Abstract
Hevea brasiliensis (Para rubber tree) is a commercially cultivated crop for latex production worldwide. Rubber trees from Southern states of India have been affected by Circular Leaf Spot (CLS) disease caused by Colletotrichum fructicola and Colletotrichum siamense causing yellowing and severe defoliation in rubber plantations in recent years. In this study, we collected infected leaf samples of CLS disease from different locations in the South Indian states of Kerala, Tamil Nadu, and Karnataka. Colletotrichum fructicola and C. siamense were identified as the causative agents of CLS disease and the isolate, C. fructicola was used for genomics analysis. We performed whole-genome sequencing (WGS) of, C. fructicola and carried out gene content analysis by comparing it with other reported Colletotrichum species. In silico analysis revealed a rich repertoire of pathogenicity genes and CAZymes in C. fructicola encoding secreted proteins, effectors, plant cell wall degrading enzymes, and secondary metabolism-associated proteins with possible roles in the host-specific interaction and pathogenicity. Our dataset provides a rich resource for understanding the pathogenicity-related genes that are involved in CLS disease progression and gives a basis for subsequent functional genomics research in C. fructicola.
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Data availability
The whole genome sequencing data from this study has been deposited to the Bioproject database of The National Centre for Biotechnology Information (NCBI) (https://www.ncbi.nlm.nih.gov/ accessed on 24 March 2021) under Project Id PRJNA727709. The raw data sequences were uploaded to the NCBI Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra accessed on 24 March 2021) database under the GenBank accession number SRR14453980. The sequence data of the Internal transcribed spacer (ITS) region from this study were deposited (https://www.ncbi.nlm.nih.gov/nuccore/ON054208 accessed on 23 March 2022) under the accession number ON054208.
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Acknowledgements
The authors are sincerely thankful to the Rubber Research Institute of India, for giving the technical support and laboratory facilities for executing the experiments and also thankful to Clevergene Biocorp Pvt. Ltd. Bangalore for the whole-genome sequencing support. The authors are also grateful to Ms. Limiya Joseph CSIR JRF and Dr. Indu M. Nair, University College, Cork Ireland for the editorial help of this manuscript.
Funding
The study was funded by the Junior Research Fellowship Programme of The Council of Scientific and Industrial Research and Human Resource Development Group (CSIR), New Delhi, India under Grant Agreement No. 09/662(0021)/2018-EMR-I.
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V.V.K.: The entire work was planned, executed the experiments, analyzed the data, and drafted as the manuscript; R.T.R., S.B. and C.M.: All the authors provided critical feedback and helped shape the research and manuscript; S.P.: Supervised the findings of this work, discussed the results, and contributed to the final manuscript.
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Vineeth, V.K., Reshma, T.R., Babu, S. et al. Comprehensive whole-genome sequencing reveals genetic characteristics of Colletotrichum fructicola (Nara gc5) the causative organism of circular leaf spot disease of rubber (Hevea brasiliensis). J Plant Pathol 106, 579–591 (2024). https://doi.org/10.1007/s42161-023-01578-9
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DOI: https://doi.org/10.1007/s42161-023-01578-9