Archives of Virology

, Volume 152, Issue 2, pp 405–413 | Cite as

Coat protein gene diversity among Chrysanthemum virus B isolates from India

  • L. Singh
  • V. Hallan
  • N. Jabeen
  • A. K. Singh
  • R. Ram
  • D. P. Martin
  • A. A. Zaidi
Brief Report


The complete coat protein (CP) sequences from 29 Indian isolates of Chrysanthemum virus B (CVB) were determined and analysed in relation to other previously characterized carlaviruses. The CP genes of the Indian CVB isolates were highly heterogeneous, sharing nucleotide sequence identities of 74–98%. Based on phylogenetic analyses, the isolates formed three groups potentially representing either two or three major CVB strain groupings. Recombination analysis revealed at least one definite recombination event involving the exchange of sequences between members of different groups. To our knowledge this is the first reported evidence of homologous recombination in carlaviruses.


Coat Protein Coat Protein Gene Coat Protein Sequence Tomato Spot Wilt Virus Turnip Mosaic Virus 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Alegria, OM, Royer, M, Bousalem, M, Chatenet, M, Peterschmitt, M, Girard, JC, Rott, P 2003Genetic diversity in the coat protein region of sugarcane mosaic virus isolates from eight countries, particularly from Cameroon and CongoArch Virol148357372PubMedCrossRefGoogle Scholar
  2. Altschul, SF, Gish, W, Miller, W, Myers, EW, Lipman, DJ 1990Basic local alignment search toolJ Mol Biol215403410PubMedCrossRefGoogle Scholar
  3. Bananej, K, Kheyr-Pour, A, Hosseini-Salekdeh, G, Ahoonmanesh, G 2004Complete nucleotide sequence of Iranian isolate of Tomato yellow leaf curl virus: further evidence for natural recombination among geminivirusesArch Virol14914351443PubMedCrossRefGoogle Scholar
  4. Chare, ER, Holmes, EC 2006A phylogenetic survey of recombination frequency in plant RNA virusesArch Virol151933946PubMedCrossRefGoogle Scholar
  5. Chenna, R, Sugawara, H, Koike, T, Lopez, R, Gibson, TJ, Higgins, DG, Thompson, JD 2003Multiple sequence alignment with the Clustal series of programsNucleic Acids Res3134973500PubMedCrossRefGoogle Scholar
  6. Choi, SA, Ryu, KH 2003The complete nucleotide sequence of the genome RNA of Lily symptomless virus and its comparison with that of other carlavirusesArch Virol14819431955PubMedCrossRefGoogle Scholar
  7. Felsenstein, J 1989PHYLIP – Phylogeny inference package (version 3.2)Cladistics5164166Google Scholar
  8. Froissart, R, Roze, D, Uzest, M, Galibert, L, Blanc, S, Michalakis, Y 2005Recombination every day: abundant recombination in a virus during a single multi-cellular host infectionPloS Biol3e89PubMedCrossRefGoogle Scholar
  9. Gibbs, MJ, Armstrong, JS, Gibbs, AJ 2000Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequencesBioinformatics16573582PubMedCrossRefGoogle Scholar
  10. Guindon, S, Gascuel, O 2003A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihoodSyst Biol52696704PubMedCrossRefGoogle Scholar
  11. Haselhof, I, Symons, RH 1981Chrysanthemum stunt viroid: primary sequence and secondary structureNucleic Acids Res927412752CrossRefGoogle Scholar
  12. Koenig R (1982) Carlavirus group. CMI/AAB Description of plant viruses no. 259Google Scholar
  13. Levay, KE, Zavriev, SK 1991Nucleotide sequence and gene organisation of the 3′-terminal region of Chrysanthemum virus B genomic RNAJ Gen Virol7223332337PubMedCrossRefGoogle Scholar
  14. Martelik, J, Mokra, V 1998Tomato spotted wilt virus in ornamental plants, vegetables and weeds in the Czech RepublicActa Virol42347351Google Scholar
  15. Martin, DP, Posada, D, Crandall, KA, Williamson, C 2005A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpointsAIDS Res Hum Retrovir2198102PubMedCrossRefGoogle Scholar
  16. Martin, DP, Rybicki, E 2000RDP: detection of recombination amongst aligned sequencesBioinformatics16562563PubMedCrossRefGoogle Scholar
  17. Martin, DP, Williamson, C, Posada, D 2005RDP2: Recombination detection and analysis from sequence alignmentsBioinformatics21260262PubMedCrossRefGoogle Scholar
  18. Maynard Smith, J 1992Analysing the mosaic structure of genesJ Mol Evol34126129Google Scholar
  19. Navas-Castillo, J, Sanchez-Camposs, S, Noris, E, Louro, D, Accotto, GP, Moriones, E 2000Natural recombination between Tomato yellow leaf curl virus-Is and Tomato leaf curl virusJ Gen Virol8127972801PubMedGoogle Scholar
  20. O’Reilly, D, Thomas, CJ, Coutts, RHA 1991Tomato aspermy virus has an evolutionary relationship with other tripartite RNA virusesJ Gen Virol7217PubMedGoogle Scholar
  21. Ohshima, K, Yamaguchi, Y, Hirota, R, Hamamoto, T, Tomimura, K, Tan, Z, Sano, T, Azuhata, F, Walsh, JA, Fletcher, J, Chen, J, Gera, A, Gibbs, A 2002Molecular evolution of Turnip mosaic virus: evidence of host adaptation, genetic recombination and geographical spreadJ Gen Virol8315111521PubMedGoogle Scholar
  22. Padidam, M, Sawyer, S, Fauquet, C 1999Possible emergence of new geminiviruses by frequent recombinationVirology265218225PubMedCrossRefGoogle Scholar
  23. Raizada, RK, Srivastava, KM, Chandra, G, Singh, BP 1989Comparative evaluation of sero-diagnostic methods for detection of Chrysanthemum virus B in chrysanthemumIndian J Exp Biol2710941096Google Scholar
  24. Romaine, CP, Horst, RK 1975Suggested viroid etiology of Chrysanthemum chlorotic mottle diseaseVirology648695PubMedCrossRefGoogle Scholar
  25. Roossinck, MJ 1997Mechanisms of plant virus evolutionAnnu Rev Phytopathol35191209PubMedCrossRefGoogle Scholar
  26. Rubio, L, Ayllon, MA, Kong, P, Fernandez, A, Polek, M, Guerri, J, Moreno, P, Falk, BW 2001Genetic variation of Citrus tristeza virus isolates from California and Spain: evidence for mixed infections and recombinationJ Virol7580548062PubMedCrossRefGoogle Scholar
  27. Simon, AE, Bujarski, JJ 1994RNA-RNA recombination and evolution in virus-infected plantsAnnu Rev Phytopathol29337361CrossRefGoogle Scholar
  28. Singh HP (2000) Current status of floriculture – national and international scenario. In: Singh HP, Dadlani NK (eds) Commercial floriculture. FAO and DAC, Ministry of Agriculture, Govt. of India, New Delhi, pp 1–26Google Scholar
  29. Smith, GR, Borg, Z, Lockhart, BEL, Braithwaite, KS, Gibbs, MJ 2000Sugarcane yellow leaf virus: a novel member of the Luteoviridae that probably arose by inter-species recombinationJ Gen Virol8118651869PubMedGoogle Scholar
  30. Strauss, JH, Strauss, EG 1988Evolution of RNA virusesAnnu Rev Microbiol42657683PubMedCrossRefGoogle Scholar
  31. Tan, Z, Wada, Y, Chen, J, Ohshima, K 2004Inter- and intralineage recombinants are common in natural populations of Turnip mosaic virus J Gen Virol8526832696PubMedCrossRefGoogle Scholar
  32. Verhoeven, JTJ, Roenhorst, JW, Cortes, I, Peters, D 1996Detection of a novel tospovirus in chrysanthemumActa Hort4324451Google Scholar
  33. Verma, N, Sharma, A, Ram, R, Hallan, V, Zaidi, AA, Garg, ID 2003Detection, identification and incidence of Chrysanthemum B carlavirus in chrysanthemum in IndiaCrop Prot22425429CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • L. Singh
    • 1
  • V. Hallan
    • 1
  • N. Jabeen
    • 1
  • A. K. Singh
    • 1
  • R. Ram
    • 1
  • D. P. Martin
    • 2
  • A. A. Zaidi
    • 1
  1. 1.Plant Virus Laboratory, Institute of Himalayan Bioresource TechnologyPalampurIndia
  2. 2.Institute of Infectious Diseases and Molecular MedicineUniversity of Cape TownCape TownSouth Africa

Personalised recommendations