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Detection, Characterization and In-Silico Analysis of Candidatus Phytoplasma australasiae Associated with Big Bud Disease of Tomato in India

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Proceedings of the National Academy of Sciences, India Section B: Biological Sciences Aims and scope Submit manuscript

Abstract

Tomato plants showing witches broom symptoms were collected from different states of India. The presence of phytoplasma infection was confirmed by PCR using phytoplasma-specific primer of 16S rRNA and SecY gene. The sequence analysis of 16S rRNA and SecY gene of eight tomato big bud phytoplasmas showed maximum nucleotide (nt) identity of 95–100% with Peanut WB group (16SrII). Further in-silico RFLP analysis of 16S rRNA gene of TBB-Pun1, TBB-Ban, TBB-mal, TBB-Guj and TBB-Vns showed similarity coefficient of 0.68–0.95. Since threshold similarity coefficient for classifying the phytoplasma into new subgroup is set at 0.97, the strain under study significantly distinct from the representative strains in the subgroups of pea nut witches broom. Further, the phylogenetic analysis of tomato big bud phytoplasmas revealed that, they are closely clustered with peanut witches’-broom strains (16Sr II), specifically within the 16Sr II-D and 16Sr II-A subgroups. A comprehensive recombination analysis showed the evidence of both intra and inter-species recombination in seven tomato big bud isolates with most part of their 16Sr RNA F2nR2 fragments descending from Ca.P.brasiliense (16Sr XV) as major parent, except isolate TBB-Vns which had an intra species recombination with Cactus witches-broom-16Sr II-L as major parent. Similarly, in case of SecY gene, all the seven isolates have intra-species recombination with major portion descending from Vinca virescence-[16Sr VI-A] and Potato purple top wilt-[16Sr XVIII-B]. The genetic similarities and the potential threat of this new phytoplasma belonging to 16Sr II group of Peanut witches’ broom’ group infecting tomato in India are discussed.

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References

  1. Singh J, Rani A, Kumar P, Baranwal VK, Saroj PL, Sirohi A (2012) First report of a 16SrII-D phytoplasma ‘Candidatus Phytoplasma australasia’ associated with a tomato disease in India. New Dis Rep 26:14

    Article  Google Scholar 

  2. Omar AF, Foissac X (2012) Occurrence and incidence of phytoplasmas of the 16SrII-D subgroup on solanaceous and cucurbit crops in Egypt. Eur J Plant Pathol 133:353–360

    Article  CAS  Google Scholar 

  3. Zamora L, Acosta K, Pinol B, Quinones M, Bertaccini A (2014) First report of ‘Candidatus Phytoplasma asteris’ (16SrI group) causing stunt of tomato in Cuba. New Dis Rep 30:10

    Article  Google Scholar 

  4. Arayamanesh N, Al- Subhi AM, Snoball R, Yan G, Siddique KHM (2011) Fairst report of bituminaria witches broom in australia caused by a 16SrII phytoplasmas. Plant Dis 956(2):226

    Article  Google Scholar 

  5. Hernandez-perez R, Noa-Carrazana JC, Gaspar R, Mata P, Flores-Estevez N (2009) Detection of phytoplasma on Indian Fig (Opuntia ficus-indics Mill) in Mexico central region. J Biol Sci 9(3):62–66

    CAS  Google Scholar 

  6. Harling R, Arocha Y, Harju V, Tobing C, Boa E, Kelly P, Peeder R (2009) First report of 16SrII Candidatus phytoplasma aurantifolia infecting chilli and tamarillo in Indonesia. New Dis Rep 19:3

    Google Scholar 

  7. Deng SJ, Hiruki C (1991) Amplification of 16S ribosomal-RNA genes from culturable and nonculturable mollicutes. J Microbiol Methods 14:53–61

    Article  CAS  Google Scholar 

  8. Lee LM, Hammond RW, Davis RE, Gundersen DE (1993) Universal amplification and analysis of pathogen 16SrDNA for classification and identification of mycoplasma like organisms. Phytopathology 83:834–842

    Article  CAS  Google Scholar 

  9. Gundersen DE, Lee IM (1996) Ultrasensitive detection of phytoplasmas by nested-PCR assays using two universal primer pairs. Phytopathol Mediterr 35:114–151

    Google Scholar 

  10. Wei W, Davis RE, Lee IM, Zhao Y (2007) Computer simulated RFLP analysis of 16SrRNA genes: identification of ten new phytoplasma groups. Int J Syst Evol Microbiol 57:1855–1867

    Article  CAS  PubMed  Google Scholar 

  11. White DT, Blackall LL, Scott PT, Walsh KB (1998) Phylogenetic positions of phytoplasmas associated with dieback, yellow crinkle and mosaic diseases of papaya, and their proposed inclusion in ‘Candidatus Phytoplasma australiense’ and a new taxon’, Candidatus Phytoplasma australasia. Int J Syst Bacteriol 48:941–951

    Article  CAS  PubMed  Google Scholar 

  12. Amaral-Mello APO, Bedendo IP, Camargo LEA (2006) Sequence heterogeneity in the 16S rDNA of tomato big bud phytoplasma belonging to group 16SrIII. J Phytopathol 154:245–249

    Article  Google Scholar 

  13. Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15

    Google Scholar 

  14. Smart CD, Schneider B, Blomquist CL, Guerra LJ, Harrison NA, Ahrens U (1996) Phytoplasma specific PCR primers based on sequences of 16S-23SrRNA spacer region. Appl Environ Microbiol 62:2988–2993

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Lee IM, Bottner-Parker KD, Zhao Y, Davis RE, Harrison NA (2010) Phylogenetic analysis and delineation of phytoplasmas based on secY gene sequences. Int J Syst Evol Microbiol 60:2887–2897

    Article  PubMed  Google Scholar 

  16. Venkataravanappa V, Reddy CNL, Swarnalatha P, Shankarappa KS, Krishna Reddy M (2017) Detection and characterization of ‘Candidatus Phytoplasma asteris’ associated with little leaf disease of bitter gourd from India by 16SrRNA phylogenetic and RFLP (in vitro and virtual) analysis. Arch Biol Sci 69(4):707–714

    Article  Google Scholar 

  17. Zhao Y, Wei W, Lee IM, Shao J, Suo X, Davis RE (2009) Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII). Int J Syst Evol Microbiol 59:2582–2593

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Galtier N, Gouy M, Gautier C (1996) SEA VIEW and PHYLO WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12:543–548

    CAS  PubMed  Google Scholar 

  19. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Article  CAS  Google Scholar 

  20. Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23:254–267

    Article  CAS  PubMed  Google Scholar 

  21. Martin DP, Murrell B, Golden M, Khoosal A, Muhire B (2015) RDP4: detection and analysis of recombination patterns in virus genomes. Virus Evol 1:vev003. https://doi.org/10.1093/ve/vev003

    Article  PubMed  PubMed Central  Google Scholar 

  22. Bertaccini A, Duduk B (2009) Phytoplasma and phytoplasma diseases: a review of recent research. Phytopathol Mediterr 48:355–378

    CAS  Google Scholar 

  23. IRPCM (2004) ‘Candidatus Phytoplasma’, a taxon for the wallless, non-helical prokaryotes that colonise plant phloem and insects. Int J Syst Evol Microbiol 54:1243–1255

    Article  CAS  Google Scholar 

  24. Lee IM, Gundersen-Rindal DE, Davis RE, Bartoszyk IM (1998) Revised classification scheme of phytoplasmas based on RFLP analysis of 16SrRNA and ribosomal protein gene sequences. Int J Syst Bacteriol 48:1153–1169

    Article  CAS  Google Scholar 

  25. Davis RI, Schneider B, Gibb K (1997) Detection and differentiation of phytoplasmas in Australia. Aust J Agric Res 48:535–544

    Article  Google Scholar 

  26. Choueiri E, Salar P, Jreijiri F, El-Zammar S, Massaad R, Abdul-Nour H (2007) Occurrence and distribution of Candidatus Phytoplasma trifoli associated with diseases of solanaceous crops in Lebanon. Eur J Plant Pathol 118:411–416

    Article  CAS  Google Scholar 

  27. Wei W, Lee IM, Davis RE, Suo X, Zhao Y (2008) Automated RFLP pattern comparison and similarity coefficient calculation for rapid delineation of new and distinct phytoplasma 16Sr subgroup lineages. Int J Syst Evol Microbiol 58:2368–2377

    Article  CAS  PubMed  Google Scholar 

  28. Nishigawa H, Oshima K, Kakizawa S, Jung H, Kuboyama T, Miyata S, Ugaki M, Namba S (2002) Evidence of intermolecular recombination between extra-chromosomal DNAs in phytoplasma: a trigger for the biological diversity of phytoplasma. Microbiology 148:1389–1396

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

The research was supported by the project “Consortium platform on Vaccines and diagnostics” funded by Indian Council of Agricultural Research (Grant No. F.No.AS/2/8/2016-ASR-IV), Government of India, New Delhi, India.

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Authors and Affiliations

  1. Division of Plant Pathology, Central Horticultural Experimental Station, Regional Station of IIHR, ICAR-Indian Institute of Horticultural Research, Chettalli, Kodagu, Karnataka, 571248, India

    V. Venkataravanappa

  2. Division of Plant Pathology, National Research Centre for Grapes, Pune, Maharashtra, 412307, India

    V. Venkataravanappa & Sujoy Saha

  3. Division of Plant Pathology, Plant Virology Laboratory, Indian Institute of Horticultural Research (IIHR), Hessaraghatta Lake PO, Bangalore, 560089, India

    P. Swarnalatha & M. Krishna Reddy

  4. Department of Plant Pathology, College of Sericulture, University of Agricultural Sciences (Bangalore), Chintamani, Karnataka, 563125, India

    C. N. Lakshminarayana Reddy

Authors
  1. V. Venkataravanappa
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  2. P. Swarnalatha
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  3. Sujoy Saha
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  4. C. N. Lakshminarayana Reddy
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  5. M. Krishna Reddy
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Correspondence to V. Venkataravanappa or M. Krishna Reddy.

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Significance statement

The phytoplasma associated with tomato big bud disease was characterized by Electron microscopy, PCR, in silico RFLP and recombination analysis showed that five new subgroup and three already existing tomato big bud phytoplasma were identified, which gives a good alarm signal to breed resistance varieties against big bud phytoplasma in India.

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Venkataravanappa, V., Swarnalatha, P., Saha, S. et al. Detection, Characterization and In-Silico Analysis of Candidatus Phytoplasma australasiae Associated with Big Bud Disease of Tomato in India. Proc. Natl. Acad. Sci., India, Sect. B Biol. Sci. 89, 493–503 (2019). https://doi.org/10.1007/s40011-017-0960-y

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  • DOI: https://doi.org/10.1007/s40011-017-0960-y

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