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A variant of Rubus yellow net virus with altered genomic organization

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Abstract

Rubus yellow net virus (RYNV) is a member of the genus Badnavirus (family: Caulimoviridae). RYNV infects Rubus species causing chlorosis of the tissue along the leaf veins, giving an unevenly distributed netted symptom in some cultivars of red and black raspberry. Recently, a strain of RYNV was sequenced from a Rubus idaeus plant in Alberta, Canada, exhibiting such symptoms. The viral genome contained seven open reading frames (ORFs) with five of them in the sense-strand, including a large polyprotein. Here we describe a graft-transmissible strain of RYNV from Europe infecting cultivar ‘Baumforth’s Seedling A’ (named RYNV-BS), which was sequenced using rolling circle amplification, enzymatic digestion, cloning and primer walking, and it was resequenced at a 5X coverage. This sequence was then compared with the RYNV-Ca genome and significant differences were observed. Genomic analysis identified differences in the arrangement of coding regions, promoter elements, and presence of motifs. The genomic organization of RYNV-BS consisted of five ORFs (four ORFs in the sense-strand and one ORF in the antisense-strand). ORFs 1, 2, and 3 showed a high degree of homology to RYNV-Ca, while ORFs 4 and 6 of RYNV-BS were quite distinct. Also, the predicted ORFs 5 and 7 in the RYNV-Ca were absent in the RYNV-BS sequence. These differences may account for the lack of aphid transmissibility of RYNV-BS.

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References

  1. R. Stace-Smith, A.T. Jones, USDA Agriculture Handbook No. 631 (USDA, Washington, 1987), p. 175

    Google Scholar 

  2. R. Stace-Smith, Can. J. Bot. 33, 267–274 (1955)

    Google Scholar 

  3. W.J. McGavin, S.A. MacFarlane, Ann. Appl. Biol. 156, 439–448 (2010)

    Article  CAS  Google Scholar 

  4. A.T. Jones, W.J. McGavin, A.D.W. Geering, B.E.L. Lockhart, Ann. Appl. Biol. 141, 1–10 (2002)

    Article  CAS  Google Scholar 

  5. M.L. Kalischuk, A.F. Fusaro, P.M. Waterhouse, H.R. Pappu, L.M. Kawchuk, Virus Res. 178(2), 306–313 (2013)

    Article  CAS  PubMed  Google Scholar 

  6. R. Hull, S.N. Covey, Virus Genes 11(2), 105–118 (1996)

    Google Scholar 

  7. D.F. Quito-Avila, D. Lightle, J. Lee, R.R. Martin, Phytopathology 102(5), 547–553 (2012)

    Article  CAS  PubMed  Google Scholar 

  8. A.T. Jones, I.M. Robert, A.F. Murrant, Ann. Appl. Biol. 77, 283–288 (1974)

    Article  Google Scholar 

  9. A.G. Laney, M. Hassan, I.E. Tzanetakis, Phytopathology 102, 1182–1189 (2012)

    Article  CAS  PubMed  Google Scholar 

  10. D.M. Sether, M.J. Melzer, W.B. Borth, J.S. Hu, Plant Dis. 96, 1798–1804 (2012)

    Article  CAS  Google Scholar 

  11. B.E.L. Lockhart, Phytopathology 80, 127–131 (1990)

    Article  CAS  Google Scholar 

  12. S.L. Medberry, B.E.L. Lockhart, N.E. Olszewski, Nucleic Acids Res. 18, 5505–5513 (1990)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  13. F.B. Dean, J.R. Nelson, T.L. Giesler, R.S. Lasken, Genome Res. 11, 1095–1099 (2001)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  14. P.M. Lizardi, X. Huang, Z. Zhu, P. Bray-Ward, D.C. Thomas, D.C. Ward, Nat. Genet. 19(3), 225–232 (1998)

    Article  CAS  PubMed  Google Scholar 

  15. M. Kearse, R. Moir, A. Wilson, S. Stones-Havas, M. Cheung, S. Sturrock, S. Buxton, A. Cooper, S. Markowitz, C. Duran, T. Thierer, B. Ashton, P. Meintjes, Bioinformatics 28(12), 1647–1649 (2012)

    Article  PubMed Central  PubMed  Google Scholar 

  16. S.F. Altschul, W. Gish, W. Miller, E.W. Myers, D.J. Lipman, J. Mol. Biol. 215, 403–410 (1990)

    Article  CAS  PubMed  Google Scholar 

  17. W. Gish, D.J. States, Nat. Genet. 3, 266–272 (1993)

    Article  CAS  PubMed  Google Scholar 

  18. A. Marchler-Bauer, S.H. Bryant, Nucleic Acids Res. 32(W), 327–331 (2004)

    Article  Google Scholar 

  19. K. Higo, Y. Ugawa, M. Iwamoto, T. Korenaga, Nucleic Acids Res. 27(1), 297–300 (1999)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  20. M.A. Larkin, G. Blackshields, N.P. Brown, R. Chenna, P.A. McGettigan, H. McWilliam, F. Valentin, I.M. Wallace, A. Wilm, R. Lopez, J.D. Thompson, T.J. Gibson, D.G. Higgins, Bioinformatics (2007). doi:10.1093/bioinformatics/btm404

    PubMed  Google Scholar 

  21. A. James, R.J. Geijskes, J.L. Dale, R.M. Harding, Plant Dis. 95(1), 57–62 (2011)

    Article  CAS  Google Scholar 

  22. D. Xu, R. Mock, G. Kinard, Virus Genes 43, 130–137 (2011)

    Article  CAS  PubMed  Google Scholar 

  23. W.P. Maddison, D.R. Maddison, Mesquite: a modular system for evolutionary analysis. (Version 0.98, 2001) http://mesquiteproject.org

  24. S. Katoh, Mol. Biol. Evol. 30, 772–780 (2013)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  25. J.P. Huelsenbeck, F. Ronquist, Bioinformatics 17, 754–755 (2001)

    Article  CAS  PubMed  Google Scholar 

  26. Y. Xiong, T.H. Eickbush, EMBO J. 9(10), 3353 (1990)

    PubMed Central  CAS  PubMed  Google Scholar 

  27. J. Zhou, R.L. Bean, V.M. Vogt, M. Summers, J. Mol. Biol. 365(2), 453–467 (2007)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  28. E. Lam, N.H. Chua, Plant Cell Online 1(12), 1147–1156 (1989)

    Article  CAS  Google Scholar 

  29. S.L. Medberry, B.E.L. Lockhart, N.E. Olszewski, Plant Cell 4, 185–192 (1992)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  30. I. Schmidt, S. Blanc, P. Esperandieu, G. Kuhl, G. Devauchelle, C. Louis, M. Cerutti, Proc. Natl. Acad. Sci. 91, 8885–8889 (1994)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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Acknowledgments

We thank Joseph Postman from the National Clonal Germplasm Repository-USDA (Corvallis, Oregon) for providing information and plant material used during this study. Also, we thank Javier F Tabima (Oregon State University) for his advice on phylogenetic analysis. The work presented here was partially funded with Grants from the Northwest Center for Small Fruits Research, the Washington Red Raspberry Commission, the Oregon Raspberry and Blackberry Commission, and USDA-NIFA-SCRI (2009-51181-06022). Diaz-Lara did most of the work reported here, with the other authors contributed equally to the work.

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Authors and Affiliations

  1. Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA

    Alfredo Diaz-Lara

  2. Horticultural Crops Research Laboratory, USDA-ARS, Corvallis, OR, 97330, USA

    Nola J. Mosier, Karen E. Keller & Robert R. Martin

Authors
  1. Alfredo Diaz-Lara
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  2. Nola J. Mosier
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  3. Karen E. Keller
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  4. Robert R. Martin
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Correspondence to Alfredo Diaz-Lara.

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Diaz-Lara, A., Mosier, N.J., Keller, K.E. et al. A variant of Rubus yellow net virus with altered genomic organization. Virus Genes 50, 104–110 (2015). https://doi.org/10.1007/s11262-014-1149-6

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  • DOI: https://doi.org/10.1007/s11262-014-1149-6

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