Güney Hindistan'da Çakal Hünnabı (Zizyphus oenoplia L.)'nın Cadı Süpürgesi Hastalığı "Candidatus Phytoplasma balanitae" ile İlişkisi

Year 2023, Volume: 54 Issue: 3 - Research in Agricultural Sciences, 113 - 123, 19.10.2023

V. Venkataravanappa K. V. Ashwathappa H. D. Vınaykumar M. Nandan M. Krıshna Reddy C. N. Lakshmınarayana Reddy

https://doi.org/10.5152/AUAF.2023.23089

Abstract

Araştırma sürecinde (2017-18), Hindistan’ın Karnataka ilçesinde fitoplazmalara özgü cadı süpürgesi (WB: Witches Broom) simptomu gösteren on iki (12) Çakal hünnap (Jackal jujube) bitkisinden örnek toplanmıştır. Örnekler fitoplazmaların 16S rRNA ve SecA genlerine sipesifik primerler kullanılarak Polymerase Chain Reaction (PCR) ile testlenmiş, amplifikasyon bölgeleri klonlanarak sekans dizilimleri çıkarılmış ve takiben NCBI veri tabanında yer alan fitoplazmaların sekans dizilimleri ile mukayese edilmiştir. Yapılan karşılaştırmada JJWB fitoplazma izolatlarının 16S rRNA gen bölgesinin Candidatus Phytoplasma balanitae gurubu (16SrV) ile %97,8-%98,2, SecA gen bölgesinin ise %89,4-%99 oranında Jujube witches broom (JWB) phytoplasma ile benzer nükleotit dizilimlerine sahip oldukları tespit edilmiş ve sonuç filogenetik analiz ile desteklenmiştir. Diğer taraftan, JJWB izolatları Alu I, Hae III ve Mse I enzimleri ile Restriction Fragmenth Length Polymorphism (RFLP) analizine tabi tutulduğunda kontrol olarak kullanılan Ca. P. balanitae (16SrV) gurubu ile 0,91 oranında benzerlik gösterdiği saptanmıştır. Bu oran yeni alt guruplar için eşik benzerlik oranını olan 0,98’den düşük bulunmuş ve bulgular bu veriler çerçevesinde tartışılmıştır.

Keywords

Candidatus Phytoplasma balanitae, çakal hünhabı, PCR, fillodi, filogenetik analiz

“Candidatus Phytoplasma balanitae” Associated with Witches’ Broom Disease of Jackal Jujube (Zizyphus oenoplia L.) in South India

Abstract

During survey, 12 Jackal jujube plant samples showing the symptoms of witches’ broom disease were collected from the Shivamogga district of Karnataka, India, between 2017 and 2018. The causal agent associated with Jackal jujube witches’ broom disease was identified through polymerase chain reaction using phytoplasma 16S rRNA-encoding and SecA gene-specific universal primers. All 12 Jackal jujube plant samples gave positive amplification for the phytoplasmaspecific primers. The amplified polymerase chain reaction products (16S rRNA-encoding gene and SecA gene) were cloned and sequenced. The nucleotide sequence 16S rRNA-encoding and SecA genes comparisons were made with the available phytoplasmas from an NCBI database. The Jackal jujube witches’ broom phytoplasma isolates shared the highest nucleotide identity of 97.8–98.2% (16S rRNA gene) with Candidatus Phytoplasma balanitae group (16SrV) and 89.4–99% (SecA gene) nucleotide identity with Jujube witches’ broom phytoplasma. This was well supported by the close clustering of Jackal jujube witches’ broom phytoplasma isolates in the current study with Candidatus Phytoplasma balanitae (16S rRNA gene) and Jujube witches’ broom-phytoplasma (SecA gene) in phylogenetic analysis. The virtual Restriction fragment length polymorphism (RFLP) pattern generated by Jackal jujube witches’ broom isolates was different (similarity coefficient of 0.91) to the reference pattern of Candidatus Phytoplasma balanitae (16SrV) group with respect to three enzymes (Alu I, Hae III, and Mse I). Based on the threshold similarity coefficient for the new subgroup, delineation should be set at 0.98. The significance of the research is discussed.

Keywords

Candidatus Phytoplasma balanitae, jackal jujube, PCR, phyllody, phylogenetic analysis

References

• Anonymous (2003). The wealth of India: A dictionary of Indian raw materials and industrial productsraw materials series, Publication and Information Directorate (pp. 49–51). Council of Scientific and Industrial Research.
• Bertaccini, A., Duduk, B., Paltrinieri, S., & Contaldo, N. (2014). Phytoplasmas and Phytoplasma diseases: A severe threat to agriculture. American Journal of Plant Sciences, 05(12), 1763–1788. [CrossRef]
• Bertaccini, A., & Lee, I.-M. (2018). Phytoplasmas: An update. In Phytoplasmas: Plant Pathogenic Bacteria-I, in Characterization and Epidemiology of Phytoplasma-Associated diseases G. P. Rao, A. Bertaccini, N. Fiore & L. Liefting (Eds.). Springer. [CrossRef]
• Dickinson, M., & Hodgetts, J. (2013). PCR Analysis of phytoplasmas based on the SecA Gene. In Phytoplasma: Methods and protocols. (pp. 205–215). Humana Press. [CrossRef]
• Doi, Y., Teranaka, M., Yora, K., & Asuyama, H. (1967). Mycoplasma or PLT grouplike microorganisms found in the phloem elements of plants infected with mulberry dwarf, potato witches’ broom, aster yellows or Pawlownia Witches’ Broom. Japanese Journal of Phytopathology, 33(4), 259–266. [CrossRef]
• Doyle, J. J., & Doyle, J. L. (1990). Isolation of plant DNA from fresh tissue. Focus, 12, 13–15. [CrossRef]
• Duduk, B., & Bertaccini, A. (2011). Phytoplasma classification: Taxonomy based on 16S ribosomal gene, is it enough? Phytopathogenic Mollicutes, 1(1), 3–13. [CrossRef]
• Eswari, M. L., Bharathi, R. V., & Jayshree, N. (2014). Pharmacognostical and physico-chemical standardization on the leaves of Ziziphus oenoplia. International Journal of Green Pharmacy, 8(4), 424. [CrossRef]
• Galtier, N., Gouy, M., & Gautier, C. (1996). SEA-VIEW and PHYLO WIN: Two graphic tools for sequence alignment and molecular phylogeny. Computer Applications in the Biosciences: CABIOS, 12(6), 543–548. [CrossRef]
• Gundersen, D. E., & Lee, I. M. (1996). Ultrasensitive detection of phytoplasmas by nested-PCR assays using two universal primer pairs. Phytopathologia Mediterranea, 35, 114–151.
• Hall, T. A. (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids, 41, 95–98.
• Jamadar, M. M., Balikai, R. A., & Sataraddi, A. R. (2009). Status of diseases on ber (Ziziphus mauritiana L.) in India and their management options. Acta Horticulturae, (840), 383–390. [CrossRef]
• Jung, H. Y., Sawayanagi, T., Kakizawa, S., Nishigawa, H., Wei, W., Oshima, K., Miyata, S. I., Ugaki, M., Hibi, T., & Namba, S. (2003). 'Candidatus phytoplasma ziziphi’, a novel phytoplasma taxon associated with jujube witches’-broom disease. International Journal of Systematic and Evolutionary Microbiology, 53(4), 1037–1041. [CrossRef]
• Khan, M. S., Raj, S. K., & Snehi, S. K. (2008). Natural occurrence of ‘Candidatus Phytoplasma ziziphi’ isolates in two species of jujube trees (Ziziphus spp.) in India. Plant Pathology, 57(6), 1173. [CrossRef]
• Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7), 1870–1874. [CrossRef]
• Kuvar, S. D., & Bapat, U. C. (2010). Medicinal plants used by Kokani tribals of Nasik district Maharashtra to cure cuts and wounds. Indian Journal of Traditional Knowledge, 9(1), 114–115.
• Lee, I. M., Bottner-Parker, K. D., Zhao, Y., Bertaccini, A., & Davis, R. E. (2012). Differentiation and classification of phytoplasmas in the pigeon pea witches’ broom group (16SrIX): An update based on multiple gene sequence analysis. International Journal of Systematic and Evolutionary Microbiology, 62(9), 2279–2285. [CrossRef]
• Lee, I. M., Davis, R. E., & Gundersen-Rindal, D. E. (2000). Phytoplasma: Phytopathogenic Mollicutes. Annual Review of Microbiology, 54, 221–255. [CrossRef]
• Lee, I.-M., Gundersen, D. E., Hammond, R. W., & Davis, R. E. (1994). Use of Mycoplasmalike Organism (MLO) group-specific oligonucleotide primers for nested-PCR assays to detect mixed-MLO infections in a single host plant. Phytopathology, 84(6), 559–566. [CrossRef]
• Lee, I.-M., Gundersen-rindal, D. E., Davis, R. E., & Bartoszyk, I. M. (1998). Revised classification scheme of phytoplasmas based on RFLP analysis of 16S rRNA and ribosomal protein gene sequences. International Journal of Systematic Bacteriology, 48(4), 1153–1169. [CrossRef]
• Lorenz, K.-H., Schneider, B., Ahrens, U., & Seemuller, E. (1995). Detection of the apple proliferation and pear decline phytoplasmas by PCR amplification of ribosomal and nonribosomal DNA. Phytopathology, 85(7), 771–776. [CrossRef]
• Makarova, O., Contaldo, N., Paltrinieri, S., Bertaccini, A., Nyskjold, H., & Nicolaisen, M. (2013). DNA bar-coding for Phytoplasma identification. Methods in Molecular Biology, 938, 301–317. [CrossRef]
• Manimekalai, R., Nair, S., Soumya, V. P., Roshna, O. M., & Thomas, G. V. (2011). Real-time PCR technique-based detection of coconut root (wilt) Phytoplasma. Current Science, 101, 1209–1213.
• Marcone, C., Lee, I. M., Davis, R. E., Ragozzino, A., & Seemüller, E. (2000). Classification of aster yellows-group phytoplasmas based on combined analyses of ribosomal RNA and tuf gene sequences. International Journal of Systematic and Evolutionary Microbiology, 50(5), 1703–1713. [CrossRef]
• Misra, D. K., Saha, J., Devidas, P. V., & Bauri, F. K. (2013). Diseases of ber (Zizyphus jujube) in Eastern India. Journal of Plant Protection Sciences, 5(1), 65–69.
• Ohashi, A., Nohira, T., Yamaguchi, K., Kusunoki, M., & Shiomi, T. (1996). Jujube (Zizyphus jujuba) witches broom caused by Phytoplasma in Gifu Prefecture. Transactions of the Japan Society for Computational Engineering and Science, 107, 309–310.
• Omar, A. F. (2017). Detection and molecular characterization of phytoplasmas associated with vegetable and alfalfa crops in Qassim region. Journal of Plant Interactions, 12(1), 58–66 . [CrossRef]
• Omar, A. F., & Foissac, X. (2012). Occurrence and incidence of phytoplasmas of the 16SrII-D subgroup on solanaceous and cucurbit crop in Egypt. European Journal of Plant Pathology, 133(2), 353–360. [CrossRef]
• Pandey, P. K., Singh, A. B., Nimbalkar, M. R., & Marathe, T. S. (1976). A witches broom diseases of jujube from India. Plant Disease Reporter, 60(4), 301–330.
• Rao, G. P., Madhupriya, V., Thorat, V., Manimekalai, R., Tiwari, A. K., & Yadav, A. (2017). A century progress of research on Phytoplasma diseases in India. Phytopathogenic Mollicutes, 7(1), 1–38. [CrossRef]
• Sambrook, J., & Russell, D. W. (2001). Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory Press.
• Suksamrarn, S., Suwannapoch, N., Aunchai, N., Kuno, M., Ratananukul, P., Haritakun, R., Jansakul, C., & Ruchirawat, S. (2005). Ziziphine N, O, P and Q, new antiplasmodial cyclopeptide alkaloids from Ziziphus oenoplia var brunoniana. Tetrahedron, 61(5), 1175–1180. [CrossRef]
• Venkataravanappa, V., Reddy, C. N. L., Swarnalatha, P., Shankarappa, K. S., & Krishna Reddy, M. (2017). Detection and characterization of ‘Candidatus Phytoplasma asteris’ associated with little leaf disease of bitter gourd from India by 16S rRNA phylogenetic and RFLP (in vitro and virtual) analysis. Archives of Biological Sciences, 4, 707–714. [CrossRef]
• Venkataravanappa, V., Swarnalatha, P., Saha, S., Lakshminarayana Reddy, C. N. L., & Krishna Reddy, M. (2019). Detection, characterization and in-silico analysis of ‘Candidatus Phytoplasma australasiae’ associated with big bud disease of tomato in India. Proceedings of the National Academy of Sciences, India Section B, 89(2), 493–503. [CrossRef]
• Wang, J., Song, L., Jiao, Q., Yang, S., Gao, R., Lu, X., & Zhou, G. (2018). Comparative genome analysis of jujube witches'-broom Phytoplasma, an obligate pathogen that causes jujube witches'-broom disease. BMC Genomics, 19(1), 689. [CrossRef]
• Wei, W., Davis, R. E., Lee, I. M., & Zhao, Y. (2007). Computer simulated RFLP analysis of 16S rRNA genes: Identification of ten new Phytoplasma groups. International Journal of Systematic and Evolutionary Microbiology, 57(8), 1855–1867. [CrossRef]
• Weintraub, P. G., & Beanland, L. (2006). Insect vectors of phytoplasmas. Annual Review of Entomology, 51, 91–111. [CrossRef]
• Win, N. K. K., Lee, S. Y., Bertaccini, A., Namba, S., & Jung, H. Y. (2013). ‘Candidatus Phytoplasma balanitae’ associated with witches broom disease of Balanites triflora. International Journal of Systematic and Evolutionary Microbiology, 63, 636–640. [CrossRef]
• Yuan, G. Q., Li, Q. Q., Wei, J. G., & Lai, C. Y. (2009). Identification of the pathogens of different diseases of Yunnan jujube Zizyphus mauritiana. South China Fruits, 3, 57–59.
• Zhao, Y., Wei, W., Lee, I. 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(10), 2582–2593. [CrossRef]