Indian Journal of Virology

, 22:117 | Cite as

Biological and Molecular Characterization of Two Distinct Tomato Strains of Cucumber mosaic virus Based on Complete RNA-3 Genome and Subgroup Specific Diagnosis

  • A. Swapna Geetanjali
  • Rakesh Kumar
  • P. S. Srivastava
  • Bikash Mandal
Original Article

Abstract

Cucumber mosaic virus (CMV) is one of the most important viral pathogen infecting several plant species in India. Five isolates of CMV obtained from cucumber, muskmelon, tobacco and tomato from distinct geographical locations in India were analysed based on host-reactions and genome sequence. The majority of the isolates were very similar and only two isolates, Tfr-In and Tss-In showed distinct symptoms in tomato and high sequence diversity (77.8%) in coat protein (CP) gene. Tfr-In was isolated from tomato fruit showing grey patches in Aurangabad and Tss-In from tomato plant showing shoe-string symptoms in New Delhi. The RNA-3 genomes of Tfr-In (2,214 nt; JF279606), shared only 70.3% nucleotide sequence identity with Tss-In (2,178 nt; JF279605. The complete RNA-3 genome of Tss-In and Tfr-In were compared with that of 65 CMV isolates reported from various plants of the world, which formed four distinct subclades-IA, -IB, -IC and -II. The Tfr-In isolate clustered with the CMV subgroup-IB and Tss-In with the subgroup-II. The comparison of the RNA-3 sequence of both the isolates revealed maximum heterogeneity in the intergenic region (IR). Reverse transcriptase polymerase chain reaction (RT-PCR) based detection of CMV subgroup-I and -II was developed designing primers from flanking IR region. The specificity of the RT-PCR detection was confirmed using Tfr-In and Tss-In representing subgroup-I and -II and validated with field samples of tomato, cucurbits and chilli. This is the first report of complete RNA-3 of subgroup-IB CMV causing grey patches in tomato fruit and subgroup-II CMV causing shoe-string symptoms in tomato in India. The present and previous studies together showed that tomato in India was affected by multiple strains of CMV.

Keywords

Cucumber mosaic virus Tomato CMV subgroups Shoe-string Grey-patch RT-PCR RNA-3 genome 

References

  1. 1.
    Aglave BA, Krishnareddy M, Patil FS, Andhale MS. Molecular identification of a virus causing banana chlorosis disease from Marathwada region. Int J Biotechnol Biochem. 2007;3:13–23.Google Scholar
  2. 2.
    Akhtar KP, Ryu KH, Saleem MY, Asghar M, Jamil FF, Haq MA. Occurrence of Cucumber mosaic virus subgroup IA in tomato in Pakistan. J Plant Dis Prot. 2008;115:2–3.Google Scholar
  3. 3.
    Aramburu J, Galipienso L, Lopez C. Reappearance of Cucumber mosaic virus isolates belonging to subgroup IB in tomato plants in North-eastern Spain. J Phytopathol. 2007;155:513–8.CrossRefGoogle Scholar
  4. 4.
    Bhargava KS. Some properties of four strains of Cucumber mosaic virus. Ann Appl Biol. 1951;38:377–88.CrossRefGoogle Scholar
  5. 5.
    Bhat AI, Hareesh PS, Madhubala R. Sequencing of coat protein gene of an isolate of Cucumber mosaic virus infecting black pepper (Piper nigrum L.) in India. J Plant Biochem Biotechnol. 2005;14:37–40.Google Scholar
  6. 6.
    Ding SW, Anderson BJ, Haase HR, Symons RH. New overlapping gene encoded by the cucumber mosaic virus genome. Virology. 1994;198:593–601.PubMedCrossRefGoogle Scholar
  7. 7.
    Dodds JA, Morris TJ, Jordan RL. Plant viral double-stranded RNA. Annu Rev Phytopathol. 1984;22:151–68.CrossRefGoogle Scholar
  8. 8.
    Eck RV, Dayhoff MO. Atlas of protein sequence and structure. Silver Springs: National Biomedical Research Foundation; 1966.Google Scholar
  9. 9.
    Kosaka Y, Hanada K, Fukunishi T, Tochihara H. Cucumber mosaic virus isolate causing tomato necrotic disease in Kyoto prefecture. Ann Phytopathol Soc Jpn. 1989;55:229–32.CrossRefGoogle Scholar
  10. 10.
    Madhubala R, Bhadramurthy V, Bhat AI, Hareesh PS, Retheesh ST, Bhai RS. Occurrence of Cucumber mosaic virus on vanilla (Vanilla planifolia Andrews) in India. J Biosci. 2005;30:339–50.PubMedCrossRefGoogle Scholar
  11. 11.
    Nei M, Kumar S. Molecular evolution and phylogenetics. New York: Oxford University Press; 2000. pp. 352.Google Scholar
  12. 12.
    Palukaitis P, Zaitlin M. Replicase-mediated resistance to plant virus disease. Adv Virus Res. 1997;48:349–77.PubMedCrossRefGoogle Scholar
  13. 13.
    Palukaitis P, Roossinck MJ, Dietzgen RG, Francki RIB. Cucumber mosaic virus. Adv Virus Res. 1992;41:281–348.PubMedCrossRefGoogle Scholar
  14. 14.
    Pratap D, Kumar S, Raj SK. First molecular identification of a Cucumber mosaic virus isolate causing shoestring symptoms on tomato in India. Aust Plant Dis Notes. 2008;3:57–58.CrossRefGoogle Scholar
  15. 15.
    Raj SK, Srivastava A, Chandra G, Singh BP. Characterisation of Cucumber mosaic virus isolate infecting Gladiolus cultivars and comparative analysis of serological and molecular methods for sensitive diagnosis. Curr Sci. 2002;83:1132–6.Google Scholar
  16. 16.
    Raj SK, Kumar S, Pratap D, Vishnoi R, Snehi SK. Natural Occurrence of Cucumber mosaic virus on Rauvolfia serpentina, a new record. Plant Dis. 2007;91:322.CrossRefGoogle Scholar
  17. 17.
    Raj SK, Kumar S, Snehi SK. First Report of Cucumber mosaic virus on Jatropha curcas in India. Plant Dis. 2008;92:171.CrossRefGoogle Scholar
  18. 18.
    Rizos H, Gunn LV, Pares RD, Gillings RM. Differentiation of Cucumber mosaic virus isolates using the polymerase chain reaction. J Gen Virol. 1992;73:2099–103.PubMedCrossRefGoogle Scholar
  19. 19.
    Roossinck MJ. Cucumber mosaic virus, a model for RNA virus evolution. Mol Plant Pathol. 2001;2:59–63.PubMedCrossRefGoogle Scholar
  20. 20.
    Roossinck MJ, Zhang L, Hellwald KH. Rearrangements in the 5′ nontranslated region and phylogenetic analyses of Cucumber mosaic virus RNA 3 indicate radial evolution of three subgroups. J Virol. 1999;73:6752–8.PubMedGoogle Scholar
  21. 21.
    Roossinck MJ, Bujarski J, Ding SW, Hajimorad R, Hanada K, Scott S, Tousignant M. Bromoviridae. In: van Regenmortel MHV, Fauquet CM, Bishop DHL, Carstens EB, Estes MK, Lemon SM, Maniloff J, Mayo MA, McGeoch DJ, Pringle CR, Wickner RB, editors. Virus taxonomy: classification and nomenclature of viruses. Seventh Report of the International Committee on the Taxonomy of Viruses. San Diego: Academic Press; 2000. p. 923–35.Google Scholar
  22. 22.
    Salamon P, Gajdos L, Balogh P, Solymoss E, Varro P, Milotay P, Kiss L, Salanki K. Isolation of a virulent strain of Cucumber mosaic virus from tomato (Lycopersicon esculentum Mill.) affected by fruit necrosis. Kertgazdasag Hortic. 2005;(special):155–61.Google Scholar
  23. 23.
    Samad A, Raj SK, Srivastava A, Chandra G, Ajayakumar PV, Zaim M, Singh BP. Characterization of a Cucumber mosaic virus isolates infecting Egyptian henbane (Hyoscyamus muticus L.) in India. Acta Virol. 2000;44:131–6.PubMedGoogle Scholar
  24. 24.
    Sambrook J, Russell DW. Molecular cloning, a laboratory manual. 3rd ed. Cold Spring Harbor: Cold Spring Harbor Laboratory Press; 2001.Google Scholar
  25. 25.
    Sharma A, Mahinghara BK, Singh AK, Kulshrestha S, Raikhy G, Singh L, Verma N, Ram R, Zaidi AA. Identification, detection and frequency of Lily viruses in northern India. Sci Hortic. 2005;106:213–27.CrossRefGoogle Scholar
  26. 26.
    Singh Z, Jones RA, Jones MGK. Identification of Cucumber mosaic virus subgroup I isolates from banana plants affected by infectious chlorosis disease using RT-PCR. Plant Dis. 1995;79:716–31.Google Scholar
  27. 27.
    Srivastava A, Raj SK. High molecular similarity among Indian isolates of Cucumber mosaic virus suggests a common origin. Curr Sci. 2004;87:1126–31.Google Scholar
  28. 28.
    Srivastava A, Chandra G, Raj SK. Coat protein and movement protein gene based molecular characterization of Amaranthus strain of Cucumber mosaic virus. Acta Virol. 2004;48:229–39.PubMedGoogle Scholar
  29. 29.
    Sudhakar N, Prasad DN, Mohan N, Murugesan K. First report of Cucumber mosaic virus subgroup II infecting Lycopersicon esculentum in India. Plant Dis. 2006;90:1457. doi:10.1094/PD-90-1457B.CrossRefGoogle Scholar
  30. 30.
    Sulistyowati E, Mitter N, Bastiaan-Net S, Roossinck MJ, Dietzgen RG. Host range, symptom expression and RNA 3 sequence analyses of six Australian strains of Cucumber mosaic virus. Aust Plant Pathol. 2004;33:505–12.CrossRefGoogle Scholar
  31. 31.
    Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 2007;24:1596–9.PubMedCrossRefGoogle Scholar
  32. 32.
    Verma N, Mahinghara BK, Ram R, Zaidi AA. Coat protein sequence shows that Cucumber mosaic virus isolate from geraniums (Pelargonium Sp.) belongs to subgroup II. J Biosci. 2006;31:47–56.PubMedCrossRefGoogle Scholar
  33. 33.
    Wahyuni WS, Dietzgen RG, Hanadat K, Francki RB. Serological and biological variation between and within subgroup I and II strains of Cucumber mosaic virus. Plant Pathol. 1992;41:282–97.CrossRefGoogle Scholar
  34. 34.
    Wang HY, Zhang HR, Du ZY, Zeng R, Chen J. Evolutionary characterization of two Cucumber mosaic virus isolates infecting Pinellia ternata of Araceae family. 2009; http://www.paper.edu.cn/index.php/default/en_releasepaper/downPaper/200902-1424.
  35. 35.
    Yu C, Wu J, Zhou X. Detection and sub grouping of Cucumber mosaic virus isolates by TAS-ELISA and immunocapture RT-PCR. J Virol Methods. 2005;123:155–61.PubMedCrossRefGoogle Scholar

Copyright information

© Indian Virological Society 2011

Authors and Affiliations

  • A. Swapna Geetanjali
    • 1
  • Rakesh Kumar
    • 1
  • P. S. Srivastava
    • 2
  • Bikash Mandal
    • 1
  1. 1.Plant Virology Unit, Division of Plant PathologyIndian Agricultural Research InstituteNew DelhiIndia
  2. 2.Department of BiotechnologyJamia Hamdard UniversityNew DelhiIndia

Personalised recommendations