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Rubus canadensis virus 1, a novel betaflexivirus identified in blackberry

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Abstract

Flexuous filaments, resembling flexivirus virions, were observed in partially purified blackberry preparations showing mild virus-like symptoms. Further tests revealed the presence of a novel betaflexivirus that is phylogenetically related to foveaviruses. The putative virus-encoded proteins shared limited similarity with orthologs of known members of the genus, indicating that the virus, provisionally named Rubus canadensis virus 1 (RuCV-1), represents a novel member of the taxon. Results of a survey in several U.S. states suggest that RuCV-1 is not widespread in the blackberry germplasm.

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References

  1. Adams MJ, Candresse T, Hammond J, Kreuze JF, Martelli GP, Namba S, Pearson MN, Ryu KH, Saldarelli P, Yoshikawa N (2011) Family Betaflexiviridae. In: King A, Adams MJ, Carstens EB, Lefkowitz E (eds) Virus taxonomy. Ninth report of the International Committee on taxonomy of viruses. Elsevier, Amsterdam, pp 920–941

    Google Scholar 

  2. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 25:3389–3402

    Article  PubMed  CAS  Google Scholar 

  3. Dovas CI, Katis NI (2003) A spot nested RT-PCR method for the simultaneous detection of members of the Vitivirus and Foveavirus genera in grapevine. J Virol Methods 107:99–106

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  5. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunesekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A (2010) The Pfam protein families database. Nucl Acids Res Database Issue 38:D211–D222

    Article  CAS  Google Scholar 

  6. Halgren A, Tzanetakis IE, Martin RR (2007) Identification, characterization and detection of Black raspberry necrosis virus. Phytopathology 97:44–50

    Article  PubMed  CAS  Google Scholar 

  7. Krogh A, Larsson B, von Heijne B, Sonnhammer ELL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305:567–580

    Article  PubMed  CAS  Google Scholar 

  8. Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH (2011) CDD: a conserved domain database for the functional annotation of proteins. Nucl Acids Res 39:D225–D229

    Article  PubMed  Google Scholar 

  9. Martelli GP, Adams MJ, Kreuze JF, Dolja VV (2007) Family Flexiviridae: a case study in virion and genome plasticity. Ann Rev Phytopathol 45:73–100

    Article  CAS  Google Scholar 

  10. Martin RR, MacFarlaine S, Sabanadzovic S, Quito D, Poudel B, Tzanetakis IE (2012) Viruses and virus diseases of Rubus. Plant Dis. doi:10.1094/PDIS-04-12-0362-FE

  11. Sabanadzovic S, Abou Ghanem-Sabanadzovic N (2009) Identification and molecular characterization of a marafivirus in Rubus spp. Arch Virol 154:1729–1735

    Article  PubMed  CAS  Google Scholar 

  12. Sabanadzovic S, Abou Ghanem-Sabanadzovic N, Tzanetakis IE (2011) Blackberry virus E: an unusual flexivirus. Arch Virol 156:1665–1669

    Article  PubMed  CAS  Google Scholar 

  13. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    PubMed  CAS  Google Scholar 

  14. Savino V, Sabanadzovic S, Scarito G, Laviola C, Martelli GP (1996) Due giallumi dell’olivo di possible origine virale in Sicilia. Informatore Fitopatologico 5:55–59

    Google Scholar 

  15. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  17. Tzanetakis IE, Susaimuthu J, Gergerich RC, Martin RR (2006) Nucleotide sequence of blackberry yellow vein associated virus, a novel member of the Closteroviridae. Virus Res 116:196–200

    Article  PubMed  CAS  Google Scholar 

  18. Tzanetakis IE, Halgren AB, Mosier N, Martin RR (2007) Identification and characterization of Raspberry mottle virus, a novel member of the Closteroviridae. Virus Res 127:26–33

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

Deep thanks to A. Lawrence for the help in electron microscopy. This work was partially supported by funds from Discover Life in America Inc., NIFA-SCRI grant 2009-51181-06022, USDA-APHIS-NCPN 10-8100-1572-CA and by the Special Research Initiative Program of the Mississippi Agricultural and Forestry Experiment Station (MAFES), Mississippi State University. This article was approved for publication as Journal Article of the Mississippi Agricultural and Forestry Experiment Station, Mississippi State University.

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Authors and Affiliations

  1. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS, 39762, USA

    Nina Abou Ghanem-Sabanadzovic

  2. Division of Agriculture, Department of Plant Pathology and Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, USA

    Ioannis E. Tzanetakis

  3. Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, 39762, USA

    Sead Sabanadzovic

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  1. Nina Abou Ghanem-Sabanadzovic
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  2. Ioannis E. Tzanetakis
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  3. Sead Sabanadzovic
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Correspondence to Sead Sabanadzovic.

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Abou Ghanem-Sabanadzovic, N., Tzanetakis, I.E. & Sabanadzovic, S. Rubus canadensis virus 1, a novel betaflexivirus identified in blackberry. Arch Virol 158, 445–449 (2013). https://doi.org/10.1007/s00705-012-1484-7

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  • DOI: https://doi.org/10.1007/s00705-012-1484-7

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