Skip to main content
Springer Nature Link
Log in

A complex virome unveiled by deep sequencing analysis of RNAs from a French Pinot Noir grapevine exhibiting strong leafroll symptoms.

  • Original Article
  • Published:
Archives of Virology Aims and scope Submit manuscript

Abstract

We have characterized the virome of a grapevine Pinot Noir accession (P70) that displayed, over the year, very stable and strong leafroll symptoms. For this, we have used two extraction methods (dsRNA and total RNA) coupled with the high throughput sequencing (HTS) Illumina technique. While a great disparity in viral sequences were observed, both approaches gave similar results, revealing a very complex infection status. Five virus and viroid isolates [Grapevine leafroll-associated viruse-1 (GLRaV-1), Grapevine virus A (GVA), Grapevine rupestris stem pitting-associated virus (GRSPaV), Hop stunt viroid (HSVd) and Grapevine yellow speckle viroid 1 (GYSVd1)] were detected in P70 with a grand total of eleven variants being identified and de novo assembled. A comparison between both extraction methods regarding their power to detect viruses and the ease of genome assembly is also provided.

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

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price includes VAT (Canada)

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  1. Abou-Ghanem N, Saldarelli P, Minafra A, Buzkan N, Castellano MA, Martelli GP (1997) Properties of Grapevine virus D, a novel putative trichovirus. J Plant Pathol 79:15–25

    Google Scholar 

  2. 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 

  3. Al Rwahnih M, Dolja VV, Daubert S, Koonin EV, Rowhani A (2012) Genomic and biological analysis of Grapevine leafroll-associated virus 7 reveals a possible new genus within the family Closteroviridae. Virus Res 163:302–309

    Article  CAS  PubMed  Google Scholar 

  4. Al Rwahnih M, Sudarshana MR, Uyemoto JK, Rowhani A (2012) Complete genome sequence of a novel vitivirus isolated from grapevine. J Virol 86:9545

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Almeida RPP, Daane KM, Bell VA, Blaisdell GK, Cooper ML, Herrbach E, Pietersen G (2013) Ecology and management of grapevine leafroll disease. Front Microbiol 4:94

    Article  PubMed  PubMed Central  Google Scholar 

  6. 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 

  7. Blouin AG, Chooi KM, Warren B, Napier KR, Barrero RA, MacDiarmid RM (2018) Grapevine virus I, a putative new vitivirus detected in co-infection with grapevine virus G in New Zealand. Arch Virol 163:1371–1374

    Article  CAS  PubMed  Google Scholar 

  8. Blouin AG, Keenan S, Napier KR, Barrero RA, MacDiarmid RM (2018) Identification of a novel vitivirus from grapevines in New Zealand. Arch Virol 163:281–284

    Article  CAS  PubMed  Google Scholar 

  9. Bratlie MS, Drabløs F (2005) Bioinformatic mapping of AlkB homology domains in viruses. BMC Genomics 6:1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Candresse T, Marais A, Faure C, Gentit P (2013) Association of Little cherry virus 1 (LChV1) with the shirofugen stunt disease and characterization of the genome of a divergent LChV1 isolate. Phytopathology 103:293–298

    Article  CAS  PubMed  Google Scholar 

  11. Candresse T, Filloux D, Muhire B, Julian C, Galzi S, Fort G, Bernardo P, Daugrois J-H, Fernandez E, Martin DP, Varsani A, Roumagnac P (2014) Appearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine context. PLoS One 9:e102945

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Candresse T, Theil S, Faure C, Marais A (2018) Determination of the complete genomic sequence of grapevine virus H, a novel vitivirus infecting grapevine. Arch Virol 163:277–280

    Article  CAS  PubMed  Google Scholar 

  13. Czotter N, Molnar J, Szabó E, Demian E, Kontra L, Baksa I, Szittya G, Kocsis L, Deak T, Bisztray G, Tusnady GE, Burgyan J, Varallyay E (2018) Ngs of virus-derived small rnas as a diagnostic method used to determine viromes of hungarian vineyards. Front Microbiol 9:122

    Article  PubMed Central  Google Scholar 

  14. du Preez J, Stephan D, Mawassi M, Burger JT (2011) The grapevine-infecting vitiviruses, with particular reference to grapevine virus A. Arch Virol 156:1495

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Fazeli CF, Rezaian MA (2000) Nucleotide sequence and organization of ten open reading frames in the genome of Grapevine leafroll-associated virus 1 and identification of three subgenomic RNAs. J Gen Virol 81:605–615

    Article  CAS  PubMed  Google Scholar 

  17. Giampetruzzi A, Roumi V, Roberto R, Malossini U, Yoshikawa N, La Notte P, Terlizzi F, Credi R, Saldarelli P (2012) A new grapevine virus discovered by deep sequencing of virus- and viroid-derived small RNAs in cv Pinot gris. Virus Res 163:262–268

    Article  CAS  PubMed  Google Scholar 

  18. 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 

  19. Goszczynski DE, Jooste AEC (2003) Identification of divergent variants of Grapevine virus A. Eur J Plant Pathol 109:397–403

    Article  CAS  Google Scholar 

  20. Goszczynski DE (2010) Divergent molecular variants of Grapevine virus B (GVB) from corky bark (CB)-affected and CB-negative LN33 hybrid grapevines. Virus Genes 41:273–281

    Article  CAS  PubMed  Google Scholar 

  21. Gugerli P, Brugger J, Bovey R (1984) L’enroulement de la vigne: mise en évidence de particules virales et développment dune méthode inmunoenzymatique pour le diagnostic rapide. Revue Suisse de Vitic Arboric Hortic 16:299–304

    Google Scholar 

  22. Habili N, Farrokhi N, Lima MF, Nicholas P, Randles JW (2006) Distribution of Rupestris stem-pitting-associated virus variants in two Australian vineyards showing different symptoms. Ann Appl Biol 148:91–96

    Article  Google Scholar 

  23. Herrbach E, Alliaume A, Prator CA, Daane KM, Cooper ML, Almeida RPP (2017) Vector transmission of grapevine Leafroll-associated viruses. In: Meng B, Martelli GP, Golino DA, Fuchs M (eds) Grapevine viruses: molecular biology, diagnostics and management. Springer International Publishing, New York, pp 483–503

    Chapter  Google Scholar 

  24. 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 Biotech J 16:208–220

    Article  CAS  Google Scholar 

  25. Hily JM, Beuve M, Vigne E, Demangeat G, Candresse T, Lemaire O (2018) A genome-wide study of grapevine rupestris stem pitting-associated virus. Arch Virol (in press)

  26. Hoefert L, Gifford M (1967) Grapevine leafroll virus—history and anatomic effects. Hilgardia 38:403–426

    Article  Google Scholar 

  27. Hommay G, Komar V, Lemaire O, Herrbach E (2008) Grapevine virus A transmission by larvae of Parthenolecanium corni. Eur J Plant Pathol 121:185–188

    Article  Google Scholar 

  28. 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. Arch Virol 160:2641–2645

    Article  CAS  PubMed  Google Scholar 

  29. Ito T, Nakaune R (2016) Molecular characterization of a novel putative ampelovirus tentatively named grapevine leafroll-associated virus 13. Arch Virol 161:2555–2559

    Article  CAS  PubMed  Google Scholar 

  30. Jo Y, Song M-K, Choi H, Park J-S, Lee J-W, Lian S, Lee BC, Cho WK (2017) Genome sequence of grapevine virus K, a novel vitivirus infecting grapevine. Genome Announc 5:e00994-17

    Article  PubMed  PubMed Central  Google Scholar 

  31. Jo Y, Song M-K, Choi H, Park J-S, Lee J-W, Lian S, Lee BC, Cho WK (2017) Genome sequence of grapevine Virus T, a novel foveavirus infecting grapevine. Genome Announc 5:e00995-17

    Article  PubMed  PubMed Central  Google Scholar 

  32. Komínek P (2008) Distribution of grapevine viruses in vineyards of the Czech Republic. J Plant Pathol 90:357–358

    Google Scholar 

  33. 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 

  34. Le Maguet J, Beuve M, Herrbach E, Lemaire O (2012) Transmission of six ampeloviruses and two vitiviruses to grapevine by Phenacoccus aceris. Phytopathology 102:717–723

    Article  PubMed  Google Scholar 

  35. Le Maguet J, Fuchs J-J, Chadœuf J, Beuve M, Herrbach E, Lemaire O (2013) The role of the mealybug Phenacoccus aceris in the spread of Grapevine leafroll-associated virus −1 (GLRaV-1) in two French vineyards. Eur J Plant Pathol 135:415–427

    Article  Google Scholar 

  36. 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 

  37. Ling R, Pate AE, Carr JP, Firth AE (2013) An essential fifth coding ORF in the sobemoviruses. Virology 446:397–408

    Article  CAS  PubMed  Google Scholar 

  38. Maree HJ, Almeida RPP, Bester R, Chooi KM, Cohen D, Dolja VV, Fuchs MF, Golino DA, Jooste AEC, Martelli GP, Naidu RA, Rowhani A, Saldarelli P, Burger JT (2013) Grapevine leafroll-associated virus 3. Front Microbiol 4:82

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Martelli GP, Ghanem-Sabanadzovic NA, Agranovsky AA, Rwahnih MA, Dolja VV, Dovas CI, Fuchs M, Gugerli P, Hu JS, Jelkmann W, Katis NI, Maliogka VI, Melzer MJ, Menzel W, Minafra A, Rott ME, Rowhani A, Sabanadzovic S, Saldarelli P (2012) Taxonomic revision of the family Closteroviridae with special reference to the grapevine leafroll-associated members of the genus Ampelovirus and the putative species unassigned to the family. J Plant Pathol 94:7–19

    Google Scholar 

  40. Martelli GP (2017) An overview on grapevine viruses, viroids, and the diseases they cause. In: Meng B, Martelli GP, Golino DA, Fuchs M (eds) Grapevine viruses: molecular biology, diagnostics and management. Springer International Publishing, Cham, pp 31–46

    Chapter  Google Scholar 

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

    Article  Google Scholar 

  42. 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 

  43. 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 

  44. Milne RG, Conti M, Lesemann D-E, Stellmach G, Tanne E, Cohen J (1984) Closterovirus-like particles of two types associated with diseased grapevines. Phytopathol Z 110:360–368

    Article  Google Scholar 

  45. Naidu RA, Maree HJ, Burger JT (2015) Grapevine leafroll disease and associated viruses: a unique pathosystem. Annu Rev Phytopathol 53:613–634

    Article  CAS  PubMed  Google Scholar 

  46. Nakaune R, Inoue K, Nasu H, Kakogawa K, Nitta H, Imada J, Nakano M (2008) Detection of viruses associated with rugose wood in Japanese grapevines and analysis of genomic variability of Rupestris stem pitting-associated virus. J Gen Plant Pathol 74:156–163

    Article  CAS  Google Scholar 

  47. Nakaune R, Toda S, Mochizuki M, Nakano M (2008) Identification and characterization of a new vitivirus from grapevine. Adv Virol 153:1827

    CAS  Google Scholar 

  48. 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. Arch Virol 151:83–96

    Article  CAS  PubMed  Google Scholar 

  49. Poojari S, Alabi OJ, Fofanov VY, Naidu RA (2013) A leafhopper-transmissible DNA virus with novel evolutionary lineage in the family Geminiviridae implicated in grapevine redleaf disease by next-generation sequencing. PLoS One 8:e64194

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Reynard JS, Brodard J, Dubuis N, Yobregat O, Kominek P, Schumpp O, Schaerer S (2017) First report of grapevine rupestris vein feathering virus in Swiss grapevines. Plant Dis 101:1062

    Article  Google Scholar 

  51. Roossinck MJ, Martin DP, Roumagnac P (2015) Plant virus metagenomics: advances in virus discovery. Phytopathology 105:716–727

    Article  CAS  PubMed  Google Scholar 

  52. van den Born E, Omelchenko MV, Bekkelund A, Leihne V, Koonin EV, Dolja VV, Falnes PØ (2008) Viral AlkB proteins repair RNA damage by oxidative demethylation. Nucleic Acids Res 36:5451–5461

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This work was supported by the Institut National de la Recherche Agronomique (INRA) and FranceAgriMer. JLM and AA were supported by Ph.D. grants respectively from the French National Association of Research and Technology and from Department SPE of INRA. Additional funds were kindly provided by three French professional committees for viticulture (the Interprofessional Committee of Champagne Wine, CIVC, Epernay; the Interprofessional Office of Burgundy Wines, BIVB, Beaune and the Interprofessional Committee of Wines from Alsace, CIVA, Colmar). This work was also partially supported by the Agence Nationale pour la Recherche, ANR Vinobodies contract: ANR- 14-CE19-0018-02. 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, Emmanuelle Vigne and Shahinez Garcia for useful input into creating a more readable manuscript.

Author information

Author notes

  1. Jean Le Maguet

    Present address: Institut Français des Productions Cidricoles (IFPC), 61500, Sées, France

  2. Monique Beuve and Jean-Michel Hily contributed equally to the work.

Authors and Affiliations

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

    Monique Beuve, Jean-Michel Hily, Antoine Alliaume, Catherine Reinbold, Jean Le Maguet, Etienne Herrbach & Olivier Lemaire

  2. UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Villenave d’Ornon Cedex, France

    Thierry Candresse

Authors
  1. Monique Beuve
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jean-Michel Hily
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Antoine Alliaume
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Catherine Reinbold
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jean Le Maguet
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Thierry Candresse
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Etienne Herrbach
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. 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: Jesús Navas-Castillo.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 680 kb)

Supplementary material 2 (PPTX 2301 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Beuve, M., Hily, JM., Alliaume, A. et al. A complex virome unveiled by deep sequencing analysis of RNAs from a French Pinot Noir grapevine exhibiting strong leafroll symptoms.. Arch Virol 163, 2937–2946 (2018). https://doi.org/10.1007/s00705-018-3949-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00705-018-3949-9

Search

Navigation