Variability of some isolates of Prunus necrotic ringspot virus and Prune dwarf virus infecting sour and sweet cherry in Ukraine

Liliia PAVLIUK, Kateryna UDOVYCHENKO, Iryna RIABA, Mykola BUBLYK

Abstract


Prunus necrotic ringspot virus (PNRSV) and Prune dwarf virus (PDV) are the most common pathogens in stone crop orchards. These diseases are easily transmitted with pollen and hence rapidly spread in orchards leading to stunting of trees, their increased susceptibility to abiotic stress factors and, eventually, to significant yield losses. In Ukraine, only monitoring studies on the spread of these viruses were conducted until now. However, phylogenetic comparison of Ukrainian isolates was lacking. In this work, total RNA was isolated from plant samples tested positive for PNRSV and PDV by ELISA. The part of viral CP gene sequences were amplified and sequenced with their subsequent phylogenetic analysis. It was determined that PNRSV isolates from Ukraine analyzed in this study belong to different groups – PV-96 (MT828889) and PV-32 (MT892676) with a maximum identity level of 100 % with known isolates from NCBI GenBank. PDV isolates (MT828888 and MT828887) showed high identity with each other (99.6 %), and Slovakian isolate from sweet cherry was shown as the most related to them with identity of 95.3 %.


Keywords


PNRV; PDV; ELISA; RT-PCR; sweet cherry virus; phylogenetic analysis

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References


Amari, K., Burgos, L., Pallás, V., Sánchez-Pina, M. A. (2007). Prunus necrotic ringspot virus early invasion and its effects on apricot pollen grains performance. Phytopathology, 97, 892-899. http://doi.org/10.1094/PHYTO-97-8-0892

Aparicio, F., & Pallás, V. (2002). Molecular variability analysis of the RNA 3 of fifteen isolates of Prunus necrotic ringspot virus sheds light on the minimal requirements for the synthesis of the subgenomic RNA. Virus Genes, 25, 75-84. http://doi.org/10.1023/a:1020126309692

Aparicio, F., Sánchez-Navarro, J. A., Pallás, V. (2006). In vitro and in vivo mapping of the Prunus necrotic ringspot virus coat protein C-terminal dimerization domain by bimolecular fluorescence complementation. Journal of General Virology, 87, 1745-1750. http://doi.org/10.1099/vir.0.81696-0

Aparicio, F., Sanchez-Pina, M. A., Sanchez-Navarro, J. A., Pallas, V. (1999). Location of Prunus necrotic ringspot ilarvirus within pollen grains of infected nectarine trees: evidence from RT-PCR, dot-blot and in situ hybridisation. European Journal of Plant Pathology, 105, 623-627

Bachman, E. J., Scott, S. W., Xin, G., Vance, V. B. (1994). The Complete Nucleotide Sequence of Prune Dwarf Ilarvirus RNA 3: Implications for Coat Protein Activation of Genome Replication in Ilarviruses. Virology, 201(1), 127–131. http://doi.org/10.1006/viro.1994.1272

Boulila, M., Tiba, S. B., Jilani, S. (2013). Molecular adaptation within the coat protein-encoding gene of Tunisian almond isolates of Prunus necrotic ringspot virus. Journal of Genetics, 92(1), 11-24. http://doi.org/10.1007/s12041-013-0211-9.

Çağlayan, K., Ulubas-Serce, C., Gazel, M., Varveri, C. (2011). Prune dwarf virus. In A. Hadidi, M. Barba, T. Candresse, W. Jelkmann (Eds.), Virus and Virus-Like Diseases of Pome and Stone Fruits (pp. 199-205). American Phytopathological Society, St. Paul, MN.

Codoñer, F. M., & Elena, S. F. (2006). Evolutionary relationships among members of the Bromoviridae deduced from whole proteome analysis. Archives of Virology, 151(2), 299-307. http://doi.org/10.1007/s00705-005-0628-4

Felsenstein, J. (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution, 39, 783-791. https://doi.org/ 10.2307/2408678

Hammond R. W. (2003). Phylogeny isolates of Prunus necrotic ringspot virus from the ilarvirus ringtest and identification of group-specific features. Archives of Virology, 148(6), 1195-1210. http://doi.org/10.1007/s00705-003-0013-0

Jakab-Ilyefalvi, Zs., Pamfil, D., Craciun, C. (2011). Transmission electron microscopy of Plum pox virus, Prunus necrotic ringspot virus, Prune dwarf virus in plum (Prunus domestica, L.). Journal of Horticulture, Forestry and Biotechnology, 15(1), 120- 125.

Kamenova, I., Borisova, A., Popov, A. (2019). Incidence and genetic diversity of Prune dwarf virus in sweet and sour cherry in Bulgaria. Biotechnology & Biotechnological Equipment, 33(1), 980–987. https://doi.org/10.1080/13102818.2019.1637278

Kozieł, E., Bujarski, J., Otulak, K. (2017). Molecular Biology of Prune Dwarf Virus—A Lesser Known Member of the Bromoviridae but a Vital Component in the Dynamic Virus–Host Cell Interaction Network. International Journal of Molecular Sciences, 18(12), 2733. http://doi.org/10.3390/ijms18122733

Kumar, S., Stecher, G., Li, M., Knyaz, C., Tamura K. (2018). MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution, 35, 1547-1549. https://doi.org/10.1093/molbev/msy096

Maliogka, V. I., Dovas, C. I., Katis, N. I. (2007). Demarcation of ilarviruses based on the phylogeny of RNA2-encoded RdRp and generic ramped annealing RT-PCR. Archives of Virology, 152(9), 1687-1698. https://doi.org/10.1007/s00705-007-0995-0

Massart, S., Brostaux Y., Barbarossa, L., César, V., Cieslinska, M., Dutrecq, O., Fonseca, F., … Jijakli M. H. (2008). Inter-laboratory evaluation of a duplex RT-PCR method using crude extracts for the simultaneous detection of Prune dwarf virus and Prunus necrotic ringspot virus. European Journal of Plant Pathology, 122, 539–547. https://doi.org/10.1007/s10658-008-9322-1

Menzel, W., Jelkmann, W., Maiss, E. (2002). Detection of four apple viruses by multiplex RT-PCR assays with coamplification of plant mRNA as internal control. Journal of Virological Methods, 99(1-2), 81-92. https://doi.org/10.1016/s0166-0934(01)00381-0

Nemeth, M. (1986). Virus, Mycoplasma and Rickettsia Diseases of Fruit Trees. Hungary Martinus Nijhoff Publishers, The Netherlands and Akademiai Kiado.

Nyland, G., Gilmer, R. M., Moore, J. D. (1976). “Prunus” ringspot group. Іn R. M. Gilmer, J. D. Moore (Eds.) Virus Diseases and Non-Infectious Disorders of Stone Fruits in North America, (рр. 104-132). USDA, Washington Agriculture Handbook.

Pallas, V., Aparicio, F., Herranz, M., Amari, K., Sanchez-Pina, M., Myrta, A., Sanchez-Navarro, J. (2012). Ilarviruses of Prunus spp.: a continued concern for fruit trees. Phytopathology, 102, 1108-1120. https://doi.org/10.1094/PHYTO-02-12-0023-RVW

Pallas, V., Aparicio, F., Herranz, M., Sanchez-Navarro, A., Scott, W. (2013). The molecular biology of ilarviruses. Advances in Virus Research, 87, 139-181. https://doi.org/10.1016/B978-0-12-407698-3.00005-3

Pavliuk, L., Riaba, I., Udovychenko, K., Triapitsyna, N., Bublyk M. (2019). Phyto-virologic state of parent plantings of cherry and mazzard cherry in Ukraine. Bulletin of Agricultural Science, 97(7). https://doi.org/20.31073/agrovisnyk201907-3

Roossinck M. J., Bujarski, J., Ding, S. W., Hajimarad, R., Hanada, K., Scott, S., Tousignant, M. (2005). Bromoviridae. In. C. M. Fauquet, M. A. Mayo, J. Maniloff, U. Desselberger, L. A. Ball (Eds.), Virus Taxonomy. Eight Report of the International Committee on Taxonomy of Viruses (pp. 1049-1058). Elsevier/Academic Press, Amsterdam, Netherlands.

Saitou, N., & Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4, 406-425. https://doi.org/10.1093/oxfordjournals.molbev.a040454

Sala-Rejczak, K., & Paduch-Cichal, E. (2013). Molecular variability of the coat protein gene of Prunus necrotic ringspot virus isolates. Acta Scientiarum Polonorum Hortorum Cultus, 12(2), 35-42.

Sanchez, R. P., Corts, R. M., Benavides, P. G., Gómez-Sánchez, M. A. (2015). Main viruses in sweet cherry plantations of Central-Western Spain. Scientia Agricola, 72(1), 83-86. https://doi.org/10.1590/0103-9016-2014-0140

Scott, S. W., Zimmerman M. T., Ge, X., MacKenzie, D. J. (1998). The coat proteins and putative movement proteins of isolates of Prunus necrotic ringspot virus from different host species and geographic origins are extensively conserved. European Journal of Plant Pathology, 104, 155–161. http://doi.org/10.1023/a:1008668129926

Smith, I. M., Dunez, J., Phillips, D. H., Lelliott, R. A., Archer, S. A. (1988). European handbook of plant diseases. Oxford (UK): Blackwell Scientific.

Sokhandan-Bashir, N., Kashiha, Z., Koolivand D., Eini, O. (2017). Detection and phylogenetic analysis of Prunus necrotic ringspot virus isolates from stone fruits in Iran. Journal of Plant Pathology, 99(3), 717–723. http://doi.org/10.4454/jpp.v99i3.3986

Song, S., Sun, P., Chen, Y., Ma, Q., Wang, X., Zhao, M., Li, Z. (2019). Complete genome sequences of five prunus necrotic ringspot virus isolates from Inner Mongolia of China and comparison to other PNRSV isolates around the world. Journal of Plant Pathology 101, 1047-1054. http://doi.org/10.1007/s42161-019-00335-1

State Service of Statistics of Ukraine (2019). Areas, gross production, and yields of agricultural crops by their type and by region. Retrieved from http://www.ukrstat.gov.ua/ (in Ukrainian)

Tamura, K., & Nei, M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10, 512-526. https://doi.org/10.1093/oxfordjournals.molbev.a040023

Ulubas-Serçe, Ç., Ertunç, F., ÖZtürk, A. (2009). Identification and genomic variability of Prune dwarf virus variants infecting stone fruit in Turkey. Journal of Phytopathology, 157, 298-305. https://doi.org/10.1111/j.1439-0434.2008.01486.x

Umer, M., Liu, J., You, H., Xu, C., Dong, K., Luo, N., … Xu, W. (2019). Genomic, Morphological and Biological Traits of the Viruses Infecting Major Fruit. Viruses, 11(6), 515. http://doi.org/10.3390/v11060515

Vaskova, D., Petrzik, K., Spak, J. (2000). Molecular variability of the capsid protein of the Prune dwarf virus. European Journal of Plant Pathology, 106, 573-580. http://doi.org/10.1023/A:1008742513754

Verderevskaya, T. D., & Marinesku, V. G. (1985). Viral and mycoplasmal diseases of fruit crops and grapes. Chisinau: Shtinitsa. (in Russian)

Wells, J. M., & Kirkpatrick, H. C. (1986). Symptomatology and incidence of Prunus necrotic ringspot virus in peach orchards in Georgia. Plant Disease, 70, 444-447. https://doi.org/10.1094/PD-70-444.




DOI: http://dx.doi.org/10.14720/aas.2021.117.1.1844

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