on the context, use of the name in either 

sense can be useful. When used in a broad sense in this paper, 

it is referred to as the C. gloeosporioides species complex or C. 

gloeosporioides s. lat. 

Colletotrichum gloeosporioides is often linked taxonomically to 

the teleomorph Glomerella cingulata, see notes under G. cingulata. 



Specimens examined: Australia, New South Wales, Tamworth, on Carya 

illinoinensis (DAR 76936; ICMP 18738). Italy, Calabria, on Citrus sinensis, 

(ex-epitype culture of C. gloeosporioides − IMI 356878 = CBS 112999 = ICMP 

17821); on Citrus limon juice, coll. G. Goidánich, 1951 (ex-holotype culture of 

Gloeosporium pedemontanum – CBS 273.51 = ICMP 19121). New Zealand, 

Auckland, Sandringham, on Citrus sp. fruit, coll. P.R. Johnston C1014.6, 2 May 

1988 (ICMP 12939); Auckland, Sandringham, on Ficus sp. fruit, coll. P.R. Johnston 

C945.2, 9 May 1988 (ICMP 12066); Auckland, on Citrus sp. fruit, coll. G. Caroll, Feb 

2010 (ICMP 18730); Northland, Kerikeri, Kapiro Rd, on Citrus sinensis fruit, coll. P.R. 

Johnston C1009.2, 10 Aug. 1988 (ICMP 12938). South Africa, on Mangifera indica, 

coll. L. Korsten Cg68 (ICMP 18694). USA, Georgia, on Pueraria lobata (AR2799 = 

CBS 119204 = BPI 871837 = ICMP 18678); Florida, on Citrus sp. leaf lesion, coll. N. 

Peres SRL-FTP-9 (ICMP 18695); Florida, on Vitis vinifera leaf lesion, coll. N. Peres 

LAGrape8 (ICMP 18697). 

Colletotrichum gloeosporioides “f. sp. aeschynomenes” 

(Daniel et al. 1973, as aeschynomene). 

Notes: See Colletotrichum aeschynomenes. 

Colletotrichum gloeosporioides “f. alatae” R.D. Singh, 

Prasad & R.L. Mathur, Indian Phytopathol. 19: 69. 1966. 

[nom. inval., no Latin description, no type designated] 

Notes: See Colletotrichum alatae. 

Colletotrichum gloeosporioides var. aleuritis Saccas & 

Drouillon [as “aleuritidis”], Agron. Trop. (Nogent-sur-Marne) 

6: 249. 1951. 

≡ Glomerella cingulata var. aleuritis Saccas & Drouillon [as “aleuritidis”], 

Agron. Trop. (Nogent-sur-Marne) 6: 251. 1951. 

Notes: Originally described from Aleurites fordii and A. montaba 

from French Equatorial Africa, these names have not been used 

since being described and the genetic relationship of this fungus 

to and within the C. gloeosporioides species complex is unknown. 

Although the original publications have not been seen, both names 

were tagged as invalid in the Index of Fungi 2: 53, 57 (1952). 

Colletotrichum gloeosporioides “f. sp. clidemiae” (Trujillo 

et al. 1986). 

Notes: See Colletotrichum clidemiae. 

Fig. 24. Colletotrichum gloeosporioides. A. ICMP 17821 

(ex IMI 356878 – ex-epitype culture). A. Cultures on PDA, 

10 d growth from single conidia, from above and below. 

Colletotrichum gloeosporioides “f. sp. cucurbitae” 

(Menten et al. 1980). 

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Notes: First described from cucumber, this fungus is widely 

regarded as a synonym of C. orbiculare in the plant pathology 

literature (e.g. Snowdon 1991, da Silva et al. 2011). 

Colletotrichum gloeosporioides “f. sp. cuscutae” (Zhang 

1985). 

Notes: A strain identified by this name was developed as a 

mycoherbicide against dodder (Cuscuta chinensis in China (Zhang 

1985). This strain referred to as “Lu Bao No.1” is apparently 

included in the study of Guerber et al. (2003) as strain 783 and 

belongs to the C. acutatum species complex. Other strains from 

dodder in the USA included in the same study were revealed to be 

C. fioriniae, while a strain from Dominica was found to represent a 

new species, both belonging to the C. acutatum species complex 

as well (Damm et al. 2012, this issue). 

Colletotrichum gloeosporioides var. gomphrenae Perera, 

Revista Fac. Agron. Univ. Nac. La Plata 41: 12. 1965. 

Notes: Originally described from Gomphrena globosa, the name has 

not been used since it was described and its genetic relationship 


Colletotrichum gloeosporioides var. hederae Pass., Atti 

Reale Accad. Italia, Rendiconti., Serie 4, 6: 469. 1889. 

Notes: The original description of this Hedera-inhabiting species, 

with fusiform, straight to curved conidia suggests that it is a 

synonym of the Hedera pathogen C. trichellum. 

Colletotrichum gloeosporioides f. heveae (Petch) Saccas, 

Agron. Trop. (Nogent-sur-Marne) 14: 430. 1959. 

Basionym: Colletotrichum heveae Petch, Ann. Roy. Bot. Gard. 

Peradeniya 3(1): 8. 1906. 

Notes: Originally described from the leaves of seedlings of Hevea 

brasiliensis from Sri Lanka, this fungus was described with very 

broad conidia, 18–24 × 7.5–8 µm. Carpenter & Stevenson (1954) 

considered this, and several other Colletotrichum, Gloeosporium 

and Glomerella species described from rubber, to be synonyms of 

C. gloeosporioides. The genetic relationship of these species to 

and within the C. gloeosporioides species complex is unknown. See 

also notes in Damm et al. (2012b, this issue) under Colletotrichum 

annelatum. 

Colletotrichum gloeosporioides “f. sp. hyperici” (Harris 

1993). 

Notes: This name was first used by Harris (1993) for strains of 

C. gloeosporioides pathogenic to Hypericum perforatum. Earlier 

studies by Hildebrand & Jensen (1991) had found the Hypericum 

pathogen to be pathogenic also on several other plants. The 

genetic relationship of the Hypericum pathogen to and within the 

C. gloeosporioides species complex is unknown. Note that the exholotype 

culture of G. cingulata var. migrans, a variety here placed 

in synonymy with C. kahawae subsp. ciggaro, was also isolated 

from Hypericum. 

154 

Colletotrichum gloeosporioides “f. sp. jussiaeae” (Boyette 

et al. 1979). 

Notes: Strains identified as C. gloeosporioides “f. sp. jussiaeae” are 

highly pathogenic, specialised pathogens of Jussiaea decurrens 

(Boyette et al. 1979). The genetic relationship of this taxon to and 

within the C. gloeosporioides species complex, or to Colletotrichum 

jussiaeae Earle, is unknown. Isolates pathogenic to Jussiaea have 

a similar conidial germination self-inhibitor profile to another isolate 

identified as C. fragariae (Tsurushima et al. 1995). The authentic 

isolate of C. gloeosporioides “f. sp. jussiaeae” deposited as ATCC 

52634, is not included in this study. 

Colletotrichum gloeosporioides “f. sp. malvae” (Makowski 

& Mortensen 1989). 

Notes: Strains identified as C. gloeosporioides “f. sp. malvae” were 

registered as a bioherbicide against round leafed mallow in Canada 

(Makowski & Mortensen 1989). The fungus was subsequently 

recognised as belonging to the C. orbiculare species complex 

(Bailey et al. 1996). 

Colletotrichum gloeosporioides “f. sp. manihotis” 

(Chevaugeon 1956). 

Notes: See Colletotrichum manihotis. 

Colletotrichum gloeosporioides f. melongenae Fournet, 

Ann. Mus. Civico Storia Nat. Genova 5: 13. 1973. 

Notes: In addition to C. gloeosporioides f. melongenae, the names 

C. gloeosporioides “f. sp. melongenae”, C. melongenae Av.- 

Saccá 1917, and C. melongenae Lobik 1928 have been used to 

refer to fungi associated with anthracnose diseases of Solanum 

melongena (e.g. Sherf & McNab 1986, Kaan 1973). Other names 

used for isolates from the same host have included Gloeosporium 

melongenae Ellis & Halst. 1891 and G. melongenae Sacc. 1916. 

The genetic relationships of these eggplant-associated taxa to and 

within the C. gloeosporioides species complex remain unknown. 

Solanum melongena associated species are known also from the 

C. boninense species complex (Damm et al. 2012b, this issue). 

Colletotrichum gloeosporioides “f. sp. miconiae” (Killgore 

et al. 1999). 

Notes: Killgore et al. (1999) reported that the isolates they 

recognised as C. gloeosporioides “f. sp. miconiae” were highly 

specialised pathogens of Miconia calvescens, unable to infect 

the closely related Clidemia hirta. The original voucher cultures 

are no longer available (pers. comm., Robert Barreto). Recently 

collected isolates from Miconia from the type locality in Brazil have 

proved to be genetically diverse across the C. gloeosporioides 

species complex, with isolates in both the Kahawae and Musae 

clades (unpubl. data). For now the genetic position of this pathogen 

remains unresolved. 

Colletotrichum gloeosporioides var. minus Simmonds, 

Queensland J. Agric. Anim. Sci. 25: 178A. 1968. 

Notes: See Colletotrichum queenslandicum.

Colletotrichum gloeosporioides var. nectrioidea Gonz. 

Frag., Bol. Soc. Brot., 2: 52. 1924. 

Notes: Originally described from Citrus aurantium from Portugal, 

the name has not been used since it was described and its genetic 

relationship to and within the C. gloeosporioides species complex 

is unknown. 

Colletotrichum gloeosporioides “f. sp. ortheziidae” 

(Marcelino et al. 2008). 

Notes: Marcelino et al. (2008) clearly show that the Orthezia 

praelonga pathogen belongs in the C. acutatum species complex, 

despite referring to the fungus only as C. gloeosporioides “f. sp. 

ortheziidae”. See also notes under C. nymphaeae in Damm et al. 

(2012a, this issue). 

Colletotrichum gloeosporioides “f. sp. pilosae” (Singh 

1974). 

Notes: First described from leaves of Bidens pilosa, this name has 

not been used since it was described and its genetic relationship 


Colletotrichum gloeosporioides f. stylosanthis Munaut, 

Mycol. Res. 106: 591. 2002. 

Notes: Placed here in synonymy with C. theobromicola; see notes 

under C. theobromicola. 

Irwin & Cameron (1978) and Munaut et al. (2002) described 

different diseases of Stylosanthes associated with Type A and Type 

B isolates of C. gloeosporioides f. stylosanthis, the two groups of 

isolates distinguished morphologically by growth rate in culture and 

by conidial morphology. Compared with Type A, the Type B isolates 

had a slower growth rate on PDA, and conidia more variable in size 

and shape (Irwin & Cameron 1978). They were also distinguished 

genetically using RFLP and similar methods (e.g. Munaut et al. 

1998, 2002). Munaut et al. (2002) used ITS1 sequences to show 

the C. gloeosporioides f. stylosanthis to be related to an isolate they 

identified as C. fragariae. We regard C. fragariae to be a synonym 

of C. theobromicola, with putatively authentic Type A (HM335, C. 

gloeosporioides f. stylosanthis “f. sp. guianensis”) and Type B (HM 

336, C. gloeosporioides f. stylosanthis “f. sp. stylosanthis”) isolates 

both also belonging to this species. From the ITS1 sequence data 

available, isolates regarded as typical of Type A (RAPD cluster I) 

and of Type B (RAPD cluster II) by Munaut et al. (1998) all belong 

in C. theobromicola in the sense that we are using the name; their 

RAPD cluster III isolate could be C. tropicale, and their RAPD 

cluster IV isolates are probably C. fructicola. 

The cultures of C. gloeosporioides f. stylosanthis that we used 

were originally studied by Irwin & Cameron (1978), and selected 

as the “types” of “f. sp. guianensis” and “f. sp. stylosanthis” by 

Munaut et al. (2002). Both isolates have a ‘stale’ growth form, no 

longer forming conidia in culture and with aerial mycelium closely 

appressed to the agar surface, resulting in an almost slimy colony 

surface. Both isolates had a slow growth rate, similar to that 

reported for Type B isolates by Irwin & Cameron (1978). Genetically 

both isolates were identical for all the genes we sequenced. This 

identity should be checked against additional isolates, especially 

some matching Type A sensu Irwin & Cameron (1978) with respect 

to both pathogenicity and growth form. 



Sherriff et al. (1994), using ITS2 and partial 28S rDNA 

sequences, found isolates they considered to represent C. 

gloeosporioides f. stylosanthis Type A and Type B respectively to 

be genetically distinct. However, their ITS2 sequences show that 

the putative Type B isolate in their study was in fact a member of 

the C. boninense species complex. 

Specimens examined: Australia, Queensland, Townsville, on Stylosanthes viscosa, 

coll. J.A.G. Irwin 21365 (HM335), 1976 (ex-holotype culture of C. gloeosporioides 

f. stylosanthis – MUCL 42294 = ICMP 17957 = CBS 124251); Samford, on 

Stylosanthes guianensis, coll. J.A.G. Irwin 21398 (HM336), 1979 (MUCL 42295 = 

ICMP 17958 = CBS 124250). 

Colletotrichum gloeosporioides f. stylosanthis “f. sp. 

guianensis” (Munaut et al. 2002) 

≡ Colletotrichum gloeosporioides “f. sp. guianensis” (Vinijsanum et al. 

1987). 

Notes: See notes and specimens examined under C. 

gloeosporioides f. stylosanthis. 

Colletotrichum gloeosporioides f. stylosanthis “f. sp. 

stylosanthis” (Munaut et al. 2002). 

Notes: See notes and specimens examined under C. 


Colletotrichum gloeosporioides “f. sp. uredinicola” 

(Singh 1975). 

Notes: Described from uredinia and telia of Ravenelia sessilis 

on pods of Albizia lebbek, this name has not been used since it 

was described and its genetic relationship to and within the C. 

gloeosporioides species complex is unknown. 

Colletotrichum gossypii Southw., J. Mycol. 6: 100. 1891. 

= Glomerella gossypii Edgerton, Mycologia 1: 119. 1909. 

Notes: This species was originally described from the USA and was 

reported to cause disease symptoms on all parts of cotton plants, 

but especially the bolls (Southworth 1891, Edgerton 1909). Isolates 

identified as C. gossypii by Shear & Wood (1907) were reportedly 

associated with a Glomerella state in culture, and Edgerton (1909) 

described Glomerella gossypii from diseased, mature cotton plants 

in the USA Edgerton (1909) discussed differences in ascospore 

shape between G. gossypii and fruit-rotting isolates of G. 

cingulata, with G. gossypii having elliptic, not curved ascospores. 

Von Arx (1957) considered C. gossypii to be a synonym of C. 

gloeosporioides and von Arx & Müller (1954) regarded G. gossypii 

to be a synonym of G. cingulata. 

Modern authors have recognised two pathogens of cotton, C. 

gossypii and C. gossypii var. cephalosporioides. Colletotrichum 

gossypii is reportedly the cause of cotton anthracnose, a damping-off 

disease of cotton seedlings, and C. gossypii var. cephalosporioides 

the cause of ramulosis, a disease causing abnormal branching 

of mature plants (Bailey et al. 1996, Silva-Mann et al. 2005). In 

a study based on ITS2 sequences, Bailey et al. (1996) found C. 

gossypii and C. gossypii var. cephalosporioides to be genetically 

distinct but with both belonging to the C. gloeosporioides species 

complex. Silva-Mann et al. (2005) also distinguished the two 

taxa genetically, based on an AFLP analysis. The only DNA 

sequences available for isolates identified as C. gossypii and C. 

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Weir et al. 

gossypii var. cephalosporioides are ITS2 and the D2 region of 

the rDNA LSU, neither of which resolves their relationships within 

the C. gloeosporioides complex. Whether the seedling pathogen 

regarded by Silva-Mann et al. (2005) and Bailey et al. (1996) to be 

C. gossypii represents the species first described from cotton in 

the USA is not known. The genetic relationship of these apparently 

biologically specialised fungi requires additional sequences to be 

generated from authentic isolates with known pathogenicity. 

Colletotrichum gossypii var. cephalosporioides A.S. 

Costa, Bragantia 6: 5. 1946. 

≡ Colletotrichum gloeosporioides “var. cephalosporioides” (A.S. Costa) 

Follin & Mangano, Coton et fibres tropicales 37: 209. 1983. [comb. inval., 

no full reference to basionym] 

Notes: See notes under Colletotrichum gossypii. 

* Colletotrichum horii B. Weir & P.R. Johnst., Mycotaxon 

111: 21. 2010. 

Weir & Johnston (2010) and Xie et al. (2010a) provide descriptions. 

Geographic distribution and host range: Associated with fruit and 

stem disease of Diospyros kaki from China, Japan, and New 

Zealand. Xie et al. (2010a) noted minor symptoms on inoculated 

fruit of Capsicum annuum, Musa acuminata, and Cucurbita pepo, 

but noted that the fungus had never been associated with disease 

symptoms on these hosts from the field. 

Genetic identification: ITS distinguishes C. horii from all other 

species. 

Specimens examined: See Weir & Johnston (2010). 

Colletotrichum hymenocallidis Yan L. Yang, Zuo Y. Liu, 

K.D. Hyde & L. Cai, Fungal Diversity 39: 138. 2009. 

Notes: Placed here in synonymy with Colletotrichum siamense. 

See notes and additional specimens examined under C. siamense. 

Yang et al. (2009) reported this species as a leaf pathogen of 

Hymenocallis americana. They distinguished C. hymenocallidis 

from C. siamense, also described from Hymenocallis, primarily 

on the basis of a multi-gene phylogeny and differences in colony 

colour. Although gene selection was appropriate for resolving 

genetic relationships within the C. gloeosporioides group, Yang 

et al. (2009) included only five isolates of the C. gloeosporioides 

complex in their phylogeny. Based on this isolate selection, the 

C. hymenocallidis isolates were genetically distinct from the 

C. siamense isolates. However, in our analysis, in which the C. 

siamense/C. hymenocallidis group is represented by 30 isolates 

from a wide range of hosts from all over the world, authentic isolates 

of the two species fall within a monophyletic clade that cannot be 

further subdivided phylogenetically. 

The Latin part of the C. hymenocallidis protologue designates 

a culture (“Holotypus: Cultura (CSSN2)”) as the holotype but 

the English citation of the type specimen corrects this apparent 

mistake, citing CSSN2 as an ex-holotype culture, with the herbarium 

specimen GZAAS 080001 as the holotype. 

Specimen examined: China, Guangxi, Nanning, on Hymenocallis americana leaf 

spot, coll. Y.L. Yang GZAAS 080001, 19 Jun 2008 (ex-holotype culture of C. 

hymenocallidis − CBS 125378 = ICMP 18642). 

156 

Colletotrichum ignotum E.I Rojas, S.A. Rehner & Samuels, 

Mycologia 102: 1331. 2010. 

Notes: Placed here in synonymy with Colletotrichum fructicola. See 

notes and additional specimens examined under C. fructicola. 

Specimen examined: Panama: Barro Colorado Monument, Tetragastris panamensis 

leaf endophyte, coll. E.I. Rojas E886, 1 Jun 2004 (ex-holotype culture of C. 

ignotum − CBS 125397 = ICMP 18646). 

Colletotrichum jasmini-sambac Wikee, K.D. Hyde, L. Cai 

& McKenzie, Fungal Diversity 46: 174. 2011. 

Notes: Placed here in synonymy with Colletotrichum siamense 

based on the ITS, GAPDH, CAL, TUB2, and ACT gene sequences 

from the ex-holotype culture, deposited in GenBank by Wikee et 

al. (2011). 

Wikee et al. (2011) discussed similarities between C. jasminisambac, 

C. siamense and C. hymenocallidis, three species 

genetically close in their phylogenetic analysis. The broader range 

of isolates representing C. siamense in our analysis shows that 

these species form a single, monophyletic clade that cannot be 

sensibly subdivided (see notes under C. siamense). 

Specimen examined: Vietnam, Cu Chi District, Trung An Ward, on living leaves of 

Jasminum sambac, Jan. 2009, coll. Hoa Nguyen Thi LLTA–01 (ex-holotype culture 

of C. jasmini-sambac – CBS 130420 = ICMP 19118). 

* Colletotrichum kahawae J.M. Waller & Bridge subsp. 

kahawae, Mycol. Res. 97: 993. 1993. Fig. 25. 

Waller et al. (1993) provide a description. 

Geographic distribution and host range: Known only from Coffea 

from Africa. 

Genetic identification: ACT, CAL, CHS-1, GAPDH, TUB2, SOD2, 

and ITS sequences are the same as those from C. kahawae 

subsp. ciggaro. The two subspecies can be distinguished by GS 

sequences; C. kahawae subsp. kahawae has a 22 bp deletion and 

a single C to T transition. Collectively, the two subspecies can be 

distinguished from all other species using ITS sequences alone. 

Notes: Colletotrichum kahawae was proposed by Waller et al. (1993) 

as a name to refer specifically to Colletotrichum isolates causing 

Coffee Berry Disease (CBD), to taxonomically distinguish these 

disease-causing isolates from the several other Colletotrichum 

spp. that can be isolated from coffee plants, including C. coffeanum 

(see notes under C. coffeanum). Colletotrichum kahawae is an 

apparently clonal population (Varzea et al. 2002), widespread on 

coffee in Africa, and with a distinctive growth form and biology 

(Waller et al. 1993). 

In this paper C. kahawae sensu Waller et al. (1993) is reduced 

to subspecies. Based on ACT, CAL, CHS-1, GAPDH, TUB2, SOD2, 

and ITS gene sequences the coffee berry pathogen cannot be 

distinguished from isolates from a wide range of other hosts that 

are not pathogenic to coffee. Those other isolates are referred to 

here as C. kahawae subsp. ciggaro. We retain a distinct taxonomic 

label for the coffee berry pathogen to reflect its biosecurity 

importance. In addition to its biology, C. kahawae subsp. kahawae 

can be distinguished metabolically, and genetically using GS gene 

sequences. Waller et al. (1993) used a metabolic test, an inability



Fig. 25. Colletotrichum kahawae subsp. kahawae. A, E. ICMP 17905 (ex IMI 361501). B–C. ICMP 17816 (ex IMI 319418 – ex-holotype culture). C. ICMP 17915 (ex CBS 

982.69). A–B. Appressoria. C. Conidia. D–E. Cultures on PDA, 10 d growth from single conidia, from above and below. Scale bar C = 20 µm. Scale bar of C applies to A–C. 

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Weir et al. 

to utilise either citrate or tartrate as a sole carbon source, to help 

characterise isolates as C. kahawae. None of our C. kahawae 

subsp. kahawae isolates were able to utilise either citrate or tartrate, 

whereas all of the C. kahawae subsp. ciggaro isolates were able 

to utilise one or both of these carbon sources (Weir & Johnston 

2009). All of the C. kahawae subsp. kahawae isolates share a 22 

bp deletion in the glutamine synthetase gene, lacking in the C. 

kahawae subsp. ciggaro isolates. Note that one of the isolates 

metabolically and genetically typical C. kahawae subsp. kahawae 

(CBS 982.69) was reported by Gielink & Vermeulen (1983) to be 

non-pathogenic to coffee, but we have not independently checked 

this result. 

The isolates we accept as C. kahawae subsp. kahawae show 

two cultural types, one matching the description of Waller et al. 

(1993), slow growing, darkly pigmented cultures with conidia 

developing mostly in the aerial mycelium. The second cultural type 

grew even more slowly, had little or no pigmentation within the agar, 

and the colony surface was covered with numerous acervuli and 

orange conidial masses. Metabolically and genetically both cultural 

types were the same, and pathogenicity tests showed that the nonpigmented 

isolates caused CBD (unpubl. data, D. Silva, Centro de 

Investigação das Ferrugens do Cafeeiro). Rodriguez et al. (1991) 

reported further variation in cultural appearance amongst CBD 

causing isolates. 

Waller et al. 1993 stated that C. kahawae was not known to form 

ascospores. However, Gielink & Vermeulen (1983) observed the 

production of perithecia on coffee berries that had been inoculated 

with CBD-causing isolates, many months after inoculation and death 

of the berries. At least one of the isolates that they cited with this 

biology, CBS 135.30, has the GS sequence typical of C. kahawae 

subsp. kahawae. Vermeulen et al. (1984) grew cultures from the 

perithecia that developed on the previously inoculated berries, and 

found that none were pathogenic to coffee. It is possible that the 

perithecia developing on inoculated berries reported by Gielink & 

Vermeulen (1983) were from other Colletotrichum spp. present on 

the berries before they were inoculated, and represented species 

distinct from C. kahawae subsp. kahawae. A similar situation has 

been noted with some of our inoculations, where species present 

on tissues prior to inoculation, either endophytic or latent, started 

to sporulate on the dead tissue following inoculation (unpubl. data, 

B.S. Weir). 

Based on ITS sequences, most of the accessions in GenBank 

identified as C. kahawae and isolated from coffee, match our 

concept of C. kahawae subsp. kahawae. There are two exceptions, 

AF534468 (from Malawi) and AY376540 (STE-U 5295 = IMI 319424 

= CBS 112985, from Kenya). The Kenyan isolate was cited as C. 

kahawae in Lubbe et al. (2004). Based on the ITS sequences, and 

the TUB2 sequence from isolate STE-U 5295 (AY376588), these 

isolates represent C. siamense. 

Specimens examined: Angola, Ganada, on Coffea arabica berry, coll. J.N.M. Pedro 

16/65, 2 Jun. 1965 (IMI 310524 = CBS 982.69 = ICMP 17915). Cameroon, on 

Coffea arabica (IMI 361501 = ICMP 17905). Kenya, Ruiru, Kakuzi Estate, on Coffea 

arabica young shoots, coll. D.M. Masaba 22/87, 29 Jan. 1987 (ex-holotype culture 

of C. kahawae – IMI 319418 = ICMP 17816); on Coffea sp., coll. E.C. Edwards, 

May 1930 (CBS 135.30 = ICMP 17982). Malawi, on Coffea arabica (IMI 301220 = 

ICMP 17811). 

* Colletotrichum kahawae subsp. ciggaro B. Weir & P.R. 

Johnst., subsp. nov. MycoBank MB563758. Figs 26, 27. 

= Glomerella cingulata var. migrans Wollenw., Z. Parasitenk. (Berlin) 14: 262. 

1949. 

= Glomerella rufomaculans var. vaccinii Shear, Bull. Torrey Bot. Club. 34: 314. 

1907. 

158 

Etymology: Based on the title of the Jim Jarmusch movie “Coffee 

and Cigarettes”, referring to the close genetic relationship between 

C. kahawae subsp. ciggaro and the coffee pathogen C. kahawae 

subsp. kahawae; ciggaro is Portuguese for cigarette. 

Holotype: Australia, on Olea europaea, coll. V. Sergeeva UWS124, 

1989, PDD 102232; ex-type culture ICMP 18539. 


after 10 d for most isolates, the ex-holotype culture of G. cingulata 

var. migrans 48–49 mm diam. Aerial mycelium cottony, grey, dense, 

or in some isolates with dark stromatic masses and associated 

orange conidial ooze showing through mycelium from agar 

surface; in reverse agar with pinkish-orange pigments (6B4–7B4), 

irregular scattered black spots, and variable levels of development 

of overlying dark grey to green-grey pigments (4C2–5D4), these 

sometimes in discrete sectors. See notes below about a divergent 

growth form single ascospore cultures from perithecia in culture. 

Conidia form on dark-based acervuli, (12–)16–19.5(–29) × (4.5–) 

5(–8) µm (av. 17.8 × 5.1 µm, n = 214), cylindric, straight, apex 

rounded, often tapering slightly towards the base. Appressoria 

typically cylindric to fusoid in shape, deeply lobed. Perithecia 

numerous, forming tightly packed clumps, individual perithecia 

globose, small, about 250 µm diam, with a short ostiolar neck. Asci 

55–100 × 10–12 µm, 8–spored. Ascospores (13.5–)17.5–20(–24) 

× (4–)4.5–5(–6.5) µm (av. 18.8 × 4.8 µm, n = 121), gently curved, 

tapering to quite narrow, rounded ends, widest point usually 

towards one end of the spore. 

Geographic distribution and host range: Known from Australia, 

Germany, New Zealand, and South Africa. Both host and geographic 

range of the isolates we accept in C. kahawae subsp. ciggaro 

are broad. Genetic identification: ACT, CAL, CHS-1, GAPDH, 

TUB2, SOD2, and ITS sequences match those from C. kahawae 

subsp. kahawae. The two subspecies can be distinguished by GS 

sequences. Collectively, the two subspecies can be distinguished 

from all other species using ITS sequences alone. 

Notes: The authentic isolate of G. cingulata var. migrans (CBS 237.49) 

differed from all other isolates we accept in C. kahawae subsp. 

ciggaro by its slower growth rate. Wollenweber & Hochapfel (1949) 

distinguished Glomerella cingulata var. migrans from G. cingulata var. 

cingulata on the basis of pathogenicity (G. cingulata var. migrans was 

pathogenic to Hypericum and not to apple) and because of its slightly 

longer ascospores and shorter conidia — ascospores average 21 × 

4.2 µm versus 18 × 4.6 µm, conidia average 14 × 5.2 µm versus 18 × 

5 µm (Wollenweber & Hochapfel 1949). We were unable to produce 

ascospores from CBS 237.49, the conidia were similar in size to that 

reported by Wollenweber & Hochapfel (1949), averaging 16.6 × 5.3 

µm. However, the average ascospore and conidial lengths of our C. 

kahawae subsp. ciggaro isolates varied across the range cited by 

Wollenweber & Hochapfel (1949) for both G. cingulata var. cingulata 

and G. cingulata var. migrans, the average ascospore length from 

individual isolates ranging from 16.6 to 20 µm, the average conidial 

length ranging from 14.9 to 21.2 µm. 

Glomerella rufomaculans var. vaccinii was described by Shear 

(1907) for a fungus isolated from cranberry that was morphologically 

identical to isolates from apple and other hosts but which appeared 

to be biologically distinct (Shear 1907, Shear & Wood 1913). A 

putatively authentic isolate of this species, deposited by Shear 

in CBS in 1922, matches C. kahawae subsp. ciggaro genetically. 

Polashock et al. (2009) discussed the diversity of Colletotrichum



Fig. 26. Colletotrichum kahawae subsp. ciggaro. A. ICMP 12952. B, D. ICMP 17932 (ex CBS 112984). E, H. ICMP 17931 (ex IMI 359911). C, F. ICMP 18539 – ex-holotype 

culture. G. ICMP 18531. A–B. Asci and ascospores. C–D. Appressoria. E. Setae. F–H. Conidia. Scale bars A, E = 20 µm. Scale bar of A applies to A–D, F–H. 

spp. associated with North American cranberry fruit rots, reporting a 

close match between their isolates and C. kahawae. Incorporation 

of their ITS sequences into our alignment confirms this. Whether or 

not there is a genetically distinct, cranberry specialised taxon within 

C. kahawae requires additional genes to be sequenced from the 

cranberry-associated isolates. 

Colletotrichum kahawae subsp. ciggaro was referred to as C. 

gloeosporioides Group B by Johnston & Jones (1997) and Johnston 

159

Weir et al. 

Fig. 27. Colletotrichum kahawae subsp. ciggaro. A. ICMP 12953. B. ICMP 18534. C. ICMP 17922 (ex CBS 237.49 – ex-holotype culture of Glomerella cingulata var. migrans). 

D. ICMP 17932 (ex CBS 112984). E. ICMP 18539 – ex-holotype culture of C. kahawae subsp. ciggaro. F. ICMP 12952 – single ascospore cultures from single conidial isolate. 

Cultures on PDA, 10 d growth from single conidia, from above and below. 

et al. (2005), and as Undescribed Group 1 by Silva et al. (2012b). 

Single ascospore isolates derived from perithecia forming in 

single conidial cultures of the avocado-associated isolates of C. 

160 

kahawae subsp. ciggaro from New Zealand showed two highly 

divergent growth forms (Fig. 27F). One typical of the “wild type” 

(cottony, grey to dark grey aerial mycelium with dark-based acervuli



Fig. 28. Colletotrichum musae. A. ICMP 12930. B. ICMP 18600. C. ICMP 17817 (ex IMI 52264). Cultures on PDA, 10 d growth from single conidia, from above and below. 

and orange conidial masses visible through the mycelium, in 

reverse with pinkish-orange pigmentation, in places this masked by 

irregular patches or sectors of dark grey pigmentation), the other 

more or less lacking aerial mycelium, the surface of the colony 

covered with small, pale-based acervuli with bright orange conidial 

ooze, in reverse bright orange from the conidial ooze. Although 

common from single ascospores, the bright, conidial cultural type 

is rarely formed by isolates from nature (unpubl. data). Similar 

dimorphic cultural types have been observed also from single 

ascospore isolates from a member of the C. boninense complex, 

C. constrictum (unpubl. data, P.R. Johnston). 

Other specimens examined: Brazil, on leaves of Miconia sp., coll. R. Barreto 

RWB1054, 2009 (ICMP 18728). Germany, Berlin-Dahlem, on stem of Hypericum 

perforatum, Jun. 1937 (ex-holotype culture of Glomerella cingulata var. migrans 

– CBS 237.49 = ICMP 17922). New Zealand, Auckland, Waitakere Ranges, on 

leaves of Kunzea ericoides, coll. S. Joshee 5Kun3.10 (ICMP 18741); Auckland, 

Waitakere Ranges, on leaves of K. ericoides, coll. S. Joshee 7Kun5.2 (ICMP 18534); 

Auckland, Waitakere Ranges, on leaves of Toronia toru, coll. G. Carroll TOROTO3 

(ICMP 18544); Te Puke, on Persea americana fruit rot, coll. W.F.T. Hartill, 19 Jan. 

1989 (ICMP 18531); Te Puke, on P. americana fruit rot, coll. W.F.T. Hartill, 8 Feb. 

1988 (ICMP 12952); Te Puke, on P. americana fruit rot, coll. W.F.T. Hartill, 28 Sep. 

1991 (ICMP 12953). South Africa, Madeira, on Dryandra sp., coll. J.E. Taylor, 1 

Apr. 2001 (CBS 112984, as C. crassipes = ICMP 17932). Switzerland, on Dryas 

octopetala, coll. P. Cannon (IMI 359911 = CBS 12988 = ICMP 17931). USA, on 

Vaccinium macrocarpum leaves, coll. C.L. Shear, Apr. 1922 (authentic culture of 

G. rufomaculans var. vaccinii – CBS 124.22 = ICMP 19122). 

Colletotrichum manihotis Henn., Hedwigia 43: 94. 1904. 

Notes: Anthracnose is an important disease of cassava (e.g. 

Chevaugeon 1956, Makambila 1994, Fokunang et al. 2000, 

Owolade et al. 2008), variously referred to Colletotrichum manihotis, 

Gloeosporium manihotis Henn., Glomerella manihotis (Sacc.) 

Petr., Glomerella cingulata “f. sp. manihotis”, or C. gloeosporioides 

“f. sp. manihotis”. The original descriptions of both C. manihotis 

and Gloeosporium manihotis are of species with short, broad 

conidia (8–15 × 4–6 µm), and Chevaugeon (1956) regarded all of 

these cassava-associated fungi as con-specific. However, based 

on Fokunang et al. (2000), a morphologically highly diverse set of 

Colletotrichum isolates are associated with diseased plants. There 

are three GenBank accessions of Colletotrichum from cassava, 

all from China, and although only ITS sequences are available for 

these isolates, they appear to represent a single, distinct species 

within the C. gloeosporioides complex. How these Chinese isolates 

relate to cassava-associated isolates from other parts of the world 

is not known. 

* Colletotrichum musae (Berk. & M.A. Curtis) Arx, Verh. 

Kon. Ned. Akad. Wetensch., Afd. Natuurk., Sect. 2 51(3): 

107. 1957. Fig. 28. 

Basionym: Myxosporium musae Berk. & M.A. Curtis, Grevillea 3: 

13. 1874. 

Su et al. (2011) provide a description. 

Geographic distribution and host range: Found in association with 

fruit lesions of Musa spp. in many regions. 

Genetic identification: ITS sequences separate C. musae from all 

other species. 

Notes: Colletotrichum musae was originally described from North 

Carolina (Berkeley 1874), and the name was recently epitypified 

by Su et al. (2011) on the basis of a specimen collected in Florida 

161

Weir et al. 

(ex-epitype culture CBS 116870). Su et al. (2011) cite several 

strains from Thailand that match their concept of C. musae, and 

isolates from anthracnose symptoms on banana fruit from several 

parts of the world are the same based on our study. These 

isolates form a well-supported clade within the C. gloeosporioides 

species complex, show low levels of genetic differentiation, and 

based on ITS sequences are consistent with C. musae sensu 

Sreenivasaprasad et al. (1996), Nirenberg et al. (2002) and Shenoy 

et al. (2007). The morphology in culture agrees with the description 

of Sutton & Waterston (1970). 

We have not seen a Glomerella state in culture and none was 

mentioned by Su et al. (2011). However, Rodriguez & Owen (1992) 

reported rare production of perithecia from crosses between two 

of 14 isolates identified as C. musae. It is not known whether the 

isolates studied by Rodriguez & Owen (1992) match our concept of 

C. musae genetically, but it is possible that this species behaves in a 

similar way to some species in the C. acutatum complex, where the 

sexual morph can be generated in culture under suitable conditions 

(Guerber & Correll 2001). The name “Glomerella musae”, used by 

Rodriguez & Owen (1992) and Krauss et al. (2001), has never been 

validly published. 

More than one species of Colletotrichum has been found 

in association with rotting banana fruit. From isolates with well 

characterised sequence data these include a species belonging to 

C. acutatum s. lat. (Sherriff et al. 1994, Johnston & Jones 1997) that 

is described as C. paxtonii (Damm et al. 2012a, this issue), and C. 

karstii that belongs to the C. boninense species complex (Damm et 

al. 2012b, this issue). The latter forms a sexual stage in culture and 

is known from Musa in South America and Australia, as well as from 

many other hosts worldwide, often as an endophyte. Species in the C. 

boninense species complex have been previously confused with C. 

gloeosporioides s. lat. Greene (1967) referred isolates pathogenic to 

banana that were not associated with a teleomorph to C. musae, and 

a second non-pathogenic species that formed fertile ascospores, to 

C. gloeosporioides. Whether Glomerella musarum Petch, described 

from leaves of banana and cited as the teleomorph of C. musae by 

Sutton (1992) and Hyde et al. (2009), is a synonym of C. musae in 

the sense we use the name here is not known, but seems unlikely 

given the rare production of perithecia by this species. 

Specimens examined: Indonesia, on Musa sp., coll. G. von Becze, Jan. 1931 (CBS 

192.31 = ICMP 17923). Kenya, on Musa sapientum, coll. R.M. Nattrass 1850, 1 

Jan. 1953 (IMI 52264 = ICMP 17817). New Zealand, Auckland (imported fruit), on 

Musa sp., coll. P.R. Johnston C1197.1, 24 May 1991 (ICMP 12931; PDD 59100); 

Auckland (fruit imported from the Phillipines), on Musa sp., coll. S. Bellgard, 5 May 

2009 (ICMP 18600); Auckland, Mt Albert Research Centre, Musa sp. spots on green 

fruit, coll. P.R. Johnston C809.2, 12 Aug. 1987 (ICMP 12930; PDD 46160); Auckland 

(fruit imported from the Phillipines), on Musa sp., coll. B. Weir, 17 May 2009 (ICMP 

18701; PDD 97438). USA, Florida, on Musa sp., coll. M. Arzanlou A-1 (ex-epitype 

culture of C. musae – CBS 116870 = ICMP 19119). 

Glomerella musarum Petch, Ann. Roy. Bot. Gard. 

Peradeniya 6(3): 223. 1917. 

Notes: See notes under C. musae. 

* Colletotrichum nupharicola D.A. Johnson, Carris & J.D. 

Rogers, Mycol. Res. 101: 647. 1997. Fig. 29. 

Johnson et al. (1997) provide a description. 

Geographic distribution and host range: Known only from the USA, 

on the aquatic plants Nuphar and Nymphaea spp. 

162 

Genetic identification: One of the two ITS haplotypes of C. 

nupharicola is identical with C. queenslandicum. All other 

genes distinguish this species well from other species in the C. 

gloeosporioides complex. 

Notes: Sequence data from the ex-holotype culture of C. nupharicola 

places it within the C. gloeosporioides complex, genetically close to 

C. fructicola and C. alienum in the Musae clade. This apparently 

host-specific species and has a distinctive, slow growth in culture 

and massive conidia (Johnson et al. 1997). 

Johnson et al. (1997) compare C. nupharicola with another 

water plant pathogen, C. nymphaeae, that is epitypified and shown 

to belong to the C. acutatum species complex by Damm et al. 

(2012a, this issue). 

Specimens examined: USA, Washington, King Co., on Nuphar lutea subsp. 

polysepala, coll. D.A. Johnson A-7, Oct. 1993 (CBS 469.96 = ICMP 17938); 

Washington, Yakima Co., on N. lutea subsp. polysepala, coll. D.A. Johnson A-2, 

Oct. 1993 (ex-holotype culture − CBS 470.96 = ICMP 17939); Rhode Island, on 

Nymphaea ordorata, coll. R.D. Goos RDG-291, 1979 (CBS 472.96 = ICMP 18187). 

Gloeosporium pedemontanum Pupillo, Ann. Sperim. Agrar. 

n.s. 6: 57. 1952. 

Notes: Placed here in synonymy with C. gloeosporioides. See 

notes under C. gloeosporioides. 

Specimen examined: Italy, on Citrus limon juice, coll. G. Goidánich, 1951 (exholotype 

culture of G. pedemontanum – CBS 273.51 = ICMP 19121). 

* Colletotrichum psidii Curzi, Atti dell’Istituto Botanico 

dell’Università di Pavia, ser. 3, 3: 207. 1927. Fig. 30. 


after 10 d, aerial mycelium dense, cottony to felted, uniform in 

height, white to off-white; in reverse uniformly pale creamy yellow 

(2A2–2A3) or in some cultures becoming dull greyish yellow (2D2– 

2E2) towards the centre. No conidiogenous cells or conidia seen. 

Geographic distribution and host range: Known from a single 

isolate, from Psidium from Italy. 

Genetic identification: Although known from only one isolate, ITS 

sequences separate C. psidii from all other taxa. 

Notes: A putatively authentic isolate of this species, deposited 

in CBS by Curzi shortly after publication of C. psidii, represents 

a genetically distinct species within the Kahawae clade. The only 

available culture is stale, no longer forming conidia. Curzi (1927) 

describes the conidia as 12–15 × 3.5–4.5 µm, cylindric with 

rounded ends, straight or rarely slightly curved. 

Anthracnose diseases have been noted for Psidium spp. 

(guava) from several tropical regions of the world (e.g. MacCaughey 

1917, Venkatakrishniah 1952, Liu 1972, Misra 2004). It is likely that 

several Colletotrichum spp. are associated with guava fruit rots. 

Whether the fungus described by Curzi from an Italian botanical 

garden represents one of the species causing a guava disease in 

the tropics is not known. All other members of the Kahawae clade 

are predominantly tropical, so perhaps this fungus was introduced 

to Italy along with its host plant. Misra (2004) uses C. psidii to refer 

to a Colletotrichum species with curved conidia. 

One other species has been described from this host, 

Glomerella psidii (basionym Gloeosporium psidii), the relationship



Fig. 29. Colletotrichum nupharicola. A. ICMP 17939 (ex CBS 470.96 – ex-holotype culture). B. ICMP 17938 (ex CBS 469.96). C. ICMP 18187 (ex CBS 472.96). Cultures on 


Fig. 30. Colletotrichum psidii (ICMP 19120, 

ex CBS 145.29 – authentic culture). 

Cultures on PDA, 10 d growth from single 

hyphal tips, from above and below. 

163

Weir et al. 

of this species to C. psidii remains unknown. A new species on 

Psidium guajava, C. guajavae, belonging to the C. acutatum 

species complex, is described elsewhere in this volume (Damm 

et al. 2012a). 

Specimen examined: Italy, Rome, on Psidium sp., coll. M. Curzi (authentic culture 

of C. psidii – CBS 145.29 = ICMP 19120). 

Glomerella psidii (Delacr.) J. Sheld., Bull. West Virginia 

Agric. Exp. Sta. 104: 311. 1906. 

Basionym: Gloeosporium psidii Delacr., Bull. Soc. Mycol. France. 

19: 144. 1903. 

Notes: Sheldon (1906) produced perithecia in culture from 

isolates he considered typical of Gloeosporium psidii and on this 

basis recombined the species described by Delacroix (1903) in 

Glomerella. The relationship of G. psidii to Colletotrichum psidii, 

also described from guava, is not known. See notes under C. psidii. 

* Colletotrichum queenslandicum B. Weir & P.R. Johnst., 

nom. nov. et stat. nov. MycoBank MB563593. Fig. 31. 

Basionym: Colletotrichum gloeosporioides var. minus Simmonds, 

Queensland J. Agric. Anim. Sci. 25: 178A. 1968. [as var. minor] 

Etymology: based on the region from which the type specimen of 

this species was collected. 

Holotype: Australia, Queensland, Ormiston, on Carica papaya, coll. 

J.H. Simmonds, Oct. 1965, IMI 117612. 

Epitype: Australia, Queensland, Brisbane, on Carica papaya, coll. 

J.H. Simmonds 11663C, Sep. 1965, epitype here designated PDD 

28797; ex-epitype culture ICMP 1778. 


after 10 d, aerial mycelium either dense, cottony, uniform, grey, 

or with aerial mycelium lacking, towards centre of colony with 

numerous, small acervuli with dark bases and orange conidial 

ooze; in reverse cultures with copious aerial mycelium uniformly 

dark grey (1F2), those with little aerial mycelium having a pinkish 

brown (8B4) pigment within the agar, the dark bases of the acervuli 

and the colour of the conidial ooze visible through the agar. Conidia 

(12–)14.5–16.5(–21.5) × (3.5–)4.5–5(–6) µm (av. 15.5 × 4.8 µm, n 

= 96), cylindric, straight, sometimes slightly constricted near centre, 

ends broadly rounded. Appressoria about 6–12 µm diam., globose 

to short-cylindric, rarely lobed. Perithecia not seen. 

Geographic distribution and host range: Known from Carica papaya 

and Persea americana from Queensland, Australia, and from 

Coffea berries from Fiji. Simmonds (1965) reported from Australia 

what he considered to be the same fungus also from Mangifera 

indica, Malus sylvestris, and “many other hosts”. 

Genetic identification: ITS sequences do not separate C. 

queenslandicum from some C. fructicola, some C. siamense, and 

some C. tropicale isolates. It is best distinguished from these taxa 

using TUB2, GAPDH, or GS. 

Notes: The ex-type cultures cited by Simmonds (1968) are no 

longer in storage at BRIP in Queensland (R. Shivas, pers. comm.) 

and presumably lost. However, we do have two cultures identified 

as C. gloeosporioides var. minus by Simmonds and isolated from 

164 

the same host from the same locality as the holotype (Simmonds 

isolates 16633C and 1647A2), that had been sent to Joan Dingley 

in 1965 and subsequently stored in the ICMP culture collection. 

The culture selected here as epitype (Simmonds 11663C = ICMP 

1778) matches the Simmonds (1965) description of this fungus as 

having “an abundance of aerial mycelium in culture”. Our conidial 

measurements from ICMP 1778 and 1780 are broader than those 

given by Simmonds (1965), but he does note that “Confusion can 

occur between narrower strains of C. gloeosporioides and broader 

strains of C. gloeosporioides var. minus …”. Simmonds (1965) also 

notes that perithecia may rarely be seen in cultures of some isolates. 

The isolates accepted here as C. queenslandicum are 

genetically distinct within the Musae clade of C. gloeosporioides s. 

lat. Colletotrichum minus Zimm. (1901) requires that we propose a 

nom. nov. for this fungus at species rank. 

Simmonds (1965) considered C. gloeosporioides var. minus 

to be the conidial state of Glomerella cingulata var. minor 

Wollenw. Wollenweber & Hochapfel (1949) used the name 

Gloeosporium elasticae Cooke & Massee for the conidial state 

of G. cingulata var. minor, the type specimens for both names 

being from Ficus. Simmonds (1965) noted that it was not possible 

to transfer G. elasticae to Colletotrichum because Colletotrichum 

elasticae had already been published for a different fungus. 

However, rather than proposing a nom. nov. for Gloeosporium 

elasticae, he described C. gloeosporioides var. minus as a new 

variety, with a different type specimen. Glomerella cingulata var. 

minor is genetically distinct from the specimen Simmonds chose 

as the type of C. gloeosporioides var. minus, see notes under G. 

cingulata var. minor. 

Other specimens examined: Australia, Queensland, Brisbane, on Carica sp., 

coll. J.H. Simmonds 16347A2 (ICMP 1780, dried culture stored as PDD 28797); 

Queensland, Home Hill, on Persea americana, coll. L. Coates 22516, Feb. 1983 

(ICMP 12564). Fiji, on Coffea sp. berry, coll. R. Gounder, Apr. 1988 (ICMP 18705). 

Glomerella rufomaculans var. vaccinii Shear, Bull. Torrey 

Bot. Club. 34: 314. 1907. 

Notes: Placed here in synonymy with Colletotrichum kahawae 

subsp. ciggaro. See notes under C. kahawae subsp. ciggaro. Note 

that Saccardo & Trotter (1913) place Shear’s variety in Glomerella 

fructigena (Clint.) Sacc., a rarely used species name, placed in 

synonymy with G. cingulata by von Arx & Müller (1954). 

Specimen examined: USA, on Vaccinium macrocarpum leaves, coll. C.L. Shear, 

Apr. 1922 (authentic isolate of G. rufomaculans var. vaccinii – CBS 124.22 = ICMP 

19122). 

* Colletotrichum salsolae B. Weir & P.R. Johnst., sp. nov. 


= Colletotrichum gloeosporioides “f. sp. salsolae” (Berner et al. 2009). 

Etymology: Based on C. gloeosporioides “f. sp. salsolae”, referring 

to the host from which this fungus was originally collected. 

Holotype: Hungary, on Salsola tragus, coll. D. Berner [specimen 

from plants inoculated with strain 96-067, originally collected I. 

Schwarczinger & L. Vajna on Salsola tragus from Bugac, near 

Kiskunsag National Park, 1996], BPI 878740; ex-holotype culture 

ICMP 19051. 


after 10 d, aerial mycelium sparse, cottony, pale grey, surface of



Fig. 31. Colletotrichum queenslandicum. A, C, E. ICMP 1778 – ex-epitype culture. B, F. ICMP 1780. D, G. ICMP 12564. H. ICMP 18705. A–B. Appressoria. C–D. Conidia. E–H. 

Cultures on PDA, 10 d growth from single conidia, from above and below. Scale bar A = 20 µm. Scale bar of A applies to A–D. 

colony dark, a more or less continuous layer of acervulus-like 

structure with deep orange brown conidial masses and numerous 

setae; in reverse dark purplish-black near centre of colony, dark 

olivaceous near the margin. Conidia (10–)14–16.5(–20.5) × (4.5–) 

5.5–6(–7.5) µm (av. 15.3 × 5.8 µm, n = 24), highly variable in size 

and shape, subglobose to long-cylindric, apex usually broadly 

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Weir et al. 

Fig. 32. Colletotrichum salsolae. A, C–H. ICMP 19051 – ex-holotype culture. B. BPI 878740 – holotype. A. Cultures on PDA, 10 d growth from single conidia, from above and 

below. B. Lesion on stem, dried type specimen. C. Conidiogenous cells. D–E. Conidia. F–G. Appressoria. Scale bars B = 1 mm, C = 20 µm. Scale bar of C applies to C–G. 

rounded, small truncate scar at base. Conidiogenous cells 13–18 

× 4–6.5 µm, cylindric to flask-shaped, tapering at apex to narrow, 

166 

phialidic conidiogenous locus, wall at base often encrusted with 

dark brown material. Appressoria sparsely developed, cylindric to

elliptic, simple; many putatively partially developed appressoria, 

similar in shape to those with dark and thick walls and also with 

an appressorial pore, but the wall remains thin and only slightly 

pigmented. Perithecia not seen. 

Geographic distribution and host range: Known from throughout the 

geographic range of Salsola tragus (Berner et al. 2009), reported in 

nature only from Salsola spp. 

Genetic identification: ITS sequences of C. salsolae are very close 

to C. alienum and some C. siamense isolates. These species can 

be distinguished using TUB2 or GAPDH. 

Notes: Isolates of C. gloeosporioides pathogenic to Salsola 

tragus were reported by Schwarczinger et al. (1998) and referred 

to as C. gloeosporioides “f. sp. salsolae” by Berner et al. (2009). 

Although mildly pathogenic to a wide range of hosts in glasshouse 

pathogenicity tests, this fungus causes severe disease only on 

Salsola spp. with the exception of S. orientalis, S. soda, and S. 

vermiculata (Berner et al. 2009). 

Colletotrichum salsolae belongs to the Musae clade, and 

although genetically close to several other species, it is biologically 

and morphologically distinctive. 

Other specimen examined: Hungary, additional isolate of strain selected as the 

holotype, recovered from inoculated Glycine max plants (MCA 2498 = CBS 119296 

= ICMP 18693). 

* Colletotrichum siamense Prihastuti, L. Cai & K.D. Hyde, 


= Colletotrichum jasmini-sambac Wikee, K.D. Hyde, L. Cai & McKenzie, Fungal 

Diversity 46: 174. 2011. 

= Colletotrichum hymenocallidis Yan L. Yang, Zuo Y. Liu, K.D. Hyde & L. Cai, 

Fungal Diversity 39: 138. 2009. 

Descriptions of this species are provided by Prihastuti et al. (2009), 

Wikee et al. (2011), and Yang et al. (2009). 

Geographic distribution and host range: Colletotrichum siamense 

was originally described from coffee from Thailand, but our concept 

of this species is biologically and geographically diverse, found on 

many hosts across several tropical and subtropical regions. 

Genetic identification: ITS sequences do not reliably separate C. 

siamense from C. alienum, C. fructicola, or C. tropicale. These 

species are best distinguished using CAL or TUB2. 

Notes: Yang et al. (2009) and Wikee et al. (2011) discussed genetic 

and morphological differences between C. siamense, C. jasminisambac, 

and C. hymenocallidis. However, both studies used a 

limited set of isolates within the C. gloeosporioides complex, making 

interpretation of the genetic differences difficult. The morphological 

differences they described are commonly seen as within-species 

variation in other Colletotrichum spp. In our analysis, C. siamense is 

represented by 30 isolates from a wide range of hosts from several 

tropical regions, and forms a monophyletic clade that cannot be 

further subdivided genetically. Variation in cultural appearance is 

broad but in part this probably reflects the different conditions under 

which the isolates had been stored. Shape and size of appressoria, 

and the characteristically small conidia are similar in all isolates. 

Based on matching translation elongation factor (TEF) and 

TUB2 sequences, isolates referred by Rojas et al. (2010) to 

Colletotrichum sp. indet. 2 also represent C. siamense. Note that 



TEF data was excluded from our phylogenetic analyses because 

the TEF gene tree was often incongruent with the trees from the 

other genes that we sequenced. For example, compare our isolate 

ICMP 17797 (GenBank GU174571) with isolates Rojas et al. (2010) 

cite as Colletotrichum sp. indet. 2, V1H1_1 (GenBank GU994297) 

and 7767 (GenBank GU994298). 

The C. siamense protologue designates the holotype as MFLU 

090230, but the culture derived from holotype as “BCC” with no 

specimen number. The ex-holotype culture is listed as BDP-I2 in 

Table 1 of Prihastuti et al. (2009) but not in the description of the 

species. Strain BDP-I2 was obtained from the authors (Prihastuti et 

al. 2009) for this study and deposited as ICMP 18578. 

Specimens examined: Australia, New South Wales, Murwillumbah, on Persea 

americana fruit rot, coll. L. Coates 23695, 1 Apr. 1990 (ICMP 12567); New South 

Wales, Muswellbrook, on Pistacia vera (DAR 76934 = ICMP 18574); Queensland, 

Mt Tamborine, on Persea americana fruit rot, coll. L. Coates T10-1, 1 Sep. 1993 

(ICMP 12565). China, Guangxi, Nanning, on Hymenocallis americana leaf spot, 

coll. Y.L. Yang CSSN2, 19 Jun. 2008 (ex-holotype culture of C. hymenocallidis 

− CBS 125378 = ICMP 18642); Guangxi Province, Nanning, on H. americana leaf, 

coll. Y.L. Yang CSSN3 (CBS 125379 = ICMP 18643). Nigeria, Ibadan, on Dioscorea 

rotundata seed, coll. M. Abang CgS2 (ICMP 18121); Ibadan, on D. rotundata seed, 

coll. M. Abang CgS6 (ICMP 18117); Ibadan, on Commelina sp. leaf, coll. M. Abang 

Cg29 (ICMP 18118). South Africa, on Carica papaya fruit, coll. L. Korsten PMS 

1 (ICMP 18739). on Persea americana, coll. L. Korsten Cg227 (ICMP 18570); on 

Persea americana, coll. L. Korsten Cg231 (ICMP 18569). Thailand, Chiang Mai, 

Mae Lod Village, on Coffea arabica berries, coll. H. Prihastuti BPD-I2, 12 Dec. 

2007 (ex-holotype culture of C. siamense – MFLU 090230 = ICMP 18578). 

Kanchanaburi, on Capsicum annuum, P.P. Than Ku4 (HKUCC 10884 = ICMP 

18575); Nakhonpathon, on C. annuum, coll. P.P. Than Ku8 (HKUCC 10881 = ICMP 

18618). USA, Florida, on Vitis vinifera leaf, coll. N. Peres ssgrape 10 (ICMP 18572); 

Florida, on Fragaria × ananassa crown, coll. N. Peres strawberry 6 (ICMP 18571); 

Florida, on V. vinifera leaf, coll. N. Peres DI-grape-6 (ICMP 18573); North Carolina, 

Wilkes County, on Malus domestica fruit, coll. T. Sutton LD Cg12 2001 (ICMP 

17795); North Carolina, Johnston County, on M. domestica fruit, coll. T. Sutton GD 

8 2002 (ICMP 17791); North Carolina, Johnston County, on M. domestica fruit, coll. 

T. Sutton GD 7 2002 (ICMP 17797); Alabama, on M. domestica fruit, coll. T. Sutton 

AL 1 2001 (ICMP 17785). Vietnam, Cu Chi District, Trung An Ward, on living leaves 

of Jasminium sambac, Jan. 2009, coll. Hoa Nguyen Thi LLTA–01 (ex-holotype 

culture of C. jasmini-sambac – CBS 130420 = ICMP 19118). 

* Colletotrichum theobromicola Delacr., Bull. Soc. Mycol. 

France. 31: 191. 1905. Fig. 34. 

= Colletotrichum fragariae A.N. Brooks, Phytopathology 21: 113. 1931. 

= Colletotrichum gloeosporioides f. stylosanthis Munaut, Mycol. Res. 106: 591. 

2002. 

= Colletotrichum gloeosporioides f. stylosanthis “f. sp. stylosanthis” (Munaut 

et al. 2002). 

= Colletotrichum gloeosporioides f. stylosanthis “f. sp. guianensis” (Munaut et 

al. 2002). 

A modern description of this species is provided by Rojas et al. 

(2010). 

Geographic distribution and host range: Broadly distributed in 

tropical and subtropical regions on a wide range of hosts. 

Genetic identification: ITS sequences distinguish C. theobromicola 


Notes: The ex-epitype culture of Colletotrichum fragariae, the exneotype 

culture of C. theobromicola, and the ex-holotype culture of 

C. gloeosporioides f. stylosanthis, selected by Buddie et al. (1999), 

Rojas et al. (2010), and Munaut et al. (2002) respectively, belong in 

a clade that we accept genetically as a single species. Also in this 

clade are authentic isolates of C. gloeosporioides f. stylosanthis 

“f. sp. stylosanthis” and C. gloeosporioides f. stylosanthis “f. sp. 

guianensis” (but see notes under C. gloeosporioides f. stylosanthis). 

167

Weir et al. 

Fig. 33. Colletotrichum siamense. A. ICMP 18642 (ex CBS 125378 – ex-holotype culture of C. hymenocallidis). B. ICMP 18578 (ex MFLU 090230 – ex-holotype culture of C. 

siamense). C. ICMP 12565. D. ICMP 18574 (ex DAR 76934). E. ICMP 18618 (ex HKUCC 10881). F. ICMP 18121. Cultures on PDA, 10 d growth from single conidia, from 

above and below. 

Colletotrichum theobromicola as accepted here contains 

several putatively specialised pathogens, including the pathogen of 

strawberry runners described by Brooks (1931) as C. fragariae, and 

168 

the pathogens of Stylosanthes referred to as C. gloeosporioides f. 

stylosanthis (Munaut et al. 2002). Future studies may show that 

the species should be segregated based on their pathogenicity



Fig. 34. Colletotrichum theobromicola. A. ICMP 17957 (ex MUCL 42294 – ex-holotype culture of C. gloeosporioides f. stylosanthis). B. ICMP 17927 (ex CBS 142.31 – ex-epitype 

culture of C. fragariae). C. ICMP 17958 (ex MUCL 42295). D. ICMP 17895. E. ICMP 18567. F. ICMP 18566. Cultures on PDA, 10 d growth from single conidia, from above and 

below. 

to specific hosts. See also notes under C. fragariae and C. 


Munaut et al. (2002) distinguished C. gloeosporioides f. 

stylosanthis from isolates they considered to represent C. 

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Weir et al. 

Fig. 35. Colletotrichum ti. A. PDD 24881 – holotype. B. PDD 30206. C, D, F, H. ICMP 4832 – ex-holotype culture. E, G. ICMP 19444. A–B. Lesions on dried herbarium 

specimens. C–E. Appressoria. F. Conidia. G. Conidiogenous cells. H. Ascospores. Scale bars A = 1 mm, C = 20 µm. Scale bar of A applies to A–B, scale bar of C applies to C–H. 

gloeosporioides f. gloeosporioides because of 2 additional C’s at 

positions 93 and 94 in the ITS1 region, giving a string of 7 C’s at 

this position. This characteristic feature of the ITS-1 is found also in 

the ex-neotype isolate of C. theobromicola, the ex-epitype isolate 

of C. fragariae and all other isolates of C. theobromicola, although 

a few isolates have 3 additional C’s rather than 2. None of the 

170 

other isolates that we sampled from the C. gloeosporioides species 

complex have this characteristic string of C’s. 

Rojas et al. (2010) provide a description for their concept of 

C. theobromicola, MacKenzie et al. (2008) for C. fragariae, and 

Irwin & Cameron (1978) for C. gloeosporioides f. stylosanthis “f. sp. 

stylosanthis” (as C. gloeosporioides Type A) and C. gloeosporioides

f. stylosanthis “f. sp. guianensis” (as C. gloeosporioides Type B). 

In cultural appearance the isolates we accept in this species are 

variable, from the very dark ex-neotype isolate of C. theobromicola 

to the slow-growing, pale coloured C. gloeosporioides f. stylosanthis 

“f. sp. guianensis”. None of the isolates that we examined formed 

perithecia in culture. All had conidia tapering slightly towards 

each end, this more pronounced towards the base, matching 

the description of C. fragariae by Gunnell & Gubler (1992), who 

regarded the conidial shape as distinctive for the species. Some 

of the isolates studied by Gunnell & Gubler (1992) were included 

in the study of MacKenzie et al. (2008), their genetic concept of C. 

fragariae matching ours. 

See also notes under C. fragariae and C. gloeosporioides f. 

stylosanthis. 

Specimens examined: Australia, Queensland, Townsville, on Stylosanthes viscosa, 

coll. J.A.G. Irwin 21365 (HM335), 1976 (ex-holotype culture of C. gloeosporioides f. 

stylosanthis − MUCL 42294 = ICMP 17957); Samford, on Stylosanthes guianensis, 

coll. J.A.G. Irwin 21398 (HM336), 1979 (MUCL 42295 = ICMP 17958); New South 

Wales, Olea europaea fruit, coll. V. Sergeeva UWS 128, 21 Apr. 2008 (ICMP 18566); 

New South Wales, O. europaea fruit, coll. V. Sergeeva UWS 130, 21 Apr. 2008 

(ICMP 18565); New South Wales, O. europaea fruit, coll. V. Sergeeva UWS 98, 8 

Apr. 2008 (ICMP 18567). Israel, on Limonium sp. leaf lesion, coll. S. Freeman P1 

(cited in Maymon et al. 2006) (ICMP 18576). Mexico, on Annona diversifolia, coll. 

R. Villanueva-Aroe Gro-7, Jul. 2003 (ICMP 17895). New Zealand, Kerikeri, on Acca 

sellowiana, coll. M.A. Manning MM317, 1 Feb. 2004 (ICMP 15445). Panama, Chiriqui 

Province, San Vicente, on Theobroma cacao pod lesion, coll. E.J. Rojas ER08-9, Jan. 

2008 (CBS 125393 = ICMP 18650); Chiriqui Province, Escobal, on T. cacao leaf spot, 

coll. E.J. Rojas GJS 08-50, Jan. 2008 (ex-neotype culture of C. theobromicola − CBS 

124945 = ICMP 18649). USA, Florida, Dover, Plant City, on Fragaria × ananassa, coll. 

S. MacKenzie 326-1, 1988 (ICMP 17099); Florida, Lake Alfred, on Quercus sp. leaf, 

coll. S. MacKenzie LA-oak-13, 2002 (ICMP 17100); Louisiana, on F. vesca, 1985 (IMI 

348152 = ICMP 17814); Florida, on F. × ananassa, coll. A.N. Brooks, 1931 (ex-epitype 

culture of C. fragariae − CBS 142.31 = ICMP 17927). 

* Colletotrichum ti B. Weir & P.R. Johnst., sp. nov. 


Etymology: Based on the Maori name for Cordyline australis, tī. 

Holotype: New Zealand, Taupo, on Cordyline sp., coll. J.M. Dingley 

65187, Sep. 1965, PDD 24881; ex-holotype culture ICMP 4832. 

Leaf spots oblong to elliptic in shape, up to about 1 × 2 mm, sometimes 

coalescing when close together on a leaf, pale grey and necrotic in 

the centre with a reddish margin; acervuli numerous, base pale to 

dark grey, with scattered, dark brown setae about 50–80 µm long. 

Perithecia not seen on infected leaves. Freshly isolated colonies on 

Difco PDA 50–55 mm diam after 10 d, margin slightly irregular and 

feathery, aerial mycelium lacking from ex-holotype culture, when 

present fine, cottony, pale grey, surface of colony dark towards the 

centre, pale pinkish orange (7A6) towards margin, conidia forming 

over all parts of culture, mostly not associated with well differentiated 

acervuli, setae not observed; in reverse purple (12E3) near centre, 

orange outside, sometimes with concentric rings of grey pigment. 

Conidiogenous cells cylindric, mostly 15–25 × 3.5–4.5 µm, towards 

centre of colony arranged in closely packed palisade, towards margin 

the conidiophores with a much looser structure, irregularly branched, 

conidiogenous loci at apex and often also at septa. Conidia (11.5– 

)14–17.5(–23.5) × (4–)5–5.5(–7.5) µm (av. 16 × 5.2 µm, n = 53), 

cylindric, ends broadly rounded, sometimes tapering towards basal 

end. Appressoria often narrow-cylindric, often tapering towards 

apex, sometimes irregularly lobed. Perithecia developing in small 

numbers in culture after about 4 wk, solitary, scattered across plate, 

dark-walled, globose with well-developed, tapering ostiolar neck. 



Asci (60–)65–75(–78) × (10–) 11(–12) µm (av. 69.6 × 11 µm, n = 5), 

cylindric to subfusoid, 8–spored. Ascospores (14.5–)15.5–16.5(–19) 

× (4.5–)5–5.5(–6) µm (av. 15.9 × 5.2 µm, n=18), broad-cylindric, 

ends broadly rounded, not tapering to the ends, in side view mostly 

flat on one side, often slightly curved. 

Geographic distribution and host range: Known only from Cordyline 

spp. from New Zealand. 

Genetic identification: ITS sequences do not distinguish C. ti from 

C. aotearoa. The two species can be distinguished using TUB2 or 

GAPDH. 

Notes: A member of the Kahawae clade, this fungus causes a leaf 

spot of Cordyline spp. in New Zealand. It is genetically distinct 

from C. cordylinicola, described from Cordyline fruticosa from 

Thailand. Based on the published description of C. cordylinicola 

(Phoulivong et al. 2011) the two fungi are morphologically similar. 

Inoculation tests using culture ICMP 5285 when freshly isolated 

(J.M. Dingley, unpublished data), showed it to be pathogenic to 

Cordyline australis, forming spots on leaves 2 wk after inoculation, 

but causing no symptoms on apple, even after wounding. 

Although only four of the specimens examined have been 

compared genetically, all of the cited specimens examined match 

in terms of associated symptoms and conidial size and shape. 

A specimen from Cordyline banksii (PDD 78360) has narrower 

conidia, forms perithecia on the infected leaves, and perhaps 

represents a different species. Specimens accepted here as C. ti 

were referred to Glomerella cingulata by Laundon (1972). 

The appearance in culture varies between isolates. The J.M. 

Dingley cultures, first isolated in the mid-1960’s, have dense, felted 

aerial mycelium and limited conidial production; one has a much 

slower growth rate than the more recent collections. 

Other specimens examined: New Zealand, Auckland, on Cordyline australis, coll. 

J.M. Dingley 6653, Mar. 1966 (PDD 30206; ICMP 5285); Taranaki, New Plymouth, 

Duncan and Davies Nursery, on C. australis × C. banksii leaf spots, coll. G.F. 

Laundon LEV 3343, 26 May 1969 (PDD 50634); Taranaki, New Plymouth, Duncan 

and Davies Nursery, on C australis × C. banksii leaf spots, coll. G.F. Laundon, 26 

May 1969 (PDD 26775); Waikato, Cambridge, Anton Nursery, on C. australis leaf 

spots, coll. L.A. Houghton, 23 Jul. 1992 (PDD 61219; ICMP 19444). 

* Colletotrichum tropicale E.I. Rojas, S.A. Rehner & 

Samuels, Mycologia 102: 1331. 2010. Fig. 37. 

Rojas et al. (2010) provide a description. 

Geographic distribution and host range: Rojas et al. (2010) noted 

that C. tropicale has been isolated from a wide range of hosts 

in forests in tropical America, from rotting fruit as well as leaf 

endophytes. We include also an isolate from tropical Japan, from 

Litchi chinensis leaves. 

Genetic identification: ITS sequences do not separate C. tropicale 

from some C. siamense or some C. queenslandicum isolates. 

Colletotrichum tropicale is best distinguished using TUB2, CHS-1, 

GS, or SOD2. 

Notes: Colletotrichum tropicale is genetically close to C. siamense 

and the two species share a number of morphological features; 

slow growth in culture, short and broad conidia with broadly 

rounded ends and often slightly constricted near the centre, and 

simple appressoria. 

171

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 on 


172

Specimens 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 GJS 

08-42 (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 isolates 

we examined (ICMP 17820) formed fertile perithecia in culture, 

a feature not mentioned in the original description. Perithecia 

are dark-walled, globose with a prominent, narrow neck, wall 

comprising several layers of pseudoparenchymatous cells 8–15 

µm diam, with several layers of densely packed hyphae outside 

this. 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 less 

elliptic, tapering to narrow, rounded ends, in side view flattened on 

one side, but generally not curved. 

Genetic identification: ITS sequences distinguish C. xanthorrhoeae 


Notes: This pathogen of Xanthorrhoea has a distinctive morphology, 

with a very slow growth rate in culture and large conidia which taper 

towards the basal end. The ascospore shape is distinct to that of 

most taxa within the C. gloeosporioides group, which typically have 

bent or curved ascospores. 

Specimens examined: Australia, Western Australia, Melville, on Xanthorrhoea 

preissii leaf spots, coll. F.D. Podger, Jan. 1994 (ex-holotype culture − BRIP 45094 

= ICMP 17903 = CBS 127831); Queensland, Cunningham’s Gap, Main Ranges 

National Park, on Xanthorrhoea sp. leaf spot (IMI 350817a = ICMP 17820). 

DISCUSSION 

The species that we accept in the Colletotrichum gloeosporioides 

species complex together form a strongly supported clade in the 

Colletotrichum ITS gene tree (fig. 1 in Cannon et al. 2012, this issue). 

All species are micro-morphologically typical of C. gloeosporioides 

sensu von Arx (1970) and Sutton (1992). However, morphology 

alone cannot unequivocally place an isolate in this complex, 

making the ITS particularly important for identification at the 

species complex level in Colletotrichum. For example, members of 

the C. boninense species complex (Damm et al. 2012b, this issue) 

and C. cliviae (Yang et al. 2009) are micro-morphologically similar 

to species in the C. gloeosporioides complex but genetically distinct 

(Cannon et al. 2012, this issue). The utility of ITS sequences is 

enhanced by their strong representation in GenBank, but this can 

also be a problem. Nilsson et al. (2006) summarised the frequency 

of inaccurately annotated data in GenBank. The diversity of 

taxonomic concepts around the name C. gloeosporioides makes 

this a particular problem. This is illustrated by the phylogeny 

presented by Hyde et al. (2010), based on GenBank accessions 

of ITS sequences identified as C. gloeosporioides and Glomerella 

cingulata, that shows the taxa represented belong to many species 

in different Colletotrichum species complexes. See notes under C. 

boehmeriae, C. crassipes, and C. kahawae subsp. kahawae for 

specific examples of misidentified GenBank accessions. 

The species we accept are based on a phylogenetic species 

concept, all species forming strongly supported, monophyletic 

clades within our multigene phylogenies. However, not all terminal 



clades are recognised as named species. In most cases any well 

supported, within-species phylogenetic structure evident in the 

multi-gene phylogeny is not resolved consistently in all gene trees. 

This lack of congruence between gene trees is a signal that the 

diversity being sampled is below the species level, according to 

the logic of the genealogical concordance phylogenetic species 

recognition (GCPSR) concept (Taylor et al. 2000). Although the 

concatenation of gene sequences is a convenient way to present 

multigene data, it masks discordance between individual gene 

phylogenies. An alternative method, using a species-tree approach 

(Figs 3, 4B, 5B) combines multi-gene data from multiple isolates 

hypothesised to represent a single species, so that the evolutionary 

history of the species rather than that of individual isolates is 

estimated. Fig. 3, shows the results of such an analysis for the C. 

gloeosporioides complex, Figs 4B and 5B show relationships within 

the Musae and Kahawae clades respectively, at an expanded 

scale. Posterior probabilities for some of the speciation events 

are low, particularly within the Musae and Kahawae clades. This 

may be because although the species-trees algorithms account 

for incomplete lineage sorting (Heled & Drummond 2010, Chung 

& Ané 2011), most do not compensate for horizontal gene transfer, 

reassortment, or introgression. Hybridisation could also result 

in discordant gene phylogenies. Hybrids are known in the C. 

acutatum complex, e.g. Glomerella acutata, a hybrid formed by 

crossing C. acutatum and C. fioriniae strains in the laboratory, 

and a putative hybrid strain between the same two species that 

had been collected from terminal crook disease on Pinus in New 

Zealand, 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 Cisar 

et al. (1994), more or less genetically equivalent to our species 

within the C. gloeosporioides complex. 

Our taxonomic conclusions are based, of necessity, on the 

limited set of genes sampled. Potentially more powerful genes, 

such as ApMAT and Apn25L (Silva et al. 2012a) may provide 

finer resolution within the species-level clades that we recognise. 

However, even with these potentially more informative genes, the 

low levels of genetic divergence across the C. gloeosporioides 

complex may always provide a technical challenge (Silva et al. 

2012a). The low level of diversity within this species complex is 

reflected by the branch lengths in fig. 2, Cannon et al. (2012, this 

volume), and is especially true across the Musae clade, where 

average pairwise identity between all isolates treated in our 5 

gene alignment is 98.6 %. Pairwise identity between isolates of 

C. siamense and C. theobromicola, two species showing strong 

within-species phylogenetic structure, are 99.4 % and 99.6% 

respectively. This suggests that the species recognised within the 

C. gloeosporioides complex are very recently evolved and Silva et 

al. (2012b) provide data supporting this. Their hypothesis of recent 

evolution of host-specialised Colletotrichum populations from more 

generalist fungi was also invoked in relation to the C. acutatum 

complex by Lardner et al. (1999) using the “episodic selection” 

framework of Brasier (1995). 

Several of the species we accept contain isolates with divergent 

lifestyles, for example C. aotearoa, C. clidemiae, C. kahawae, and 

C. theobromicola. Each of these species includes isolates capable 

of causing specific diseases. In the case of C. kahawae, recent 

pathogenicity tests have shown that only some isolates are able 

to cause coffee berry disease (Silva et al. 2012a, Silva & Weir, 

unpubl. data) and that these isolates can be distinguished using GS 

sequences (this study), Apn25L and MAT1-2-1 (Silva et al. 2012b). 

Because of the well understood pathogenicity of isolates within 

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Weir et al. 

Fig. 38. Colletotrichum xanthorrhoeae. ICMP 17903 (ex BRIP 45094 – ex-holotype culture). A. Cultures on PDA, 10 d growth from single conidia, from above and below. B. 

Culture on PDA at 4 wk showing sectoring with variation in pigmentation and growth form. C–D. Asci and ascospores. E. Perithecial wall in squash mount. Scale bar C = 20 

µm. Scale bar of C applies to C–E. 

174

C. kahawae, the biosecurity importance of coffee berry disease, 

and the ability to distinguish the disease-causing isolates using 

carefully selected genetic markers, we recognise the diseasecausing 

isolates taxonomically at the subspecific level. Future study 

of the comparative pathogenicity of isolates within C. aotearoa, C. 

clidemiae, and C. theobromicola may reveal genetically distinct, 

host-specialised pathogenic populations within these species that 

future workers may also choose to recognise taxonomically. 

The classification we accept here is deliberately taxonomically 

conservative, minimising nomenclatural changes. This reflects 

continuing uncertainty about sensible species limits within the 

C. gloeosporioides complex that relate to low levels of genetic 

divergence across the complex, gene selection, isolate selection, 

and a lack of understanding of the mechanisms driving species 

and population divergence amongst these fungi. For example, 

the two haplotype subgroups of C. fructicola are not distinguished 

taxonomically because collectively they form a monophyletic clade, 

both subgroups include sets of isolates with similar geographic and 

host diversity, and there is no practical need to distinguish them 

taxonomically. 

Molecular tools are increasingly being used for day-to-day 

identification by biosecurity officers and plant pathology researchers, 

providing a need for both a taxonomy that closely reflects groups that 

are resolved genetically, as well as simple and reliable protocols for 

identifying those taxa. The internal transcribed spacer region (ITS) 

has been proposed as the official fungal barcoding gene (Schoch 

et al. 2012). Although ITS is useful at the species complex level, it 

does a poor job of resolving species within the C. gloeosporioides 

complex, resolving only 10 of 22 accepted species. This reflects 

the low number of base changes in the ITS region across the C. 

gloeosporioides complex; species often distinguished by only one 

or two base changes. In some cases, chance variation in the ITS 

sequence within or between species means that some species 

cannot be distinguished (Fig. 6). Examples of taxa with identical 

ITS sequences include C. clidemiae, C. tropicale, C. ti and some 

C. siamense isolates; C. fructicola and some C. siamense isolates; 

and C. alienum, C. aenigma and some C. siamense isolates. 

Protein-coding genes and their introns often have more 

variation than ITS, and the need for secondary barcodes based 

on these kinds of genes has been discussed in relation to some 

groups of fungi (Fitzpatrick et al. 2006, Aguileta et al. 2008, Weir 

& Johnston 2011). Ideally, one of the seven protein coding genes 

that were used in this study could be proposed as a secondary 

barcode to obtain an accurate identification of species within the 

C. gloeosporioides complex. A preliminary analysis of the genes 

performance as barcodes was conducted as part of Cai et al. 

(2009) with GAPDH, CAL, and ACT performing well, but CHS- 

1, ITS, and TEF (EF1α) poorly. However, the analysis (Cai et al. 

2009) included only five species within the C. gloeosporioides 

complex, the Musae and Kahawae clades being treated at the level 

of species. With the final classification presented here, none of 

the genes we analysed provides an effective barcode ont its own 

across the entire complex. Of the single genes, TUB2, GS, and 

GAPDH are amongst the most effective at distinguishing species. 

However, C. clidemiae is polyphyletic in the TUB2 gene tree and 

GS sequences are needed to distinguish C. fructicola and C. 

alienum. With GS, C. aotearoa, C. kahawae subsp. ciggaro, and C. 

siamense are paraphyletic. GAPDH is the easiest of all the genes 

tested to amplify and sequence, however when using this gene GS 

sequences are needed to distinguish C. fructicola from C. alienum 

and C. aeschynomenes from C. siamense, and C. tropicale is 

paraphyletic. In the species descriptions we provide notes on which 



genes are the best for genetic identifications, and in Table 4 these 

are summarised for all species and genes. For species represented 

by a single or only a few isolates the species boundaries may not 

be accurate, we recommend two protein-coding genes in addition 

to ITS for sequence-based identifications. A meta-analysis of 

DNA barcodes across the whole genus will be required to find the 

combination of genes that are effective for all species of the genus 

that distinguish all Colletotrichum species. 

Several studies have shown that cultural morphology can be 

useful for grouping isolates when they are sampled at a local or 

regional level (e.g. Johnston & Jones 1997, Prihastuti et al. 2009). 

However, our experience is that such groups often break down 

when the geographic sample within a clade is extended to a global 

scale. Many of the species we accept have few or no diagnostic 

morphological or cultural features that can be consistently and 

reliably used to identify them. Our morphological examinations 

were confined to cultures on Difco PDA agar plates, and we will 

have missed any features that develop solely in association with 

plant material. In addition, the cultures we used have been sourced 

from different labs and collections from around the world, many 

with no information on storage history. Storage history and method 

has a major impact on the appearance of Colletotrichum in culture. 

Cultures can become “stale” during storage, losing the ability to 

produce pigments, the aerial mycelium often becoming very dense 

and felted, and losing the ability to form well-differentiated acervuli, 

conidia, or perithecia. In some clades, even freshly isolated cultures 

are highly variable, forming distinct sectors with differences in the 

production of pigment, aerial mycelium, acervuli, and conidia. 

Some isolates form two very different cultural types from single 

conidia or ascospores derived from colonies themselves started 

from single ascospores. Figure 27F shows single ascospore 

cultures from an isolate of C. kahawae subsp. ciggaro. One has 

the typical appearance of cultures of this fungus isolated from the 

field. The other, with a uniform, dense layer of conidia across the 

colony surface without well differentiated acervuli and more or less 

no aerial mycelium, is common from single ascospore isolates in 

culture, but rarely found in cultures isolated directly from the field. 

This kind of variation, and that revealed from sectoring during 

colony growth, makes morphological variation difficult to interpret 

for accurate identification. 

Many of the species recognised in this work remain poorly 

understood in terms of their pathogenicity and host preference. 

This in part reflects a lack of certainty about the biological 

relationship between the fungi and the plants from which they 

were isolated. Species that are pathogenic on one host can 

also be isolated from others following opportunistic colonisation 

of senescing tissue, such as the C. salicis example discussed 

by Johnston (2000, as Glomerella miyabeana). The multiple 

Colletotrichum spp. associated with a single host are likely to 

have a variety of life styles: primary pathogens of healthy tissue, 

species with the ability to invade and cause minor disease 

when the host plant is under stress, species that develop latent 

infections and fruit only following senescence of the host tissue 

or ripening of host fruit and endophytic species that sporulate 

only following host tissue death. The combination of this range of 

distinct life styles, the fact that several Colletotrichum spp. may 

become established on a single host, and the ability of most of 

these species to also establish on a range of other hosts, has 

been a large part of the confusion surrounding species limits 

within Colletotrichum. 

In some cases, apparently clear differences in pathogenicity 

of isolates in the C. gloeosporioides complex are not reflected 

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Weir et al. 

Table 4. Performance of individual genes at resolving species within the Colletotrichum gloeosporioides species complex. Y – species 

distinguished from all others. N – species not distinguished from all others. N* – distinguishes at the subspecies level. 

Species ITS GAPDH CAL TUB2 ACT CHS-1 GS SOD 

C. fructicola N N Y N N Y Y Y 

C. nupharicola N Y Y Y Y Y Y Y 

C. alienum N N Y N N Y Y Y 

C. musae Y Y Y Y Y Y Y Y 

C. aenigma N Y Y Y N Y Y Y 

C. siamense N N Y Y N N N N 

C. aeschynomenes N N N Y N Y Y Y 

C. tropicale N N N Y Y N Y Y 

C. queenslandicum N Y Y Y N N Y N 

C. salsolae N Y Y Y Y Y N Y 

C. asianum Y Y Y Y Y Y Y Y 

C. gloeosporioides Y Y Y Y Y Y Y Y 

C. alatae Y Y Y Y Y Y Y Y 

C. theobromicola Y Y Y Y Y Y Y Y 

C. xanthorrhoeae Y Y Y Y Y Y Y Y 

C. horii Y Y Y Y Y Y Y Y 

C. aotearoa N N Y Y N Y Y N 

C. ti N Y Y Y N Y Y Y 

C. kahawae N Y N Y Y N N* N 

G. cingulata “f. sp. camelliae” Y N Y Y Y N Y Y 

C. clidemiae N N N N Y Y Y N 

C. psidii Y Y Y Y N Y Y Y 

C. cordylinicola Y Y Y Y N Y Y Y 

genetically. For example, the fungi referred to as C. gloeosporioides 

f. stylosanthis “f. sp. guianensis” and C. gloeosporioides f. 

stylosanthis “f. sp. stylosanthis”, are reportedly associated with two 

distinct diseases of Stylosanthes (Irwin & Cameron 1978; Munaut 

et al. 2002), but both taxa genetically match C. theobromicola and 

are here placed in synonymy with C. theobromicola. It is possible 

that screening additional genes across a set of isolates from 

Stylosanthes with known pathogenicity will reveal one or more 

genes that generate a phylogeny that correlates with pathogenicity. 

This is the case with another specialised pathogen, C. kahawae. 

Originally described as a pathogen of green coffee berries, almost 

genetically identical isolates have subsequently been found on a 

wide range of hosts (see notes under C. kahawae). The isolates 

from other hosts are not pathogenic to coffee berries (Silva et al. 

2012b). The difference in pathogenicity correlates with a genetic 

difference in the GS gene, and we taxonomically recognise this 

biologically specialised population at the subspecies level. A similar 

approach could potentially be taken for other biologically distinct 

populations within a genetically strongly supported species. 

Despite the epitypification of C. gloeosporioides in 2008, web 

search hits on the name C. gloeosporioides from papers published 

over the past 12 mo show that many authors will continue to use 

the name in the sense of the C. gloeosporioides species complex, 

presumably regarding this level of identification as sufficient for their 

research. All of the isolates that we accept in the C. gloeosporioides 

complex share the string 5’–GGGCGGGT–3’ about 139–142 bases 

after the ITS1F primer binding site. Based on a comparison with 

GenBank data, this string appears to be specific to isolates that 

we would accept as members of the C. gloeosporioides complex. 

176 

Several authors have developed PCR-based, rapid identification 

tools for distinguishing members of the C. gloeosporioides complex 

from members of the C. acutatum species complex. This has been 

prompted because some members of the C. acutatum complex 

have conidia without the acute ends characteristic of this species as 

described by Simmonds (1965), and have at times been confused 

with C. gloeosporioides (Damm et al. 2012, this issue). Primers 

reportedly specific to C. gloeosporioides include the CgInt primer for 

ITS (Mills et al. 1992). In our data set this primer sequence is found 

in C. gloeosporioides s. str., C. fructicola, and C. siamense but all 

of the other taxa that we recognise within the C. gloeosporioides 

complex have one or more bases not matching the CgInt primer. 

The practical impact of these differences will depend in part on 

the position of the mismatch and stringency of the PCR reaction. 

Talhinas et al. (2005) discussed the TBCG primer for β-tubulin, 

and this is found within all of our taxa within the C. gloeosporioides 

group except C. musae and C. asianum. Liu et al. (2011) describe 

characteristic RFLP bands from glutamine synthetase using the 

restriction enzyme Pst1. Based on our sequences, this method will 

generate the characteristic C. gloeosporioides bands reported by Liu 

et al. (2011) for C. aenigma, C. alienum, C. aotearoa, C. asianum, 

C. clidemiae, C. cordylinicola, C. fructicola, C. gloeosporioides s. 

str., C. horii, C. queenslandicum, C. salsolae, C. siamense, C. ti, 

and C. tropicale. Different banding patterns will be produced by C. 

aeschynomenes (band sizes 253, 316, 388), the two C. kahawae 

subspp. (band sizes 112, 388, 457), G. cingulata “f. sp. camelliae” 

(band sizes 51, 112, 337, 457), and C. musae (band sizes 388, 

552), but none match the bands reported for C. acutatum by these 

authors.

Comparison of our data with gene sequences reported as 

C. gloeosporioides in recent papers allows most to be placed 

with confidence in one of the species that we accept. There are 

exceptions, such as the pecan-associated isolates from Liu et al. 

(2011), and the pistachio-associated isolates reported by Yang et 

al. (2011), both of which appear to represent undescribed species 

within the C. gloeosporioides complex. Clearly, more species remain 

to be described within the C. gloeosporioides complex. In addition, 

taxonomic issues still to be resolved amongst the species discussed 

in this paper include the relationship between G. cingulata “f. sp. 

camelliae” and C. camelliae, the identity of the cotton pathogens 

referred to C. gossypii, the identity of the cassava pathogens referred 

to C. manihotis, the relationship between C. aeschynomenes and C. 

gloeosporioides “f. sp. jussiaeae”, whether the various yam diseases 

discussed in the literature are all caused by C. alatae, and whether 

the isolates of C. aotearoa from Meryta leaf spots form a biologically 

distinct population. A more general question relates to better 

understanding the frequency of hybrids within the C. gloeosporioides 

complex and the impact of this on the interpretation of the phylogenies 

within the complex. The impact of hybridisation on the evolution of 

disease specialised populations has barely been explored. 

ACKNOWLEDGEMENTS 

This study was funded by AGMARDT (The Agricultural and Marketing Research 

and Development Trust) grant no. 892, the New Zealand Ministry of Science and 

Innovation through backbone funding of the “Defining New Zealand’s Land Biota” 

programme, and the New Zealand Tertiary Education Commission through the 

“Molecular diagnostics: capitalising on a million DNA barcodes” project. Shaun 

Pennycook, Landcare Research, provided valuable nomenclatural advice, Duckchul 

Park and Paula Wilkie, Landcare Research, provided valuable technical assistance. 

Diogo Silva, Centro de Investigação das Ferrugens do Cafeeiro, Portugal, carried 

out the C. kahawae pathogenicity tests. David Cleland, ATCC, provided DNA 

sequences for ATCC 96723. This study has been possible only through the provision 

of cultures by the DAR, ICMP, CBS, CABI, and MAFF culture collections, as well 

as by many individual researchers — Matthew Abang, Deutsche Sammlung von 

Mikroorganismen und Zellkulturen, Braunschweig, Germany; Robert Barreto, 

Universidade Federal de Viçosa, Brazil; George Carroll, University of Oregon, 

USA; Dana Berner, Foreign Disease-Weed Science Research Unit, USDA-ARS, Ft. 

Detrick, USA; Lindy Coates, Brad McNeil and Roger Shivas, Queensland Primary 

Industries and Fisheries, Indooroopilly, Queensland, Australia; W.E. Copes, USDA- 

ARS Small Fruit Research Unit, Poplarville, Massachusetts, USA; Kerry Everett 

and Mike Manning, Plant and Food Research, Auckland, New Zealand; David Farr, 

Gary Samuels and Steve Rehner, Systematic Mycology & Microbiology Laboratory 

USDA, Beltsville, USA; Steve Ferriera and K. Pitz, University of Hawaii, USA; Stan 

Freeman, Dept. of Plant Pathology and Weed Research, The Volcani Center, Israel; 

Hideo Ishii, National Institute for Agro-Environmental Sciences, Tsukuba, Japan; 

Sucheta Joshee and Nick Waipara, Landcare Research, Auckland, New Zealand; 

Lisa Korsten, University of Pretoria, South Africa; Lei Cai, State Key Laboratory of 

Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; 

Frank Louws and Turner Sutton, North Carolina State University, USA; Stephen 

Mackenzie and Natalia Peres, University of Florida, USA; Nelson Massola, Escola 

Superior de Agricultura “Luiz de Queiroz”, Brazil; Jean-Yves Meyer, Department of 

Research Ministère d’Education, de l’Enseignement Supérieur et de la Recherche 

Gouvernement de Polynésie française, French Polynesia; François Munaut, 

Université Catholique de Louvain, Belgium; Vera Sergeeva, University of Western 

Sydney, New South Wales, Australia; Amir Sharon, Tel Aviv University, Israel; Po 

Po Than, Chinese Academy of Forestry, Kunming, China; Ramon Villanueva-Aroe, 

University of València, Spain; Jing-Ze Zhang, Zhejiang University, Hangzhou, China. 

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