Abstract
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.
References
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.
Boom, R., Sol, C. J. A., Salimans, M. M. M., Jansen, C. L., Wertheim-Van Dillen, P. M. E., & van der Nordaa, J. (1990). Rapid and simple method for purification of nucleic acids. Journal of Clinical Microbiology, 28, 495–503.
Callaway, A., Giesman-Cookmeyer, D., Gillock, E. T., Sit, T. L., & Lommel, S. A. (2001). The multifunctional capsid proteins of plant RNA viruses. Annual Review of Phytopathology, 39, 419–460.
Chen, J., Zheng, H. Y., Antoniw, J. F., Adams, M. J., Chen, J. P., & Lin, L. (2004). Detection and classification of allexiviruses from garlic in China. Archives of Virology, 149, 435–445.
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.
Domingo, E., & Holland, J. J. (1997). RNA virus mutations and fitness for survival. Annual Review of Microbiology, 51, 151–178.
Domingo, E., Biebricher, K., Eigen, M., & Holland, J. (2001). Quasispecies and RNA virus evolution: principles and consequences. Georgetown: Landes Bioscience.
Dovas, C. I., & Vovlas, C. (2003). Viruses infecting allium spp. in southern italy. Journal of Plant Pathology, 85, 135.
Galiakparov, N., Tanne, E., Mawassi, M., Gafny, R., & Sela, I. (2003). ORF5 of Grapevine virus A encodes a nucleic acid-binding protein and affects pathogenesis. Virus Genes, 27, 257–262.
García-Arenal, F., Fraile, M., & Malpica, J. M. (2001). Variability and genetic structure of plant virus populations. Annual Review of Phytopathology, 39, 157–186.
García-Arenal, F., Fraile, A., & Malpica, J. M. (2003). Variation and evolution of plant virus populations. International Microbiology, 6, 225–232.
Gieck, S. L., Hamm, P. B., David, N. L., & Pappu, H. R. (2009). First report of Garlic virus B and Garlic virus D in garlic in the Pacific Northwest. Plant Disease, 93, 431.
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.
Koo, B. J., Kang, S. G., & Chang, M. U. (2002). Survey of garlic virus disease and phylogenetic characterization of garlic viruses of the genus Allexivirus isolated in Korea. Journal of Plant Pathology, 18, 237–243.
Kosakovsky Pond, S. L., Frost, S. D. W., & Muse, S. V. (2005). HyPhy: hypothesis testing using phylogenies. Bioinformatics, 21, 676–679.
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.
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.
Malpica, J. M., Fraile, A., Moreno, I., Obies, C. I., Drake, J. W., & García-Arenal, F. (2002). The rate and character of spontaneous mutation in an RNA virus. Genetics, 162, 1505–1511.
Martin, D. P. (2009). Recombination detection and analysis using RDP3. Methods in Molecular Biology, 537, 185–205.
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.
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.
Shahraeen, N., Lesemann, D. E., & Ghotbi, T. (2008). Survey for viruses infecting onion, garlic and leek crops in Iran. EPPO Bulletin, 38, 131–135.
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). MEGA5: molecular evolutionary genetics using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731–2739.
Torres, A. C., Eiras, M., & Resende, R. (2004). Detection of three Allexivirus species infecting garlic in Brazil. Pesquisa Agropecuária Brasileira, 39, 735–740.
Vives, M. C., Rubio, L., Galipienso, L., Navarro, L., Moreno, P., & Guerri, J. (2002). Low genetic variation between isolates of Citrus leaf blotch virus from different host species and of different geographical origins. Journal of General Virology, 83, 2587–2591.
Ward, L. I., Perez-Egusquiza, Z., Fletcher, J. D., & Clover, G. R. G. (2009). A survey of viral diseases of Allium crops in New Zealand. Australasian Plant Pathology, 38, 533–539.
Zhou, Z. S., Dell’Orco, M., Saldarelli, P., Turturo, C., Minafra, A., & Martelli, G. P. (2006). Identification of an RNA silencing suppressor in the genome of Grapevine virus A. Journal of General Virology, 87, 2387–2395.
Acknowledgment
Research supported by grant 2012/07/N/NZ9/00037 from National Science Center, Poland.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Bereda, M., Kalinowska, E., Paduch-Cichal, E. et al. Low genetic diversity of a natural population of Garlic virus D from Poland. Eur J Plant Pathol 142, 411–417 (2015). https://doi.org/10.1007/s10658-015-0615-x
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10658-015-0615-x