Skip to main content
SpringerLink
Log in

Complete nucleotide sequence of a Spanish isolate of alfalfa mosaic virus: evidence for additional genetic variability

  • Brief Report
  • Published:
Archives of Virology Aims and scope Submit manuscript

Abstract

Alfalfa mosaic virus (AMV) is a plant virus that is distributed worldwide and can induce necrosis and/or yellow mosaic on a large variety of plant species, including commercially important crops. It is the only virus of the genus Alfamovirus in the family Bromoviridae. AMV isolates can be clustered into two genetic groups that correlate with their geographic origin. Here, we report for the first time the complete nucleotide sequence of a Spanish isolate of AMV found infecting Cape honeysuckle (Tecoma capensis) and named Tec-1. The tripartite genome of Tec-1 is composed of 3643 nucleotides (nt) for RNA1, 2594 nt for RNA2 and 2037 nt for RNA3. Comparative sequence analysis of the coat protein gene revealed that the isolate Tec-1 is distantly related to subgroup I of AMV and more closely related to subgroup II, although forming a distinct phylogenetic clade. Therefore, we propose to split subgroup II of AMV into two subgroups, namely IIA, comprising isolates previously included in subgroup II, and IIB, including the novel Spanish isolate Tec-1.

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

References

  1. Bergua M, Luis-Arteaga M, Escriu F (2010) Variabilidad biológica y estructura genetica de poblaciones españolas del virus del mosaico de la alfalfa. In: XV Congreso de la Sociedad Española de Fitopatología. Vitoria, p 125

  2. Bol JF (1999) Alfalfa mosaic virus and ilarviruses: involvement of coat protein in multiple steps of the replication cycle. J Gen Virol 80:1089–1102

    PubMed  CAS  Google Scholar 

  3. Bol JF, van Vloten-Doting L, Jaspars EMJ (1971) A functional equivalence of top component a RNA and coat protein in the initiation of infection by Alfalfa mosaic virus. Virology 46:73–85

    Article  PubMed  CAS  Google Scholar 

  4. Boulila M (2009) Recombination structure and genetic relatedness among members of the family Bromoviridae based on their RNas 1 and 2 sequences analyses. Virus Genes 38:435–444

    Article  PubMed  CAS  Google Scholar 

  5. Brederode FT, Koper-Zwarthoff EC, Bol JF (1980) Complete nucleotide sequence of Alfalfa mosaic virus RNA 4. Nucleic Acids Res 8:2213–2223

    Article  PubMed  CAS  Google Scholar 

  6. Bruen TC, Philippe H, Bryant D (2006) A simple and robust statistical test for detecting the presence of recombination. Genetics 172:2665–2681

    Article  PubMed  CAS  Google Scholar 

  7. Codoner FM, Elena SF (2006) Evolutionary relationships among members of the Bromoviridae deduced from whole proteome analysis. Arch Virol 151:299–307

    Article  PubMed  CAS  Google Scholar 

  8. de Graaff M, Houwing CJ, Lukacs N, Jaspars EM (1995) RNA duplex unwinding activity of Alfalfa mosaic virus RNA-dependent RNA polymerase. FEBS Lett 371:219–222

    Article  PubMed  Google Scholar 

  9. Edwardson JR, Chistie RG (1997) Alfamovirus genus-Alfalfa mosaic virus species. In: Virus infecting peppers and other solanaceous crops. University of Florida, Agricultural Experiment Station, Monograph 18-I, pp 63–94

  10. Erny C, Schoumacher F, Jung C, Gagey M-J, Godeefroy-Colburn T, Stussi-Garaud C, Berna A (1992) An N-proximal sequence of the Alfalfa mosaic virus movement protein is necessary for association with cell walls in transgenic plants. J Gen Virol 73:2115–2119

    Article  PubMed  CAS  Google Scholar 

  11. Gunn MR, Symons RH (1980) Sequence homology at the 3′- termini of the four RNAs of Alfalfa mosaic virus. FEBS Lett 109:145–150

    Article  PubMed  CAS  Google Scholar 

  12. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95–98

    CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  14. Jaspars EMJ (1985) Interaction of alfalfa mosaic virus nucleic acid and protein. In: Davies JW (ed) Molecular plant virology. CRC Press, New York, pp 155–221

    Google Scholar 

  15. Jaspars EM, Bos L (1980) Alfalfa mosaic virus. No. 229. In: Descriptions of plant viruses. Commonwealth Mycology Institute/Association of Applied Biologists, Kew, England

  16. Jeffries CJ (1998) FAO/IPGRI technical guidelines for the safe movement of germplasm: potato no. 19. Food and Agriculture Organization of the United Nations/International Plant Genetic Resources Institute, Rome

  17. Pond SLK, Frost SD, Muse SV (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics 21:676–679

    Article  PubMed  CAS  Google Scholar 

  18. Langereis K, Mugnier M-A, Cornelissen BJC, Pink L, Bol JF (1986) Variable repeats and poly (A)-stretches in the leader sequence of Alfalfa mosaic virus RNA 3. Virology 154:409–414

    Article  PubMed  CAS  Google Scholar 

  19. Lozano G, Moriones E, Navas-Castillo J (2006) Complete sequence of the RNA2 of the crinivirus tomato chlorosis virus. ArchVirol 151:581–587

    CAS  Google Scholar 

  20. Marck C (1988) “DNA Strider”: a “C” programme for the fast analysis of DNA and protein sequences on the Apple Macintosh family computers. Nucleic Acids Res 16:1829–1830

    Article  PubMed  CAS  Google Scholar 

  21. Martin DP, Williamson C, Posada D (2005) RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21:260–262

    Article  PubMed  CAS  Google Scholar 

  22. Maydt J, Lengaurer T (2006) Recco: recombination analysis using cost optimization. Bioinformatics 22:1064–1071

    Article  PubMed  CAS  Google Scholar 

  23. McLaughlin MR (1991) A greenhouse method for aphid inoculation of Alfalfa mosaic virus in white clover by co-culture of virus, vector, and clover. In: Peters DC, Webster JA, Chloubers CS (eds) Aphid plant interaction: populations to molecules. Okla. Agric. Exp. Stn., Stillwater, p 318

  24. Parrella G, Lanave C, Marchoux G, Sialer MM, Di Franco A, Gallitelli D (2000) Evidence for two distinct subgroups of Alfalfa mosaic virus (AMV) from France and Italy and their relationships with other AMV strains. Arch Virol 145:2659–2667

    Article  PubMed  CAS  Google Scholar 

  25. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Biol Mol Evol 24:1596–1599

    Article  CAS  Google Scholar 

  26. Tenllado F, Bol JF (2000) Genetic detection of the multiple functions of Alfalfa mosaic virus coat protein in viral RNA replication, encapsidation, and movement. Virology 268:29–40

    Article  PubMed  CAS  Google Scholar 

  27. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    Article  PubMed  CAS  Google Scholar 

  28. Valkonen JPT, Pehu E, Watanabe K (1992) Symptom expression and seed transmission of Alfalfa mosaic virus, Potato yellowing virus and Potato yellowing virus SB-22 in Solanum brevidens and S. tuberosum. Potato Res 35:403–410

    Article  Google Scholar 

  29. van der Vossen EAG, Neeleman L, Bol JF (1994) Early and late functions of Alfalfa mosaic virus coat protein can be mutated separately. Virology 202:891–903

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

We thank Anna Giulia Nappo for technical assistance. N. A. was supported by a fellowship from the National Research Council (RSTL n. 690). A.F.O. is recipient of a JAE predoctoral fellowship from the CSIC, Spain.

Author information

Authors and Affiliations

  1. Istituto per la Protezione delle Piante, CNR, Via Università 133, 80055, Portici, NA, Italy

    Giuseppe Parrella & Nadia Acanfora

  2. Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29750, Algarrobo-Costa, Málaga, Spain

    Anelise F. Orílio & Jesús Navas-Castillo

Authors
  1. Giuseppe Parrella
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Nadia Acanfora
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Anelise F. Orílio
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jesús Navas-Castillo
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Giuseppe Parrella.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Parrella, G., Acanfora, N., Orílio, A.F. et al. Complete nucleotide sequence of a Spanish isolate of alfalfa mosaic virus: evidence for additional genetic variability. Arch Virol 156, 1049–1052 (2011). https://doi.org/10.1007/s00705-011-0941-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00705-011-0941-z

Keywords

Search

Navigation