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A Polyphasic Approach for Studying Colletotrichum

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A Polyphasic Approach for Studying Colletotrichum Online advance Fungal Diversity A polyphasic approach for studying Colletotrichum Cai, L.1*, Hyde, K.D.2,3, Taylor, P.W.J.4, Weir, B.S.5, Waller, J.M.6, Abang, M.M.7, Zhang, J.Z.8, Yang, Y.L.9, Phoulivong, S.3, Liu, Z.Y.9, Prihastuti, H.3, Shivas, R.G.10, McKenzie, E.H.C.5 and Johnston, P.R.5 1Novozymes China, No. 14, Xinxi Road, Shangdi, HaiDian, Beijing, 100085, PR China 2International Fungal Research & Development Centre, The Research Institute of Resource Insects, Chinese Academy of Forestry, Bailongsi, Kunming 650224, PR China 3School of Science, Mae Fah Luang University, Thasud, Chiang Rai 57100, Thailand 4BioMarka/Center for Plant Health, Melbourne School of Land and Environment, The University of Melbourne, Victoria 3010 Australia 5Landcare Research New Zealand Ltd, Private Bag 92170, Auckland Mail Centre, Auckland 1142, New Zealand 6CABI Europe UK, Bakeham Lane, Egham, Surrey, TW20 9TY. 7AVRDC-The World Vegetable Center, Regional Center for Africa, PO Box 10 Duluti, Arusha, Tanzania 8Institute of Biotechnology, College of Agriculture & biotechnology, Zhejiang University, Kaixuan Rd 258, Hangzhou 310029, PR China 9 Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou 550006 P.R. China 10Plant Pathology Herbarium, Queensland Primary Industries and Fisheries, 80 Meiers Road, Indooroopilly 4068, Queensland, Australia Cai, L., Hyde, K.D., Taylor, P.W.J., Weir, B.S., Waller, J., Abang, M.M., Zhang, J.Z., Yang, Y.L., Phoulivong, S., Liu, Z.Y., Prihastuti, H., Shivas, R.G., McKenzie, E.H.C. and Johnston, P.R. (2009). A polyphasic approach for studying Colletotrichum. Fungal Diversity 39: 183-204. Colletotrichum is the causal agent of anthracnose and other diseases on leaves, stems and fruits of numerous plant species, including several important crops. Accurate species identification is critical to understand the epidemiology and to develop effective control of these diseases. Morphologically-based identification of Colletotrichum species has always been problematic, because there are few reliable characters and many of these characters are plastic, dependent upon methods and experimental conditions. Rapid progress in molecular phylogenetic methods is now making it possible to recognise stable and well-resolved clades within Colletotrichum. How these should be reflected in a classification system remains to be resolved. An important step in providing a stable taxonomy for the genus is to epitypify existing names, and in so doing link them to genetically defined clades. We recommend a polyphasic approach to the recognition and identification of species within Colletotrichum, matching genetic distinctness with informative morphological and biological characters. This paper reviews various approaches in the study of Colletotrichum complexes including morphology, pathogenicity, physiology, phylogenetics and secondary metabolite production. A backbone phylogenetic tree using ITS sequence data from 42 ex-type specimens has been generated. Phylogenetic analysis using ITS sequence data is a useful tool to give a preliminarily identification for Colletotrichum species or place them in species complexes. However, caution must be taken here as the majority of the ITS sequences deposited in GenBank are wrongly named. Multi-gene phylogenetic data provides much better understanding of the relationships within Colletotrichum and should be employed where possible. We propose that an ideal approach for Colletotrichum systematics should be based on a multi-gene phylogeny, with comparison made with type specimens, and a well-defined phylogenetic lineage should be in conjunction with recognisable polyphasic characters, such as morphology, physiology, pathogenicity, cultural characteristics and secondary metabolites. Finally a set of protocols and methodologies is provided as a guideline for future studies, epitypification and the description of new species. Key words: barcoding, epitypification, molecular phylogeny, morphology, pathogenicity, physiology, systematics Article Information Received 30 November 2009 Accepted 4 December 2009 Published online 9 December 2009 *Corresponding author: [email protected] Introduction Colletotrichum Corda is one of the eco- nomically most important genera of fungi, The need for species recognition being responsible for anthracnose and other 183 diseases of a wide range of plant species Lee et al., 2006; Hu et al., 2007; Tesjevi et al., (Sutton, 1980; Hyde et al., 2009). The impor- 2007). Such data is especially important in tance of a rigid and stable taxonomy for the species differentiation and understanding the determination of Colletotrichum species is, species relationships in Colletotrichum. therefore, a significant practical concern (She- One potential solution for poor type noy et al., 2007). However, there has been material is to designate an epitype for the considerable difficulty surrounding Colletotri- species; this stabilises the species name and chum systematics, due to the lack of reliable should provide sequence data as well as living morphological features, making species boun- specimens for future research (Hyde and Zhang, daries ambiguous and confusing. Traditionally 2008). Thirteen species of Colletotrichum have many Colletotrichum species have been named been epitypified and/or newly combined in the after their host, which suggests host specificity genus (Crouch et al., 2006; Shenoy et al., 2007; amongst species. In what some considered a Cannon et al., 2008; Than et al., 2008a; Crouch drastic move, von Arx (1957) reduced the et al., 2009b; Damm et al., 2009; Weir and number of Colletotrichum species from several Johnston, in press), while recently described hundred to 11 based on morphological charac- new species have ex-type cultures (Crouch et ters, with many taxa treated as synonyms of C. al., 2009b; Damm et al., 2009; Prihastuti et al., gloeosporioides and C. dematium. Several 2009; Shivas and Tan, 2009; Yang et al., 2009). additional species have been since accepted, The use of sequences from type specimens is based on morphological criteria (Sutton, 1980; essential when diagnosing Colletotrichum 1992). species or studying their phylogenetic relation- The difficulty in recognising Colletotri- ships. Where possible, all previously desig- chum species has resulted from: 1) few and nated Colletotrichum gloeosporioides strains variable morphological characters; 2) an exten- should be compared against the recently desig- sive host range and variability in pathogenicity nated epitype of C. gloeosporioides (Cannon et (Bailey and Jeger, 1992; Freeman et al., 2000; al., 2008) to establish if they are correctly Latunde-Dada, 2001; Du et al., 2005; Thaung, named. 2008); 3) type specimens are often missing or Colletotrichum taxonomy is presently in poor condition thus they can not be used for unsatisfactory and there is a pressing need for a molecular study and; 4) numerous rDNA ITS polyphasic approach for identification, which (ITS) and other sequences of Colletotrichum reflects the natural classification of species and strains in NCBI are often erroneously named subspecific taxa within the genus (Sutton, (Crouch et al., 2009d; Damm et al., 2009). To 1992; Cannon et al., 2000). In this paper a solve the problem of few morphologically taxonomic framework for describing Colleto- informative characters, researchers have trichum epitypes and new species is proposed. utilised other characters such as nucleic acid This utilises a multi-gene phylogeny based on sequence data, physiology, secondary metabo- type specimens, and well-defined phylogenetic lites and pathogenicity, as part of a polyphasic lineages which correlate with recognisable approach (Sutton, 1992; Cannon et al. 2000; polyphasic characters such as morphology, Than et al., 2008a,b; Crouch et al., 2009b; cultural characteristics, physiology and Prihastuti et al., 2009). Phylogenetic analysis pathogenicity. The various approaches that based on nucleic acid sequences have been have been used or could be incorporated in the successfully used to differentiate species in study of Colletotrichum species, with recom- other difficult genera or groups (e.g. mended methodologies and discussion on Fusarium—Shenoy et al., 2007; Kvas et al., correlation of characters with phylogenetic 2009; O’Donnell et al., 2009; Botryosphaeria- types are discussed. A phylogenetic analysis ceae—Slippers et al., 2004a,b; Crous et al., based on the internal transcribed spacers and 2006; Alves et al., 2006, 2008; Phillips et al., the 5.8S ribosomal RNA gene (ITS) from 2007); although unsuccessfully in other genera specimens including 42 ex-type strains is also (e.g. Pestalotiopsis—Jeewon et al., 2002, 2003; provided (Fig. 1). 184 Fungal Diversity Established methodology Colletotrichum cultivation. For example, Baxter et al. (1983) described species of Morphology Colletotrichum based on growth on MSA and Traditional identification systems in CDY at 20ºC; Sutton (1980) used potato Colletotrichum have relied heavily on morpho- dextrose agar (PDA) under alternating 12 hours logical and cultural characteristics (von Arx, near ultra violet irradiation / 12 hour dark at 1957; Sutton, 1980, 1992; Bailey and Jeger, 25ºC; others have used PDA in the dark at 1992; Freeman et al., 1998). Sutton (1992) 25ºC (Shivas et al., 1998; Nirenberg et al., noted that morphology alone does not provide 2002) or; synthetic nutrient-poor agar (SNA) sufficient information for a precise identi- medium and Anthriscus stems incubated under fication, especially for those species in the
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