Skip to main content
SpringerLink
Log in

Multilocus genes based characterization of phytoplasma strains associated with Mexican and French marigold species in India

  • Published:
European Journal of Plant Pathology Aims and scope Submit manuscript

Abstract

During the winters of 2018 to 2020, witches’ broom, phyllody, flat stem, little leaf, yellowing and stunting symptoms were recorded in Mexican and French marigold fields in four states of India. The average recorded disease incidence ranged from 3 to 30% in different states. The ~1.2 kb product of 16S rRNA gene was amplified in symptomatic marigold samples using universal phytoplasma-specific nested primer pairs. Sequence comparison, phylogenetic and virtual RFLP analysis of 16S rRNA gene sequences identified the phytoplasmas in marigold samples as enclosed in the 16SrII-C subgroup for the strains from Delhi and in the 16SrI-B subgroup for the strains from Tripura, Uttar Pradesh and Maharashtra. Phytoplasma presence was further confirmed amplifying four genes (secA, rp, secY and tuf) in the symptomatic marigold species from all the surveyed places. Moreover, six weed species growing in marigold fields resulted positive for phytoplasmas. Phyllanthus niruri (Delhi) was tested positive for 16SrII-C subgroup phytoplasma, however, Ageratum conyzoides, Acmella calva and Ludwigia perennis (Tripura), Cannabis sativa (Uttar Pradesh) and Parthenium hysterophorus (Maharashtra) were tested positive with 16SrI-B subgroup related phytoplasma strains. Four leafhopper species were also detected positive for 16SrI-B subgroup collected from marigold fields at Tripura, Uttar Pradesh and Maharashtra and were identified as putative vectors for identified marigold phytoplasma strains. The report of association of 16SrII-C subgroup phytoplasma in Mexican marigold and P. niruri and 16SrI-B subgroup phytoplasma in L. perennis and A. calva are new reports in world.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10
Fig. 11

Similar content being viewed by others

References

  • Ahrens, U., & Seemüller, E. (1992). Detection of DNA of plant pathogenic mycoplasma like organisms by a polymerase chain reaction that amplifies a sequence of the 16S rRNA gene. Phytopathology, 82, 828–832.

    Article  CAS  Google Scholar 

  • Alp, S., Usta, M., Sipahioglu, H. M., & Guller, A. (2016). First report of ‘Candidatus Phytoplasma solani’ on a new host marigold (Tagetes erecta L.). Turkish Journal of Agriculture and Forestry, 40(3), 311–318.

    Article  CAS  Google Scholar 

  • Al-Subhi, A. M., Hogenhout, S. A., Al-Yahyai, R. A., & Al-Sadi, A. M. (2018). Detection, identification, and molecular characterization of the 16SrII-D phytoplasmas infecting vegetable and field crops in Oman. Plant Disease, 102(3), 576–588.

    Article  CAS  PubMed  Google Scholar 

  • Anonymous. (2017). Horticultural statistics at a glance. National Horticulture Board, Gurugram, Haryana, India. http://nhb.gov.in. Accessed 12 March 2020.

  • Ayman, O. F., Kumar, Y., Hallan, V., & Zaidi, A. A. (2010). Molecular characterization of the phytoplasmas associated with toon trees and periwinkle in India. Journal of General Plant Pathology, 76(5), 351–354.

    Article  Google Scholar 

  • Bekele, B., Hodgetts, J., Tomlinson, J., Boonham, N., Nikolić, P., Swarbrick, P., & Dickinson, M. (2011). Use of a real-time LAMP isothermal assay for detecting 16SrII and XII phytoplasmas in fruit and weeds of the Ethiopian Rift Valley. Plant Pathology, 60(2), 345–355.

    Article  CAS  Google Scholar 

  • Bellardi, M. G., Bertaccini, A., Madhupriya, & Rao, G. P. (2018). Phytoplasma diseases in ornamental crops. In Phytoplasmas: Plant pathogenic bacteria-I (pp. 191–233). Springer.

  • Bertaccini, A., Duduk, B., Paltrinieri, S., & Contaldo, N. (2014). Phytoplasmas and phytoplasma diseases: A severe threat to agriculture. American Journal of Plant Sciences, 5, 1763–1788.

    Article  Google Scholar 

  • Bhat, S. K. S., Vandana, Y., Kiran, K., Vipool, T., Bhavesh, T., Amit, Y., & Ramanayaka, J. G. (2020). Molecular detection and identification of a strain related to 'Candidatus Phytoplasma australasia' in marigold in India. Phytopathogenic Mollicutes, 10(1), 82–88.

    Article  Google Scholar 

  • Bohunická, M., Valentová, L., Suchá, J., Nečas, T., Eichmeier, A., Kiss, T., & Cmejla, R. (2018). Identification of 17 ‘Candidatus Phytoplasma pyri’ genotypes based on the diversity of the imp gene sequence. Plant Pathology, 67(4), 971–977.

    Article  CAS  Google Scholar 

  • Bos, T. K., & Yadav L. P. (1998). Commercial Flowers. Naya Prokash Publisher. 

  • Cai, H., Wang, L. C., Yang, Z. X., Wan, Q. L., Wei, W., Davis, R. E., & Zhao, Y. (2016). Evidence for the role of an invasive weed in widespread occurrence of phytoplasma diseases in diverse vegetable crops: Implications from lineage-specific molecular markers. Crop Protection, 89, 193–201.

    Article  Google Scholar 

  • Chaube, S., Mall, S., Dubey, D. K., & Rao, G. P. (2015). Phyllanthus niruri L.: A new host of ‘Candidatus Phytoplasma asteris’ in India. Phytopathogenic Mollicutes, 5(1), 87–88.

    Article  Google Scholar 

  • Danet, J. L., Balakishiyeva, G., Cimerman, A., Sauvion, N., Marie-Jeanne, V., Labonne, G., Laviňa, A., Batlle, A., Križanac, I., & Foissac, X. (2011). Multilocus sequence analysis reveals the genetic diversity of European fruit tree phytoplasmas and supports the existence of inter-species recombination. Microbiology, 157(2), 438–450.

    Article  CAS  PubMed  Google Scholar 

  • Deng, S., & Hiruki, C. (1991). Amplification of 16S rRNA genes from culturable and nonculturable mollicutes. Journal of Microbiological Methods, 14, 53–61.

    Article  CAS  Google Scholar 

  • Galetto, L., Marzachì, C., Demichelis, S., & Bosco, D. (2011). Host plant determines the phytoplasma transmission competence of Empoasca decipiens (Hemiptera: Cicadellidae). Journal of Economic Entomology, 104(2), 360–366.

    Article  CAS  PubMed  Google Scholar 

  • Gopala, & Rao, G. P. (2018). Molecular characterization of phytoplasma associated with four important ornamental plant species in India and identification of natural potential spread sources. 3 Biotech, 8(2), 116.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gundersen, D. E., & Lee, I. M. (1996). Ultrasensitive detection of phytoplasmas by nested-PCR assays using two universal primer pairs. Phytopathologia Mediterranea, 144–151.

  • Hemmati, C., Al-Subhi, A. M., & Al-Sadi, A. M. (2020). Multigene characterization of a ‘Candidatus Phytoplasma australasia’strain associated with Roystonea regia in Oman. Canadian Journal of Plant Pathology, 1-10.

  • Hodgetts, J., Boonham, N., Mumford, R., Harrison, N., & Dickinson, M. (2008). Phytoplasma phylogenetics based onanalysis of secA and 23S rRNA gene sequences for improved resolution of candidate species of ‘Candidatus Phytoplasma’. International Journal of Systematic and Evolutionary Microbiology, 58, 1826–1837.

    Article  CAS  PubMed  Google Scholar 

  • Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33, 1870–1874.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee, I.-M., Bottner-Parker, K. D., Zhao, Y., Davis, R. E., & Harrison, N. A. (2010). Phylogenetic analysis and delineation of phytoplasmas based on secY gene sequences. International Journal of Systematic and Evolutionary Microbiology, 60(12), 2887–2897.

    Article  PubMed  Google Scholar 

  • Lee, I.-M., Gundersen-Rindal, D. E., Davis, R. E., Bottner, K. D., Marcone, C., & Seemüller, E. (2004). ‘Candidatus Phytoplasma asteris’, a novel phytoplasma taxon associated with aster yellows and related diseases. International Journal of Systematic and Evolutionary Microbiology, 54(4), 1037–1048.

    Article  CAS  PubMed  Google Scholar 

  • Lee, I. -M., Zhao, Y., & Bottner, K. D. (2006). SecY gene sequence analysis for finer differentiation of diverse strains in the aster yellows phytoplasma group. Molecular and Cellular Probes, 20(2), 87–91.

  • Mall, S., Kumar, S., Jadon, V., & Rao, G. P. (2015). Identification of phytoplasmas associated with weed species in India. Indian Phytopathology, 68, 449–453.

    Google Scholar 

  • Martini, M., Lee, I.-M., Bottner, K. D., Zhao, Y., Botti, S., Bertaccini, A., Harrison, N. A., Carraro, L., Marcone, C., Khan, A. J., & Osler, R. (2007). Ribosomal protein gene-based phylogeny for finer differentiation and classification of phytoplasmas. International Journal of Systematic and Evolutionary Microbiology, 57(9), 2037–2051.

    Article  CAS  PubMed  Google Scholar 

  • Martini, M., Quaglino, F., & Bertaccini, A. (2019). Multilocus genetic characterization of phytoplasmas. In Phytoplasmas: Plant pathogenic Bacteria-III (pp. 161–200). Springer.

  • Mergenthaler, E., Fodor, J., Kiss, E., Bodnár, D., Kiss, B., & Viczián, O. (2020). Biological and molecular evidence for the transmission of aster yellows phytoplasma to French marigold (Tagetes patula) by the flatid planthopper Metcalfa pruinosa. Annals of Applied Biology, 176(3), 249–256.

    Article  CAS  Google Scholar 

  • Nabi, S., Madhupriya, Dubey, D., & Rao, G. P. (2015). Identification of Canabis sativa L. ssp. sativa as putative alternate host of sesame phyllody phytoplasma belongs to 16SrI group in India. Medicinal Plants, 7, 68–70.

    Google Scholar 

  • Panda, P., Nigam, A., & Rao, G. P. (2019). Multilocus gene characterization of phytoplasmas in 16SrII-D subgroup associated with Coreopsis grandiflora little leaf disease in India. Phytopathogenic Mollicutes, 9(2), 295–301.

    Article  Google Scholar 

  • Panda, P., Rihne, T., Singh, A. K., & Rao, G. P. (2020). Mussaenda erythrophylla: A new host of ‘Candidatus Phytoplasma asteris’ in India. Indian Phytopathology, 73(4), 781–785.

    Article  Google Scholar 

  • Raj, S. K., Snehi, S. K., Khan, M. S., Singh, M., Chaturvedi, Y., Tiwari, A. K., & Rao, G. P. (2011). Molecular detection and identification of phytoplasmas associated with little leaf and witches’ broom disease of marigold (Tagetes erecta L.) in India. Phytopathogenic Mollicutes, 1(1), 41–46.

    Article  Google Scholar 

  • Ranebennur, H., Rihne, T., & Rao, G. P. (2020). Detection of a ‘Candidatus phytoplasma trifolii’-related strain in Xerochrysum bracteatum showing a leaf yellowing disease. Phytopathogenic Mollicutes, 10(1), 96–99.

    Article  Google Scholar 

  • Madhupriya, & Rao, G. P. (2017). Phytoplasma diseases of ornamental plants: An Indian overview. Journal of Ornamental Horticulture, 20(3/4), 87–102.

    Article  Google Scholar 

  • Rao, G. P., Panda, P., Reddy, M. G., & Mishra, S. (2019). Identification and management of 16SrII-D phytoplasmas in cluster bean and sesame crops in the Haryana province of India. Phytopathogenic Mollicutes, 9 (1), 175.

  • Rao, G. P., Panda, P., & Reddy, M. G. (2020). First report of the association of a 'Candidatus Phytoplasma asteris' strain with Crossandra infundibuliformis. New Disease Reports, 41(1), 38–38.

    Article  Google Scholar 

  • Rao, G. P., Tiwari, A. K., Kumar, S., & Baranwal, V. K. (2014). Identification of sugarcane grassy shoot-associated phytoplasma and one of its putative vectors in India. Phytoparasitica, 42(3), 349–354.

    Article  Google Scholar 

  • Rojas-Martínez, R. I., Zavaleta-Mejía, E., Lee, M., Martini, M., & Aspiros, H. S. (2003). Detection and characterization of the phytoplasma associated with marigold phyllody in Mexico. Journal of Plant Pathology, 85(2), 81–86.

    Google Scholar 

  • Schneider, B., & Gibb, K. S. (1997). Sequence and RFLP analysis of the elongation factor Tuf gene used in differentiation and classification of phytoplasmas. Microbiology, 143(10), 3381–3389.

  • Schneider, B., Seemüller, E., Smart, C. D., & Kirkpatrick, B. C. (1995). Phylogenetic classification of plant pathogenic mycoplasma-like organisms or phytoplasmas. In Molecular and diagnostic procedures in Mycoplasmology, vol 1 (pp. 369–380). Academic Press.

  • Šeruga Musić, M., Duc Nguyen, H., Černi, S., Mamula, Đ., Ohshima, K., & Škorić, D. (2014). Multilocus sequence analysis of ‘Candidatus Phytoplasma asteris’ strain and the genome analysis of turnip mosaic virus co-infecting oilseed rape. Journal of Applied Microbiology, 117(3), 774–785.

    Article  PubMed  CAS  Google Scholar 

  • Sharma, A. K., Misra, S., Raychaudhury, S. P., & Parameswaran, N. (1985). Phyllody of marigold, a disease associated with mycoplasma-like organisms. International Journal of Tropical Plant Diseases, 3, 45–49.

    Google Scholar 

  • Shukla, A., & Thakur, R. (2018). First report of Septoria leaf spot on marigold (Tagetes erecta L.) from Himachal Pradesh, India. International Journal of Current Microbiology & Applied Sciences, 7(1), 1744-1748.

  • Siampour, M., Izadpanah, K., Martini, M., & Salehi, M. (2019). Multilocus sequence analysis of phytoplasma strains of 16SrII group in Iran and their comparison with related strains. Annals of Applied Biology, 175(1), 83–97.

    Article  CAS  Google Scholar 

  • Singh, V. K., Singh, Y., & Kumar, P. (2012). Diseases of ornamental plants and their management. In V. K. Singh, Y. Singh, & A. Singh (Eds.), Eco-friendly innovative approaches in plant disease management (pp. 543–572). International Book Distributors and Publisher.

  • Sultana, R., Akanda, A. M., Haque, M. A. S., Majumdar, A., & Munsur, M. A. Z. A. (2014). An investigation to virus like diseases of marigold. Journal of Bioscience and Agriculture Research, 2(01), 23–35.

    Article  Google Scholar 

  • Taloh, A., Raju, D. V. S., Banyal, N., Kumar, G., Panda, P., Manimekalai, R., Marcone, C., & Rao, G. P. (2020). Genetic diversity of phytoplasma strains infecting chrysanthemum varieties in India and their possible natural reservoirs. 3. Biotech, 10(9), 1–13.

    Google Scholar 

  • Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22), 4673–4680.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thorat, V., Bhale, U., Sawant, V., More, V., Jadhav, P., Mane, S. S., Nandanwar, R. S., Tripathi, S., & Yadav, A. (2016). Alternative weed hosts harbors 16SrII group phytoplasmas associated with little leaf and witches’ broom diseases of various crops in India. Phytopathogenic Mollicutes, 6(1), 50–55.

    Article  Google Scholar 

  • Tiwari, A. K., Kumar, S., Mall, S., Jadon, V., & Rao, G. P. (2017). New efficient natural leafhopper vectors of sugarcane grassy shoot phytoplasma in India. Sugar Tech, 19(2), 191–197.

    Article  CAS  Google Scholar 

  • Tiwari, A. K., Vishwakarma, S. K., Singh, S. P., Kumar, P., Khan, M. S., Chun, S. C., & Rao, G. P. (2012). First report of a 'Candidatus Phytoplasma asteris' associated with little leaf disease of Ageratum conyzoides in India. New Disease Reports, 26, 18.

    Article  Google Scholar 

  • Viczián, O., Kiss, E., Szabó, M., & Mergenthaler, E. (2018). First report of aster yellows phytoplasma infection of marigold plants in Hungary. Journal of Plant Pathology, 100(2), 327.

    Article  Google Scholar 

  • Viraktamath, C. A., & Meshram, N. M. (2019). Leafhopper tribe Coelidiini (Hemiptera: Cicadellidae: Coelidiinae) of the Indian subcontinent. Zootaxa, 4653, 1–91.

    Article  Google Scholar 

  • Zhao, Y., Wei, W., Lee, M., Shao, J., Suo, X., & Davis, R. E. (2009). Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII). International Journal of Systematic and Evolutionary Microbiology, 59, 2582–2593.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The authors are thankful to the Head, Division of Plant Pathology, and the Director, Indian Agricultural Research Institute, for providing laboratory facilities.

Author information

Authors and Affiliations

  1. Discipline of Life Sciences, Indira Gandhi National Open University, New Delhi, 110068, India

    Priyam Panda & Amrita Nigam

  2. Department of Plant Pathology, College of Agriculture Tripura, Lembucherra, Agartala, 799210, India

    Prasenjit Debnath

  3. Department of Botany, DDU Gorakhpur University, Gorakhpur, Uttar Pradesh, 273009, India

    Smriti Mall

  4. Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India

    Govind Pratap Rao

Authors
  1. Priyam Panda
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Prasenjit Debnath
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Smriti Mall
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Amrita Nigam
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Govind Pratap Rao
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Govind Pratap Rao.

Ethics declarations

Conflict of interest

No potential conflict of interest was reported by the authors.

Supplementary Information

ESM 1

(DOCX 17 kb)

ESM 2

(DOCX 15 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Panda, P., Debnath, P., Mall, S. et al. Multilocus genes based characterization of phytoplasma strains associated with Mexican and French marigold species in India. Eur J Plant Pathol 161, 313–330 (2021). https://doi.org/10.1007/s10658-021-02323-7

Download citation

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10658-021-02323-7

Keywords

Search

Navigation