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Five phylogenetic groups identified in the coat protein gene of grapevine leafroll-associated virus 3 obtained from Portuguese grapevine varieties

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Abstract

The genetic variability and population structure of grapevine leafroll-associated virus 3 (GLRaV-3) variants were updated by examining the diversity within the viral coat protein (CP) gene among 174 isolates belonging to a collection of Vitis vinifera representing most of the Portuguese varieties. Phylogenetic analysis revealed the existence of five well-defined clusters. Three of these correspond to previously defined groups, another corresponds to variants from Chile for which only one sequence has been previously identified, and an additional new group includes only Portuguese variants. A typing tool based on asymmetric PCR-ELISA (APET) was developed within the frame of this population structure. This tool was used to assess the prevalence of each phylogenetic group among the infected grapevine varieties. Although most of the isolates harbour variants from groups 1 and 2, variants from the remaining three groups exist in a number of varieties, reinforcing the notion that they are genuine genomic variants and are not isolated, atypical cases.

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References

  1. Cabaleiro C, Segura A (1997) Field transmission of grapevine leafroll associated virus 3 (GLRaV-3) by the mealybug Planococcus citri. Plant Dis 81:283–287

    Article  Google Scholar 

  2. Chooi KM, Pearson MN, Cohen D, Pong JCH (2009) Sequence variation in Grapevine leafroll-associated virus 3 (GLRaV-3) New Zealand isolates. In: Extended abstracts 16th meeting ICVG, Dijon, France, 31 August–4 September 2009, pp 290–291

  3. Engel EA, Girardi C, Escobar PF, Arredondo V, Dominguez C, Perez-Acle T, Valenzuela PD (2008) Genome analysis and detection of a Chilean isolate of Grapevine leafroll associated virus-3. Virus Genes 37:110–118

    Article  PubMed  CAS  Google Scholar 

  4. Fajardo TVM, Dianese ÉC, Eiras M, Cerqueira DM, Lopes DB, Ferreira MASV, Martins CRF (2007) Variability of the coat protein gene of Grapevine leafroll-associated virus 3 in Brazil. Fitopatologia Brasileira 32:335–340

    Google Scholar 

  5. Fuchs M, Martinson TE, Loeb GM, Hoch HC (2009) Survey for the three major leafroll disease-associated viruses in Finger Lakes vineyards in New York. Plant Dis 93:395–401

    Article  CAS  Google Scholar 

  6. Gouveia P, Esteves F, Santos MT, Fonseca F, Eiras-Dias JE, Nolasco G (2009) Assessment of GLRaV-3 variants occurring in Portuguese grapevine varieties according to the coat protein gene. In: Extended abstracts 16th meeting ICVG, Dijon, France, 31 August–4 September 2009. pp 316–317

  7. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  8. Jooste AE, Maree HJ, Bellstedt DU, Goszczynski DE, Pietersen G, Burger JT (2010) Three genetic grapevine leafroll-associated virus 3 variants identified from South African vineyards show high variability in their 5’UTR. Arch Virol. doi:10.1007/s00705-00010-00793-y (in press)

  9. Kosakovsky Pond SL, Frost SD (2005) Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 21:2531–2533

    Article  Google Scholar 

  10. Ling KS, Zhu HY, Alvizo H, Hu JS, Drong RF, Slightom JL, Gonsalves D (1997) The coat protein gene of grapevine leafroll associated closterovirus-3: cloning, nucleotide sequencing and expression in transgenic plants. Arch Virol 142:1101–1116

    Article  PubMed  CAS  Google Scholar 

  11. Ling KS, Zhu HY, Gonsalves D (2004) Complete nucleotide sequence and genome organization of Grapevine leafroll-associated virus 3, type member of the genus Ampelovirus. J Gen Virol 85:2099–2102

    Article  PubMed  CAS  Google Scholar 

  12. MacKenzie DJ, McLean MA, Mukerji S, Green M (1997) Improved RNA extraction from woody plants for the detection of viral pathogens by reverse transcription-polymerase chain reaction. Plant Dis 81:222–226

    Article  CAS  Google Scholar 

  13. Magalhaes N, Oliveira A, Carvalho JB, Toscano E, Correia MJ, Pereira AM, Carneiro LC, Martins A, Sequeira OAd, Sequeira JC, Santos MT (1997) Evolution of leafroll (GLRaV-3) effect on grapevine yield and potential ethanol. In: Extended abstracts 12th meeting ICVG, Lisbon, Portugal, 29 September–2 October 1997. pp 175–176

  14. Mannini F, Credi R, Symons RH (2000) Appraisal of agronomic and enological modifications in the performances of grapevine clones after virus eradication. In: Extended abstracts 13th meeting ICVG, Adelaide, Australia, 12–17 March 2000. pp 151–152

  15. Markham NR, Zuker M (2005) DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res 33:W577–W581

    Article  PubMed  CAS  Google Scholar 

  16. Martelli GP, Agranovsky AA, Bar-Joseph M, Boscia D, Candresse T, Coutts RH, Dolja VV, Falk BW, Gonsalves D, Jelkmann W, Karasev AV, Minafra A, Namba S, Vetten HJ, Wisler GC, Yoshikawa N (2002) The family Closteroviridae revised. Arch Virol 147:2039–2044

    Article  PubMed  CAS  Google Scholar 

  17. Martin DP, Williamson C, Posada D (2005) RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21:260–262

    Article  PubMed  CAS  Google Scholar 

  18. Nolasco G, Santos C, Silva G, Fonseca F (2009) Development of an asymmetric PCR-ELISA typing method for citrus tristeza virus based on the coat protein gene. J Virol Methods 155:97–108

    Article  PubMed  CAS  Google Scholar 

  19. Schutz E, von Ahsen N (1999) Spreadsheet software for thermodynamic melting point prediction of oligonucleotide hybridization with and without mismatches. Biotechniques 27:1218–1222, 1224

    Google Scholar 

  20. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599

    Article  PubMed  CAS  Google Scholar 

  21. Thompson JD, Higgins DG, Gibson TJ (1994) Clustal-W—improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    Article  PubMed  CAS  Google Scholar 

  22. Turturo C, Saldarelli P, Yafeng D, Digiaro M, Minafra A, Savino V, Martelli GP (2005) Genetic variability and population structure of Grapevine leafroll-associated virus 3 isolates. J Gen Virol 86:217–224

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

This work partially supported by the grant from Fundação para a Ciência e Tecnologia PTDC/AGR-AAM/65094/2006 and by the grant PTDC/AGR-GPL/67844/2006. Paulo Gouveia is the recipient of the PhD grant SFRH/BD/41826/2007.

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Authors and Affiliations

  1. Center for Biodiversity, Functional & Integrative Genomics, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal

    Paulo Gouveia & Gustavo Nolasco

  2. INRB, L-INIA, Quinta do Marquês, 2784-505, Oeiras, Portugal

    Margarida Teixeira Santos

  3. INRB, L-INIA, Quinta da Almoinha, 2565-191, Dois Portos, Portugal

    José Eduardo Eiras-Dias

  4. Faculdade de Ciências e Tecnologia, Universidade do Algarve Campus de Gambelas, 8005-139, Faro, Portugal

    Gustavo Nolasco

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  1. Paulo Gouveia
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  2. Margarida Teixeira Santos
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  3. José Eduardo Eiras-Dias
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  4. Gustavo Nolasco
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Correspondence to Gustavo Nolasco.

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Gouveia, P., Santos, M.T., Eiras-Dias, J.E. et al. Five phylogenetic groups identified in the coat protein gene of grapevine leafroll-associated virus 3 obtained from Portuguese grapevine varieties. Arch Virol 156, 413–420 (2011). https://doi.org/10.1007/s00705-010-0878-7

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  • DOI: https://doi.org/10.1007/s00705-010-0878-7

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