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Molecular characterization of Prune dwarf virus cherry isolates from Slovakia shows their substantial variability and reveals recombination events in PDV RNA3

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Abstract

Although Prune dwarf virus (PDV) is one of the most common viruses infecting stone fruits (Prunus spp.), most of the molecular diversity studies have so far focused on the capsid protein (CP) gene. An alternative diagnostic primer pair targeting the movement protein (MP) gene was used in the present work, increasing then polyvalence of PDV detection in cherry samples from Slovakia as compared to the previously published primers amplifying 5′MP-intergenic region-CP-3′UTR fragment. The nearly complete sequence of the RNA3 from 24 Slovak PDV isolates was determined, together with 19 partial sequences of the MP gene for other isolates. Even though the isolates originated from a geographically limited region, analyses showed a high degree of nucleotide sequence diversity between isolates. No clear-cut phylogenetic grouping based on host or geographical origin could be observed. The topology of the MP and CP trees were incongruent for some isolates. Highly supported recombination signals were detected in five PDV isolates, with breakpoints located at different positions in the central part of RNA3, within or close to the intergenic region. Taken together these results extend our understanding of the variability of PDV and for the first time highlight the contribution of recombination to the evolutionary history of this virus.

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Acknowledgments

This work was supported by the grant APVV-0174-12 from the Slovak Research and Development Agency and partially by the grant VEGA2/0036/16 and bilateral Slovak-French Action SK-FR-2013-0021. KŠ was supported by the grant Revogene (ITMS 26240220067) from the Research & Development Operational Programme funded by the ERDF.

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Correspondence to Miroslav Glasa.

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Lukáš Predajňa and Nina Sihelská contributed equally to this work.

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Supplementary Table 1

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Supplementary Fig. 1A, B

The neighbor-joining phylogenetic trees generated from the complete nucleotide sequences coding for CP (127 isolates) (A) and partial nucleotide sequences of the MP gene (62 isolates) (B). The isolates are identified by their Genbank accession number, original host and country. The Slovak isolates characterised in this work are in bold. Bootstrap values >70 % (500 bootstrap resamplings) are indicated on the branches. An isolate of Apple mosaic virus (acc. number NC_003480) was used as the outgroup. (PPTX 49 kb)

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Predajňa, L., Sihelská, N., Benediková, D. et al. Molecular characterization of Prune dwarf virus cherry isolates from Slovakia shows their substantial variability and reveals recombination events in PDV RNA3. Eur J Plant Pathol 147, 877–885 (2017). https://doi.org/10.1007/s10658-016-1055-y

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  • DOI: https://doi.org/10.1007/s10658-016-1055-y

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