Fungal Diversity

, Volume 61, Issue 1, pp 117–138 | Cite as

The ApMat marker can resolve Colletotrichum species: a case study with Mangifera indica

  • Gunjan Sharma
  • Navinder Kumar
  • Bevan S. Weir
  • Kevin D. Hyde
  • Belle Damodara Shenoy


Anthracnose disease caused by the Colletotrichum gloeosporioides species complex is a major problem worldwide. In this study, we investigated the phylogenetic diversity of 207 Indian Colletotrichum isolates, associated with symptomatic and asymptomatic tissues of mango, belonging to this species complex. Phylogenetic analyses were performed based on a 6-gene dataset (act, cal, chs1, gapdh, ITS and tub2), followed by ApMat sequence-analysis. The ApMat-based phylogeny was found to be superior as it provided finer resolution in most of the species-level clades. Importantly, the ApMat marker identified seven lineages within C. siamense sensu lato, including C. jasmini-sambac, C. hymenocallidis, C. melanocaulon, C. siamense sensu stricto and three undesignated, potentially novel lineages. In this study, C. fragariae sensu stricto, C. fructicola, C. jasmini-sambac, C. melanocaulon and five undesignated, potentially novel lineages were found to be associated with mango tissues. There is a need to develop a consensus among mycologists as to which genes should be used to define and delimit a Colletotrichum species and in the mean time mycologists should voluntarily restrain from describing new species based on inadequate datasets.


Anthracnose Identification Phylogeny Polyphasic taxonomy Secondary barcode Systematics 



We thank Institute of Microbial Technology (CSIR-IMTECH) for the financial support. We thank Dr. Eric McKenzie from International Collection of Microorganisms from Plants, New Zealand and Dr. Makoto Kawase from National Institute Agrobiological Sciences Japan for providing some Colletotrichum type strains as gifts. Dr. D. Ananthapadmanaban, Deepak Bhatt, Amandeep Kaur, Deepinder Kaur and Yamini Agrawal from CSIR-IMTECH are thanked for their encouragement. Drs. Lei Cai and Roger Shivas are thanked for the inspiration and useful discussions on Colletotrichum taxonomy. We also thank Dr. Rakesh Pandey and Mr. Ashwin Nannaware (CSIR-NBRI, Lucknow, Uttar Pradesh), Mr. Pradip Kumar Singh (Banaras, Uttar Pradesh), Mr. Chittarjeet Singh (CSIR-CSIO, Chandigarh), Mr. Jignesh Patel (Gujrat), Mr. Srinivas Kamath (Maharashtra), Dr. S. Siddharthan (Chennai, Tamil Nadu), Ms. Sonika Verma (Patna, Bihar); Mr. Arun Prabhu and Pai (Goa) for their help in sample collections from the respective states. We acknowledge the help of Dr. V. Shanmugham, CSIR-IHBT, Palampur, India in performing the pathogenicity testing. Gavin Blyth, Landcare Research, New Zealand provided some sequences. This work was supported by CSIR-IMTECH-OLP0071 project and CSIR-SRF fellowship awarded to GS and UGC-SRF fellowship to NK. K.D. Hyde thanks the National Research Council of Thailand for the award of grant No. 54201020003 and a grant from the National Plan of Science and Technology, King Abdulaziz City of Science and Technology, Riyadh, Saudi Arabia, project No. 10-Bio-965-02 to study Colletotrichum.

Supplementary material

13225_2013_247_MOESM1_ESM.doc (436 kb)
Supplementary Table 1 List of Colletotrichum isolates associated with Mangifera indica included in this study with information on taxon, substrate, variety, geographic location, collector’s name and GenBank accession number for the 5 ′tef 1 gene sequenced (DOC 436 kb)
13225_2013_247_MOESM2_ESM.doc (54 kb)
Supplementary Table 2 List of the Colletotrichum type strains included in this study with information on taxon, host, geographic location and GenBank accession number for the 5′tef1 gene sequence (GenBank accession numbers highlighted in bold have been generated in this study, * = Type strain) (DOC 54 kb)


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Copyright information

© Mushroom Research Foundation 2013

Authors and Affiliations

  • Gunjan Sharma
    • 1
  • Navinder Kumar
    • 1
  • Bevan S. Weir
    • 2
  • Kevin D. Hyde
    • 3
  • Belle Damodara Shenoy
    • 4
  1. 1.Microbial Type Culture Collection and Gene BankCSIR-Institute of Microbial TechnologyChandigarhIndia
  2. 2.Landcare ResearchAucklandNew Zealand
  3. 3.Institute of Excellence in Fungal Research and School of ScienceMae Fah Luang UniversityChiang RaiThailand
  4. 4.CSIR-National Institute of OceanographyDona PaulaIndia

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