Low genetic diversity of a natural population of Garlic virus D from Poland
- 219 Downloads
Thirty Garlic virus D isolates collected on a local scale over a 2-year period were analysed and compared to others available in GenBank. In total, 1139 nt were sequenced for each isolate, representing about 13 % of the complete virus genome. Bioinformatic analysis revealed that despite the wide geographic distribution and different growing conditions of hosts, GarV-D maintains an amino acid similarity between 95 to 100 % and 88 to 100 %, indicating high spatial and temporal genetic stability of the coat protein (CP) and nucleic acid binding protein (NABP) genes. The sequence alignments of all isolates of GarV-D were also searched for evidence of recombination and diversifying selection. The ratio of non-synonymous to synonymous polymorphic sites indicated that mostly purifying selection has acted within the analysed genes. However, three codons (two in CP and one in NABP sequences) showed to be under positive selection, including codon located inside conserved zinc-motif finger.
KeywordsGarV-D Selection CP NABP Recombination
Research supported by grant 2012/07/N/NZ9/00037 from National Science Center, Poland.
- Adams, M. J., Zerbini, F. M., French, R., Rabenstein, F., Stenger, D. C., & Valkonen, J. P. T. (2012). Family Flexiviridae. In A. M. Q. King, M. J. Adams, E. B. Carstens, & E. J. Lefkowitz (Eds.), Virus taxonomy. Ninth report of the international committee on taxonomy of viruses (pp. 1069–1089). San Diego: Elsevier.Google Scholar
- Chodorska, M., Paduch-Cichal, E., Szyndel, M. S., & Kalinowska, E. (2012). First report of Garlic virus D, E, and X on garlic in Poland. Journal of Plant Pathology, 95, S4.70.Google Scholar
- Domingo, E., Biebricher, K., Eigen, M., & Holland, J. (2001). Quasispecies and RNA virus evolution: principles and consequences. Georgetown: Landes Bioscience.Google Scholar
- Dovas, C. I., & Vovlas, C. (2003). Viruses infecting allium spp. in southern italy. Journal of Plant Pathology, 85, 135.Google Scholar
- King, A. M. Q., Adams, M. J., Carstens, E. B., & Lefkowitz, E. J. (2012). Ninth report of the international committee on taxonomy of viruses. San Diego: Elsevier.Google Scholar
- Lanzoni, C., Ratti, C., Turina, M., Pisi, A., Tedeschi, P., & Autonell, C. R. (2006). Molecular characterisation of Allexiviruses from garlic in Italy. Journal of Plant Pathology, 88, 47.Google Scholar
- Malinowski, T. (1997). Silica capture-reverse transcription-polymerase chain reaction (SC-RT-PCR): application for the detection of several plant viruses. In H. W. Dehne, G. Adam, M. Diekmann, J. Frahm, A. MaulerMachnik, & P. VanHalteren (Eds.), Diagnosis and identification of plant pathogens, proceedings of 4th international EFPP symposium Bonn, 9–12 September 1996 (pp. 445–448). Budapest: Kluwer Academic Publishers.Google Scholar
- Melo-Filho, P. A., Nagata, T., Dusi, A. N., Buso, J. A., Torres, A. C., Eiras, M., & Resende, R. O. (2004). Detection of three Allexivirus species infecting garlic in Brazil. Pesquisa Agropecuária Brasileira, 39, 375–340.Google Scholar
- Sánchez-Campos, S., Díaz, J. A., Monci, F., Bejarano, E. R., Reina, J., Navas-Castillo, J., Aranda, M. A., & Moriones, E. (2002). High genetic stability of the begomovirus Tomato yellow leaf curl Sardinia virus in southern Spain over an 8-year period. Phytopathology, 92, 842–849.CrossRefPubMedGoogle Scholar
- Torres, A. C., Eiras, M., & Resende, R. (2004). Detection of three Allexivirus species infecting garlic in Brazil. Pesquisa Agropecuária Brasileira, 39, 735–740.Google Scholar