Pathogenicity and rDNA-ITS sequence analysis of the Corynespora cassiicola isolates from rubber plantations in Indonesia

  • Fetrina Oktavia Sembawa Research Centre, Indonesian Rubber Research Institute, Palembang, Indonesia
  • Kuswanhadi . Sembawa Research Centre, Indonesian Rubber Research Institute, Palembang, Indonesia
  • Widodo . Department of Plant Pathology, Bogor Agricultural University, Dramaga, Bogor, Indonesia
  • Diny Dinarti Plant Molecular Biology Laboratory, Department of Agriculture, Bogor Agricultural University, Dramaga, Bogor, Indonesia
  • Sudarsono . Plant Molecular Biology Laboratory, Department of Agriculture, Bogor Agricultural University, Dramaga, Bogor, Indonesia


Corynespora cassiicola is an important pathogen causing Corynespora leaf fall disease on the rubber tree. Analysis of virulence, rDNA-ITS sequence and identification of cas gene were undertaken to investigate the effect of agro-climatic conditions and host rubber clones to virulence of 23 C. cassiicola isolates on six clones (RRIC 100, BPM 24, BPM 1, PB 260, GT 1 and RRIM 600) and to observed the evolution pattern of C. cassiicola isolates. Virulence analysis showed that there is an interaction between isolates and clones, indicating the differences of each isolates virulence to six clones. Agro-climatic conditions and host clones influenced the virulence of isolates and rDNA-ITS sequence variation. Analysis of rDNA-ITS showed that there were three of Single Nucleotide Polymorphism (SNP) that separated of isolates into 5 haplotypes. Most of the isolates belonging to the haplotype 1. Phylogenetic analysis indicated that C. cassiicola have a high diversity, however the clustering did not indicate country and host species of isolates. This information will be very useful on developing strategies of disease management and rubber plant breeding towards resistance to CLF disease.

Keywords: Cassiicolin, CLF disease, Genetic diversity, Hevea brasiliensis, rDNA-ITS


Akpaja, E., D. Omorogbe and N. Nwogu. 2015. Field and in-vitro studies on corynespora leaf fall disease of Hevea brasiliensis in Nigeria. British Microb. Res. J. 7: 322-328.
Atan S. and N. Hamid. 2003. Differentiating Races of Corynespora cassiicola using RAPD and Internal Transcribed Spacer Markers. J. Rubber Res. 6: 58-64.
Bandelt H.J., P. Forster and A. Rohl. 1999. Median joining networks for inferring intraspecific phylogenies. Mol. Bio. Evol. 6: 37-47.
Breton F., C. Sanier, and J. D'Auzac. 2000. Role of cassiicolline. a host-selective toxin. in pathogenicity of Corynespora cassiicola. causal agent of a leaf fall disease of Hevea. J. Rubber Res. 3: 115-128.
Cutrim F. and G. Silva. 2003. Pathogenicity of Corynespora cassiicola to different Plant Species. Phytopathology. 28: 193-103.
de Lamotte F., M.P. Duviau, C. Sanier, R. Thai, J. Poncet, D. Bieysse, F. Breton and V. Pujade-Renaud. 2007. Purification and characterization of cassiicollin toxin produced by Corynespora cassiicola causal agent of the leaf fall disease of rubber tree. J. Chrom. 849: 357-362.
Déon M., A. Scomparin, A. Tixier, C.R. Mattos, T. Leroy, M. Seguin, P. Roeckel-Drevet and V. Pujade-Renaud. 2012a. First characterization of endophytic Corynespora cassiicola isolates with variant cassiicolline genes recovered from rubber trees in Brazil. Fungal Diver. 54: 87-99.
Déon M., Y. Bourré, S. Gimenez, A. Berger, D. Bieysse, F. de Lamotte, J. Poncet, V. Roussel, F. Bonnot, G. Oliver, et al. 2012b. Characterization of a cassiicolline-encoding gene from Corynespora cassiicola pathogen of rubber tree (Hevea brasiliensis). Plant Sci. 185-186: 227-237.
Déon M., B. Fumanal, S. Gimenez, D. Bieysse, R.R. Oliveira, S. S. Shuib, F. Breton, S. Elumalai, J.B. Vida, M. Seguin,. et al. 2014. Diversity of the cassiicolline gene in Corynespora cassiicola and relation with the pathogenicity in Hevea brasiliensis. Fungal Bio. 118:32-47.
Dixon L.J., R. L. Schlub, K. Pernezny, and L.E. Datnoff. 2009. Host specialization and phylogenetic diversity of Corynespora cassiicola. Phytopathology. 99: 1015-1027.
Fairuzah Z., B. Setyawan and T. R. Febbyanti. 2009. Resistance and susceptibility of recomendation and promising rubber clones to Corynespora cassiicola isolates. In: Proceedings of the National Breeding Seminar. Publisher Indonesian Rubber Institute, Indonesia. p 269-275.
Farr D. and A. Rossman. 2015. Fungal Databases. Systematic Mycology and Microbiology Laboratory. ARS. USDA. Available at: (accessed: Dec 7, 2015).
Fernando T., C. Jayasinghe, R. Wijesundera and D. Siriwardana. 2009. Variability of Hevea isolates of Corynespora cassiicola from Sri Lanka. J. Plant Dis. Protec. 116: 115-117.
Fernando T. H. P. S., C. K. Jayasinghe, R. L. C. Wijesundera, W. P. K. Silva and E. A. D. N. Nishantha. 2010. Evaluation of screening methods against Corynespora leaf fall disease of rubber (Hevea brasiliensis). J. Plant Dis. Protec. 117: 24-29.
Fernando T., C. Jayasinghe, R. Wijesundera and D. Siriwardane. 2012. Some factors affecting in vitro production, germination and viability of conidia of Corynespora cassiicola from Hevea brasiliensis. J. Nat. Sci. Sri Lanka. 40:241-249.
Furukawa T., K. Ushiyama and K. Kishi. 2008. Corynespora leaf spot of scarlet sage caused by Corynespora cassiicola. J. Gen. Plant Pathol. 4: 117-119.
Ganley A. and T. Kobayashi. 2007. Highly efficient concerted evolution in the ribosomal DNA repeats: total rDNA repeat variation evealed by whole-genome shotgun sequence data. Gen. Res. 17: 184-191.
Gazis R., S. Rehner and P. Chaverri. 2011. Species delimitation in fungal endophyte diversity studies and its implications in ecological and biogeographic inferences. Mol. Ecol. 20: 3001-3013.
Glass D., N. Takebayashi, L. Olson and D. Taylor. 2013. Evaluation of the authenticity of a highly novel environmental sequence from boreal forest soil using ribosomal RNA secondary structure modeling. Mol. Phyl. Evol. 67: 234-245.
Glass N. and G. Donaldson. 1995. Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous ascomycetes. App. Env. Microbio. 61: 1323–1330.
Harrington T., M. Kazmi, A. Al-Sadi and S., Ismail 2014. Intraspecific and intragenomic variability of ITS rDNA sequences reveals taxonomic problems in Ceratocytsis fimbriata sensu stricto. Mycologia. 106: 224-242.
Hieu N., N. Nghia, V. Chi and P. Dung. 2014. Genetic diversity and pathogenicity of Corynespora cassiicola isolates from rubber trees and other hosts in Vietnam. J. Rubber Res. 17:187-202.
Hinrikson H., S. Hurst, T. Lott, D. Warnock and C. Morrisson. 2005. Assessment of ribosomal large-subunit D1–D2. internal transcribed spacer 1. and internal transcribed spacer 2 regions as targets for molecular identification of medically important Aspergillus species. J. Clin. Microb. 43:2092-2103.
Isabel N., J. Beaulieu, P. Theriault and J. Bousquet. 1999. Direct evidence for biased gene diversity estimates from dominant Random Amplified Polymorphic DNA (RAPD) fingerprints. Mol. Ecol. 8: 477-482.
Katoch A., C. S. Prabhakar and P. N. Sharma. 2015. Metageographic population analysis of Colletotrichum truncatum associated with chili fruit rot and other hosts using ITS region nucleotide sequences. J. Plant Biochem. Biotech. 25: 64-72.
Munir M., H. Suryaningtyas, A. Situmorang and T. R. Febbyanti. 2009. Resistance of rubber clones IRR series 100 to Corynespora and Colletotrichum leaf fall disease. Proceedings of the National Breeding Seminar. Publisher Indonesian Rubber Institute, Indonesia. p 262-268.
Munir M., H. Suryaningtyas and Kuswanhadi. 2011. Genetic variability Analysis of Corynespora cassiicola (Berk & Curt) Wei. isolates in Indonesia using ISSR. Indon. J. Nat. Rubber Res. 30: 86-99.
Murali T., T. Suryanarayanan and R. Geeta. 2006. Endophytic Phomopsis species: host range and implications for diversity estimates. Canadian J. Microb. 57: 673-680.
Nghia N., J. Kadir, E. Sunderasan, M. Abdullah, A. Malik and S. Napis. 2008. Morphological and inter Simple Sequence Repeat (ISSR) Markers Analyses of Corynespora cassiicola Isolates from Rubber Plantations in Malaysia. Mycopathologia. 166: 189-201.
Nghia N., J. Kadir, E. Sunderasan, M. Abdullah, A. Malik and S. Napis. 2010. Intraspecific variability of Corynespora cassiicola inferred from single nucletide polymorphisms in ITS region of ribosomal DNA. J. Rubber Res. 13: 257-264.
Nilsson H., E. Kristiansson, M. Ryberg, N. Hallenbergand and K. Larsson. 2008. Intraspecific ITS variability in the kingdom Fungi as expressed in the international sequence databases and it‘s implications for molecular species identification. Evol. Bioinfo. 4: 193-201.
Nilsson R., M. Ryberg, K. Abarenkov, E. Sjokvist and Kristiansson. 2009. The ITS region as a target for characterization of fungal communities using emerging sequencing technologies. FEMS Microbiol. Let. 296: 97-101.
Ogbebor O.N. 2010: The status of three common leaf disease of Para rubber in Nigeria. J. An. Plant Sci. 6: 567-570.
Oktavia F., M. Munir, H. Suryaningtyas and Kuswanhadi. 2011. Characterization of DNA finger printing of Corynespora cassiicola isolates from varians regions of rubber plantation. Indon. J. Nat. Rubber Res. 29: 118-128.
Othman R. 2013. Development of high yielding disease resistance clones. IRRDB Agronomy Workshop. Indonesia.
Oubraim S., H. S. Moulay and H. B. Lazrek. 2016. A relationship between bayoud disease severity and toxin susceptibility of date palm cultivars. Emir. J. Food Agric. 28: 45-51.
Qi Y. X., X. Zhang, J. J. Pu, X. M. Liu, Y. Lu, H. Zhang, H. Q. Zhang, Y. C. Lv and Y. X. Xie 2011. Morphological and molecular analysis of genetic variability within isolates of Corynespora cassiicola from different hosts. Europe J. Plant Pathol. 130: 83-95.
Rampersad S.N., D. Perez-Brito, C. Torres-Calzada, R. Tapia-Tussell and C. V. Carrington. 2013. Genetic structure and demographic history of Colletotrichum gloeosporioides sensu lato and C. truncatum isolates from Trinidad and Mexico. BMC Evol. Bio. 13: 1-17.
Romruensukharom P., S. Tragoonrung, A. Vanavichit and T. Toojinda. 2005. Genetic variability of Corynespora cassiicola populations in Thailand. J. Rubber Res. 8: 38-49.
Saha T., A. Kumar, B. Roy, M. Ravindran, A. Joseph, C. K. Jacob, M. A. Nazeer, K. Sreedharan, K. Vinod and B. Chulaki. 2002. Molecular characterisation of fungal pathogens causing leaf diseases in rubber (Hevea brasiliensis). Proceeding of the 15th Plantation Crops Symposium Placrosym XV. India. p 195-203.
Savita Virk, G. S. And A. Nagpal. 2011. In vitro selection of calli of Citrus jambhiri Lush. For tolerance to culture filtrate of Phytophthora parasitica and their regeneration. Physiol. Mol. Biol. Plants. 17: 41-47.
Schoch C., K. Seifert, S. Huhndorf, V. Robert, J. Spouge, C. Levesque, W. Chen and F.B. Consortium. 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. PNAS. 109: 6241-6246.
Shimomoto Y., R. Adachi, Y. Morita, K. Yano, A. Kiba, Y. Hikichi and S. Takeuchi. 2008. Corynespora blight of sweet pepper (Capsicum annuum) caused by Corynespora cassiicola (Berk. & Curt.) Wei. J. Gen. Plant Pathol. 74: 335–337.
Shimomoto Y., T. Sato, H. Hojo, Y. Morita, S. Takeuchi, H. Mizumoto, A. Kiba and Y. Hikichi. 2011. Pathogenic and genetic variation among isolates of Corynespora cassiicola in Japan. Plant Pathol. 60: 253-260.
Shuib S., M. Deon, M. M. Mahyuddin, A. Izhar, B. Fumanal, E. Sunderasan and V. Pujade-Renaud. 2015. Cassiicolline genes among Corynespora cassiicola isolates from rubber plantations in Malaysia. J. Rubber Res. 18: 6241-6246.
Silva W. P. K., E. H. Karunanayake, R. L. C. Wijesundera and U. M. S Priyanka. 2003. Genetic variation in Corynespora cassiicola: a possible relationship between host origin and virulence. Mycol. Res. 107: 567-571.
Situmorang A. 2002. Spreading of the Corynespora leaf fall disease, virulence and genetic of Corynespora cassiicola were collected from rubber plantation in Indonesia. Ph.D. dissertation, Bogor Agricultural University, Indonesia.
Situmorang A., M. Sinaga, R. Suseno, S. Hidayat, Siswanto and A. Darussamin. 2007. Spreading of corynespora leaf fall disease in the Indonesian rubber plantation. Indon. J. Nat. Rubber Res. 25: 76-82.
Smith L. and R. Schlub. 2005. Foliar fungi on weeds of Guam and the potential for Corynespora cassiicola as a bioherbicide for Stachytarpheta jamaicensis. (Abstract). Phytopathology. 95: S93.
Tran D. M., A. Clement-Demange, M. Deon, D. Garcia, V. Le Guen, A. Clement-Vidal, M. Souahoro, A. Masson, P. Label, M. T. Le and V. Pujade-Renaud. Plos One. 11: e0162807.
U‘ren J., J. Dalling, R. Gallery, D. Maddison, E. Davis, C. Gibson and A. Arnold. 2009. Diversity and evolutionary origins of fungi associated with seeds of a Neotropical pioneer tree: a case study for analyzing fungal environmental samples. Mycol. Res. 113: 432-449.
White T. J., S. Bruns, Lee and J. Taylor. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M. A., D. Gelland, J. J. Sninsky, and T. J. White, editors. PCR protocols: A guide to methods and applications, Academic Pr, N. Y., pp. 315-322.
Yusnita, Y., W. Widodo and S. Sudarsono. 2009. In vitro selection of peanut somatic embryos on medium containing culture filtrate of Sclerotium rolfsii and planlet regeneration. Hayati. J. Biosci. 12: 50-56
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Oktavia, F., K. ., W. ., D. Dinarti, and S. . “Pathogenicity and RDNA-ITS Sequence Analysis of the Corynespora Cassiicola Isolates from Rubber Plantations in Indonesia”. Emirates Journal of Food and Agriculture, Vol. 29, no. 11, Oct. 2017, pp. 872-83, doi: Accessed 15 Aug. 2020.
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