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Resolving the Colletotrichum siamense species complex using ApMat marker

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Abstract

Colletotrichum gloeosporioides sensu lato has been associated with anthracnose in diverse commercial crops. It is now established that C. gloeosporioides sensu lato comprises 33 phylogenetic species and C. gloeosporioides sensu stricto is not a common pathogen of tropical fruits. In this study, we investigated the phylogenetic relationships of 85 Colletotrichum isolates associated with select tropical fruits and flowering plants from India. In the ApMat marker analysis, the 85 isolates clustered with 7 known Colletotrichum species (C. aotearoa, C. dianesei, C. endomangiferae, C. musae, C. siamense, C. theobromicola, Glomerella cingulata f. sp. camelliae) and six novel lineages. One of the novel lineages is described and illustrated in this paper as Colletotrichum communis sp. nov., while new-host pathogen associations for C. aotearoa, C. endomangiferae, C. dianesei and C. theobromicola are reported from India. Out of the 85 isolates analysed in this paper, 73 isolates clustered within the C. siamense species complex, indicating that C. siamense species complex, not C. gloeosporioides sensu stricto, is common on tropical fruits. In comparison with act, cal, gapdh, ITS and tub2 gene markers, we recommend the use of the ApMat marker for accurate identification of cryptic species within the C. siamense species complex. We believe that the ApMat marker, in combination with one or two similar ‘phylogenetically superior’ gene markers, is a better candidate for species-level classification of fungi that were traditionally identified as ‘Colletotrichum gloeosporioides’.

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Acknowledgments

The authors would like to thank CSIR-Institute of Microbial Technology, Chandigarh for the financial support, Dr. D. Ananthapadmanaban for his help in the microscopy and Mr. Deepak Bhatt for DNA sequencing assistance. Drs. Kevin D. Hyde, Lei Cai and Bevan Weir are thanked for the inspiration and useful discussions on Colletotrichum taxonomy. This work was supported by IMTECH-OLP0071 project and CSIR-SRF fellowship awarded to GS. This is NIO contribution no. 7636 and IMTECH communication no. IMT2014/21.

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  1. Belle Damodara Shenoy

    Present address: Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403004, India

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  1. Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036, India

    Gunjan Sharma, Anil Kumar Pinnaka & Belle Damodara Shenoy

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  1. Gunjan Sharma
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Correspondence to Belle Damodara Shenoy.

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Sharma, G., Pinnaka, A.K. & Shenoy, B.D. Resolving the Colletotrichum siamense species complex using ApMat marker. Fungal Diversity 71, 247–264 (2015). https://doi.org/10.1007/s13225-014-0312-7

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