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Virus Genes

, Volume 51, Issue 1, pp 112–121 | Cite as

Detection and molecular characterisation of Grapevine Syrah virus-1 isolates from Central Europe

  • Miroslav GlasaEmail author
  • Lukáš Predajňa
  • Katarína Šoltys
  • Sead Sabanadzovic
  • Antonio Olmos
Article

Abstract

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.

Keywords

GSyV-1 Vitis vinifera Marafivirus siRNA-based next-generation sequencing Diversity 

Notes

Acknowledgments

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.

Supplementary material

11262_2015_1201_MOESM1_ESM.docx (15 kb)
Supplementary material 1 (docx 15 kb)
11262_2015_1201_MOESM2_ESM.pptx (34 kb)
Supplementary Fig. A Phylogenetic tree generated from the sequences encompassing the 5′end proximal part of the genome (nucleotides 37-654). (pptx 33 kb)

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Miroslav Glasa
    • 1
    Email author
  • Lukáš Predajňa
    • 1
  • Katarína Šoltys
    • 2
  • Sead Sabanadzovic
    • 3
  • Antonio Olmos
    • 4
  1. 1.Department of Plant Virology, Institute of VirologySlovak Academy of SciencesBratislavaSlovakia
  2. 2.Department of Molecular Biology, Faculty of Natural SciencesComenius University in BratislavaBratislavaSlovakia
  3. 3.Department of Biochemistry, Molecular Biology, Entomology and Plant PathologyMississippi State UniversityMississippi StateUSA
  4. 4.Department of Plant PathologyInstituto Valenciano de Investigaciones AgrariasValenciaSpain

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