Detection and molecular characterisation of Grapevine Syrah virus-1 isolates from Central Europe
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Grapevine Syrah virus-1 (GSyV-1) was identified by small-RNA deep sequencing in Slovak grapevine co-infected by several other viruses. The RT-PCR assays developed in this work substantially improved the virus detection and allowed the identification of GSyV-1 in tested grapevine samples from Slovakia and the Czech Republic at an unexpectedly high rate (ca. 30 %). Subsequently, complete genome sequences of 3 GSyV-1 isolates (2 Slovak and 1 Czech) were determined by Sanger sequencing, showing a typical marafivirus genome organization. Analyses of complete genome sequences showed a higher intra-group diversity among these 3 central European GSyV-1 isolates (differences reaching 7.1 % at the nucleotide level) in comparison to 3 previously characterized North American isolates (only 1.2 % intra-group divergence). A substantially higher divergence among central European isolates and their clustering into two major phylogenetic groups was further confirmed by the partial genome analysis of additional 26 isolates. The CP-centered study did not support the geography-based clustering among central European and American isolates. Nevertheless, the sequence data of the highly variable 5′-proximal portion of the genome obtained for few additional isolates from Slovakia and Czech Republic showed the presence of both, “European-” and “north American-like”, GSyV-1 isolates in the analyzed grapevine samples.
KeywordsGSyV-1 Vitis vinifera Marafivirus siRNA-based next-generation sequencing Diversity
This work was supported by Grant VEGA 2/0060/13 from the Scientific Grant Agency of the Ministry of Education and Slovak Academy of Sciences. AO received the support from the INIA project RTA2011-00067-C04. KŠ was partially supported by the Grant REVOGENE (ITMS 26240220067) supported by the Research & Development Operational Programme funded by the ERDF. We thank Dr. P. Kominek for providing the grapevine samples from the Czech Republic.
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