Skip to main content
SpringerLink
Log in

A genome-wide diversity study of grapevine rupestris stem pitting-associated virus

  • Brief Report
  • Published:
Archives of Virology Aims and scope Submit manuscript

Abstract

Over the last decade, many scientific disciplines have been impacted by the dawn of new sequencing techniques (HTS: high throughput sequencing). Plant pathology and more specifically virology have been greatly transformed by this ‘metagenomics’ paradigm shift. Such tools significantly facilitate disease diagnostics with tremendous sensitivity, providing invaluable information such as an exhaustive list of viruses being present in a sample as well as their relative concentration. In addition, many new plant viruses have been discovered. Using RNAseq technology, in silico reconstruction of complete viral genome sequences is easily attainable. This step is of importance for taxonomy, population structure analyses, phylogeography and viral evolution studies. Here, after assembling 81 new near-complete genome sequences of grapevine rupestris stem pitting-associated virus (GRSPaV), we performed a genome-wide diversity study of this ubiquitous virus of grapevine worldwide.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2: Nucleotide diversity index (π) study and location of recombination events within all grapevine rupestris stem pitting-associated virus (GRSPaV) genomes.

References

  1. Al Rwahnih M, Daubert S, Golino D, Rowhani A (2009) Deep sequencing analysis of RNAs from a grapevine showing Syrah decline symptoms reveals a multiple virus infection that includes a novel virus. Virology 387:395–401

    Article  CAS  PubMed  Google Scholar 

  2. Alabi OJ, Martin RR, Naidu RA (2010) Sequence diversity, population genetics and potential recombination events in grapevine rupestris stem pitting-associated virus in Pacific North-West vineyards. J Gen Virol 91:265–276

    Article  CAS  PubMed  Google Scholar 

  3. Beuve M, Moury B, Spilmont A-S, Sempé-Ignatovic L, Hemmer C, Lemaire O (2013) Viral sanitary status of declining grapevine Syrah clones and genetic diversity of Grapevine rupestris stem pitting-associated virus. Eur J Plant Pathol 135:439–452

    Article  Google Scholar 

  4. Beuve M, Hily JM, Alliaume A, Reinbold C, Le Maguet J, Candresse T, Herrbach E, Lemaire O (2018) A complex virome unveiled by deep sequencing analysis of RNAs from a French Pinot Noir grapevine exhibiting strong leafroll symptoms. Arch Virol. https://doi.org/10.1007/s00705-018-3949-9.

    Article  PubMed  Google Scholar 

  5. Bol JF (2008) Role of capsid proteins. In: Foster GD, Johansen IE, Hong Y, Nagy PD (eds) Plant virology protocols: from viral sequence to protein function. Humana Press, Totowa, NJ, pp 21–31

    Chapter  Google Scholar 

  6. Bouyahia H, Boscia D, Savino V, La Notte P, Pirolo C, Castellano MA, Minafra A, Martelli GP (2005) Grapevine rupestris stem pitting-associated virus is linked with grapevine vein necrosis. Vitis 44:133–137

    CAS  Google Scholar 

  7. Byrd AL, Segre JA (2016) Adapting Koch’s postulates. Science 351:224–226

    Article  CAS  PubMed  Google Scholar 

  8. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl Acids Res 32:1792–1797

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Gambino G, Cuozzo D, Fasoli M, Pagliarani C, Vitali M, Boccacci P, Pezzotti M, Mannini F (2012) Co-evolution between Grapevine rupestris stem pitting-associated virus and Vitis vinifera L. leads to decreased defence responses and increased transcription of genes related to photosynthesis. J Exp Bot 63:5919–5933

    Article  CAS  PubMed  Google Scholar 

  10. Glasa M, Predajňa L, Šoltys K, Sihelská N, Nagyová A, Wetzel T, Sabanadzovic S (2017) Analysis of Grapevine rupestris stem pitting-associated virus in Slovakia reveals differences in intra-host population diversity and naturally occurring recombination events. Plant Pathol J 33:34–42

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Golino DA, Fuchs M, Sim S, Farrar K, Martelli GP (2017) Improvement of grapevine planting stock through sanitary selection and pathogen elimination. In: Meng B, Martelli GP, Golino DA, Fuchs M (eds) Grapevine viruses: molecular biology, diagnostics and management. Springer, Cham, pp 561–579

    Chapter  Google Scholar 

  12. Goszczynski DE (2010) Rugose wood-associated viruses do not appear to be involved in Shiraz (Syrah) decline in South Africa. Adv Virol 155:1463–1469

    CAS  Google Scholar 

  13. Hily J-M, Demanèche S, Poulicard N, Tannières M, Djennane S, Beuve M, Vigne E, Demangeat G, Komar V, Gertz C, Marmonier A, Hemmer C, Vigneron S, Marais A, Candresse T, Simonet P, Lemaire O (2018) Metagenomic-based impact study of transgenic grapevine rootstock on its associated virome and soil bacteriome. Plant Biotechnol J 16:208–220

    Article  CAS  PubMed  Google Scholar 

  14. Hu G-J, Dong Y-F, Zhu H-J, Zhang Z-P, Fan X-D, Ren F, Zhou J (2015) Molecular characterizations of two grapevine rupestris stem pitting-associated virus isolates from China. Adv Virol 160:2641–2645

    CAS  Google Scholar 

  15. Kalinowska E, Paduch-Cichal E, Chodorska M (2012) Low genetic diversity of the coat protein gene among blueberry red ringspot virus isolates. J Phytopathol 160:603–605

    Article  Google Scholar 

  16. King AMQ, Adams MJ, Cartens EB, Lefkowitz EJ (2012) Family—betaflexiviridae. Virus taxonomy. Elsevier, San Diego, pp 920–941

    Google Scholar 

  17. Korber B (2000) HIV signature and sequence variation analysis. In: Rodrigo AG, Learn GH (eds) Computational analysis of HIV molecular sequences. Kluwer Academic Publishers, Dordrecht, pp 55–72

    Google Scholar 

  18. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis Version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452

    Article  CAS  PubMed  Google Scholar 

  20. Lima MF, Alkowni R, Uyemoto JK, Golino D, Osman F, Rowhani A (2006) Molecular analysis of a California strain of Rupestris stem pitting-associated virus isolated from declining Syrah grapevines. Adv Virol 151:1889–1894

    CAS  Google Scholar 

  21. Lunden S, Meng B, Avery J, Qiu W (2009) Association of Grapevine fanleaf virus, Tomato ringspot virus and Grapevine rupestris stem pitting-associated virus with a grapevine vein-clearing complex on var, Chardonnay. Eur J Plant Pathol 126:135

    Article  Google Scholar 

  22. Mann K, Meng B (2013) The triple gene block movement proteins of a grape virus in the genus Foveavirus confer limited cell-to-cell spread of a mutant Potato virus X. Virus Genes 47:93–104

    Article  CAS  PubMed  Google Scholar 

  23. Martin DP, Murrell B, Golden M, Khoosal A, Muhire B (2015) RDP4: detection and analysis of recombination patterns in virus genomes. Virus Evolut 1:1–5

    Article  Google Scholar 

  24. Meng B, Pang SZ, Forsline PL, McFerson JR, Gonsalves D (1998) Nucleotide sequence and genome structure of grapevine rupestris stem pitting associated virus-1 reveal similarities to apple stem pitting virus. J Gen Virol 79:2059–2069

    Article  CAS  PubMed  Google Scholar 

  25. Meng B, Gonsalves D (2003) Rupestris stem pitting-associated virus of grapevines: genome structure, genetic diversity, detection, and phylogenetic relationship to other plant viruses. Current Top Virol 3:125–135

    CAS  Google Scholar 

  26. Meng B, Rebelo AR, Fisher H (2006) Genetic diversity analyses of grapevine Rupestris stem pitting-associated virus reveal distinct population structures in scion versus rootstock varieties. J Gen Virol 87:1725–1733

    Article  CAS  PubMed  Google Scholar 

  27. Meng B, Gonsalves D (2007) Grapevine rupestris stem pitting-associated virus: a decade of research and future perspectives. Plant Virus 1:52–62

    Google Scholar 

  28. Meng B, Rowhani A (2017) Grapevine rupestris stem pitting-associated virus. In: Meng B, Martelli GP, Golino DA, Fuchs M (eds) Grapevine viruses: molecular biology, diagnostics and management. Springer, Cham, pp 257–287

    Chapter  Google Scholar 

  29. Nolasco G, Santos C, Petrovic N, Teixeira Santos M, Cortez I, Fonseca F, Boben J, Nazaré Pereira AM, Sequeira O (2006) Rupestris stem pitting associated virus isolates are composed by mixtures of genomic variants which share a highly conserved coat protein. Adv Virol 151:83–96

    CAS  Google Scholar 

  30. Pacifico D, Stigliano E, Sposito L, Spinelli P, Garfì G, Gristina AS, Fontana I, Carimi F (2016) Survey of viral infections in spontaneous grapevines from natural environments in Sicily. Eur J Plant Pathol 145:189–197

    Article  CAS  Google Scholar 

  31. Petrovic N, Meng B, Ravnikar M, Mavric I, Gonsalves D (2003) First detection of Rupestris stem pitting associated virus particles by antibody to a recombinant coat protein. Plant Dis 87:510–514

    Article  CAS  PubMed  Google Scholar 

  32. Reynolds AG, Lanterman WS, Wardle DA (1997) Yield and Berry composition of five vitis cultivars as affected by Rupestris stem pitting virus. Am J Enol Vitic 48:449–458

    Google Scholar 

  33. Rubio L, Abou-Jawdah Y, Lin H-X, Falk BW (2001) Geographically distant isolates of the crinivirus Cucurbit yellow stunting disorder virus show very low genetic diversity in the coat protein gene. J Gen Virol 82:929–933

    Article  CAS  PubMed  Google Scholar 

  34. Saldarelli P, Giampetruzzi A, Maree HJ, Al Rwahnih M (2017) High-throughput sequencing: advantages beyond virus identification. In: Meng B, Martelli GP, Golino DA, Fuchs M (eds) Grapevine viruses: molecular biology, diagnostics and management. Springer, Cham, pp 625–642

    Chapter  Google Scholar 

  35. Terlizzi F, Li C, Ratti C, Qiu W, Credi R, Meng B (2011) Detection of multiple sequence variants of Grapevine rupestris stem pitting-associated virus using primers targeting the polymerase domain and partial genome sequencing of a novel variant. Ann Appl Biol 159:478–490

    Article  CAS  Google Scholar 

  36. Zhang Y-P, Uyemoto JK, Golino DA, Rowhani A (1998) Nucleotide sequence and RT-PCR detection of a virus associated with grapevine rupestris stem-pitting disease. Phytopathology 88:1231–1237

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by the Institut National de la Recherche Agronomique (INRA). Additional funds were kindly provided by three French professional committees for viticulture (Interprofessional Committee of Champagne Wine, CIVC, Epernay; Interprofessional Office of Burgundy Wines, CIVB, Beaune and Interprofessional Committee of Wines from Alsace, CIVA, Colmar) and by Moët & Chandon. The authors acknowledge Jacky Misbach and the greenhouse team for technical support, Lionel Ley and the members of the experimental unit of INRA-Colmar for the production of plants.

Author information

Authors and Affiliations

  1. SVQV, Université de Strasbourg, 68000, Colmar, France

    Jean-Michel Hily, Monique Beuve, Emmanuelle Vigne, Gérard Demangeat & Olivier Lemaire

  2. UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, 20032, 33882, Villenave d’Ornon Cedex, France

    Thierry Candresse

Authors
  1. Jean-Michel Hily
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Monique Beuve
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Emmanuelle Vigne
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Gérard Demangeat
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Thierry Candresse
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Olivier Lemaire
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jean-Michel Hily.

Ethics declarations

Conflict of interest

The authors declare there are no conflicts of interest.

Research involving human participants and/or animals

The research did not involve human participants or animals.

Informed consent

The research did not involve human participants or animals.

Additional information

Handling Editor: Sead Sabanadzovic.

Electronic supplementary material

Below is the link to the electronic supplementary material.

‘Per codon’ analysis

of the average behavior of each codon for all pairwise comparisons for synonymous (blue line) and non-synonymous (orange) mutations along the replicase polyprotein (A), TGBp1 (B), TGBp2 (c), TGBp3 (D) and CP (E), using SNAP v2,1,1 software. Overlapping sequence between TGBp2 and TGBp3 is shown (blue background) and between CP and ORF6 (green background). Nucleotide diversity index (π) study was evaluated by sliding window analyses using DnaSP v. 5.10 between the 71 genomes for which ORF6 was predicted (orange) and the 32 genomes for which ORF6 was missing (blue). 1 (PDF 431 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Hily, JM., Beuve, M., Vigne, E. et al. A genome-wide diversity study of grapevine rupestris stem pitting-associated virus. Arch Virol 163, 3105–3111 (2018). https://doi.org/10.1007/s00705-018-3945-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00705-018-3945-0

Search

Navigation