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Molecular characterization of a new tymovirus from Diascia ornamental plants

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Abstract

Two tymoviruses were identified in plants of Diascia × hybrida ‘Sun Chimes™ Coral’ that exhibited chlorotic mottling and reduced growth. A strain of Nemesia ring necrosis virus (NeRNV) designated NeRNV-WA was detected in symptomatic plants; the deduced amino acid sequence is virtually identical to that of the previously reported NeRNV-Nf from Nemesia fruticosa. Sequence analysis also revealed the presence of a new tymovirus, and the entire genomic sequence of this virus was determined. The genome of 6,290 nucleotides was organized into three potential open reading frames (ORFs) typical of viruses in the genus Tymovirus. Based on sequence identity to tymovirus sequences, ORFs I to III encoded the replicase, movement protein and coat protein, respectively. Amino acid sequence identities to those of NeRNV-Nf were 84.8, 50.3 and 94.8%, respectively. The 5′-untranslated region could potentially form four hairpin structures. Secondary structure analysis of the 3′-terminus showed that the RNA can form a transfer-RNA-like structure that has an anticodon specific for histidine. Only 77.9% nucleotide identity was found when complete genomic sequences of this tymovirus from diascia and NeRNV-Nf were compared. The name Diascia yellow mottle virus (DiaYMV) is proposed for this new tymovirus.

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References

  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  3. Batten A (1986) Flowers of Southern Africa. Frandsen Publishers, Sandton

    Google Scholar 

  4. Benham S (1987) Diascia—a survey of the species in cultivation. Plantsman 9:1–17

    Google Scholar 

  5. Benson DA, Karsch-Mizrach I, Lipman DJ, Ostell J, Wheeler DL (2005) GenBank. Nucleic Acids Res 33:D34–D38

    Article  PubMed  CAS  Google Scholar 

  6. Bernal JJ, Jimenez I, Moreno M, Hord M, Rivera C, Koenig R, Rodriguez-Cerezo E (2000) Chayote mosaic virus, a new virus infecting Cucurbitaceae. Phytopathology 90:1098–1104

    Article  CAS  PubMed  Google Scholar 

  7. Bozarth CS, Weiland JJ, Dreher TW (1992) Expression of ORF-69 of Turnip yellow mosaic virus is necessary for viral spread in plants. Virology 187:124–130

    Article  PubMed  CAS  Google Scholar 

  8. Brakke MK, Van Pelt N (1970) Linear-log sucrose gradients for estimating sedimentation coefficients of plant viruses and nucleic acids. Anal Biochem 38:6–64

    Article  Google Scholar 

  9. Cabot E, Beckenback AT (1989) Simultaneous editing of multiple nucleic acid and protein sequences with XEsee. Comp Appl Bios 5:233–234

    CAS  Google Scholar 

  10. Ding S, Howe J, Keese P, Mackenzie A, Meek D, Osorio-Keese M, Skotnicki M, Srifah P, Torronen M, Gibbs A (1990) The tymobox, a sequence shared by most tymoviruses: its use in molecular studies of tymoviruses. Nucleic Acids Res 18:1181–1187

    Article  PubMed  CAS  Google Scholar 

  11. Ding S, Keese P, Gibbs A (1989) Nucleotide sequence of the Ononis yellow mosaic tymovirus genome. Virology 172:555–563

    Article  PubMed  CAS  Google Scholar 

  12. Dreher TW (1999) Functions of the 3′-untranslated regions of the positive strand RNA viral genomes. Annu Rev Phytopathol 37:151–174

    Article  PubMed  CAS  Google Scholar 

  13. Dreher TW (2004) Turnip yellow mosaic virus: transfer RNA mimicry, chloroplasts and C-rich genome. Mol Plant Path 5:367–375

    Article  CAS  Google Scholar 

  14. Dreher TW, Edwards MC, Gibbs AJ, Haenni A-L, Hammond RW, Jupin I, Koenig R, Sabanadzovic S, Abou Ghanem-Sabanadzovic N, Martelli GP (2004) Tymoviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy. Eighth report of the ICTV. Elsevier, San Diego, pp 1067–1076

    Google Scholar 

  15. Dunn DB, Hitchborn JH (1965) The use of Bentonite in the purification of plant viruses. Virology 25:171–192

    Article  PubMed  CAS  Google Scholar 

  16. Felsenstein J (2004) PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle

  17. Finn RD, Mistry J, Schuster-Böckler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer ELL, Bateman A (2006) Pfam: clans, web tools and services. Nucleic Acids Res 34:D247–D251

    Article  PubMed  CAS  Google Scholar 

  18. Gaillard C, Strauss F (1990) Ethanol precipitation of DNA with linear polyacrylamide as carrier. Nucleic Acids Res 18:378

    Article  PubMed  CAS  Google Scholar 

  19. Gibbs A (1994) Tymoviruses. In: Webster RG, Granoff A (eds) Encyclopedia of virology, vol 3. Academic Press, San Diego, pp 1500–1502

    Google Scholar 

  20. Koenig R, Barends S, Gultyaev AP, Lesemann D-E, Vetten HJ, Loss S, Pleij CWA (2005) Nemesia ring necrosis virus, a new virus with genomic RNA having a histidylatable tobamovirus-like 3′end. J Gen Virol 86:1827–1833

    Article  PubMed  CAS  Google Scholar 

  21. Koenig R, Pleij CWA, Lesemann D-E, Loss S, Vetten HJ (2005) Molecular characterization of isolates of Anagyris vein yellow virus, Plantago mottle virus and Scrophularia mottle virus—comparison of various approaches for tymovirus classification. Arch Virol 150:2325–2338

    Article  PubMed  CAS  Google Scholar 

  22. Lin H, Rubio L, Smythe A, Jiminez M, Falk BW (2003) Genetic diversity and biological variation among California isolates of Cucumber mosaic virus. J Gen Virol 84:249–258

    Article  PubMed  CAS  Google Scholar 

  23. Marchler-Bauer A, Anderson JB, Derbyshire MK, DeWeese-Scott C, Gonzales NR, Gwadz M, Hao L, He S, Hurwitz DI, Jackson JD, Ke Z, Krylov D, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Thanki N, Yamashita RA, Yin JJ, Zhang D, Bryant SH (2007) CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res 35:D237–D240

    Article  PubMed  CAS  Google Scholar 

  24. Martelli GP, Sabanadzovic S, Abou Ghanem-Sabanadzovic N, Edwards MC, Dreher T (2002) The family Tymoviridae. Arch Virol 147:1837–1846

    Article  PubMed  CAS  Google Scholar 

  25. Mathews DM, Dodds JA (2006) First report of Nemesia ring necrosis virus in North America in Ornamental plants from California. Plant Dis 60:1263

    Article  Google Scholar 

  26. Morch MD, Boyer JC, Haenni AL (1988) Overlapping open reading frames revealed by complete nucleotide sequencing of turnip yellow mosaic virus genomic RNA. Nucleic Acids Res 16:6157–6174

    Article  PubMed  CAS  Google Scholar 

  27. Morris TJ, Dodds JA (1979) Isolation and analysis of double-stranded RNA from virus infected and fungal tissue. Phytopathology 69:854–858

    Article  CAS  Google Scholar 

  28. Mushegian AR, Koonin EV (1993) Cell-to-cell movement of plant viruses: Insights from amino acid sequence comparisons of movement proteins and from analogies with transport systems. Arch Virol 133:239–257

    Article  PubMed  CAS  Google Scholar 

  29. Ranjith-Kumar CT, Gopinath K, Jacob ANK, Srividhya V, Elango P, Savithri HS (1998) Genomic sequence of physalis mottle virus and its evolutionary relationship with other tymoviruses. Arch Virol 143:1489–1500

    Article  PubMed  CAS  Google Scholar 

  30. Rudinger-Thirion J, Olsthoorn RCL, Giegé R, Barends S (2006) Idiosyncratic behaviour of tRNA-like structures in translation of plant viral RNA genomes. J Mol Biol 355:873–878

    Article  PubMed  CAS  Google Scholar 

  31. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Plainview

    Google Scholar 

  32. Schirawski J, Voyatzakis A, Zaccomer B, Bernardi F, Haenni AL (2000) Identification and functional analysis of the Turnip yellow mosaic tymovirus subgenomic promoter. J Virol 74:11073–11080

    Article  PubMed  CAS  Google Scholar 

  33. Skelton AL, Jarvis B, Koenig R, Lesemann D-E, Mumford RA (2004) Isolation and identification of a novel tymovirus from nemesia in the UK. Plant Path 53:798

    Article  Google Scholar 

  34. Skotnicki ML, Ding SW, Mackenzie AM, Gibbs AJ (1993) Infectious eggplant mosaic tymovirus and ononis yellow mosaic virus tymovirus from cDNA. Arch Virol 131:47–60

    Article  PubMed  CAS  Google Scholar 

  35. Skotnicki ML, Mackenzie AM, Gibbs A (1996) Genetic variation in populations of kennedya yellow mosaic tymovirus. Arch Virol 141:99–110

    Article  PubMed  CAS  Google Scholar 

  36. 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 

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Acknowledgments

We thank A. Karasev and R. Larsen for reviewing this manuscript. This is contribution PPNS #0479 of the Department of Plant Pathology, College of Agricultural, Human, and Natural Resource Sciences Agricultural Research Center Project No. WNP00290, Washington State University, Pullman, WA, 99164–6240, USA. The financial support from the Botswana College of Agriculture in partnership with Washington State University is gratefully acknowledged.

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Author notes

  1. A. T. Segwagwe

    Present address: Department of Crop Science and Production, Botswana College of Agriculture, Gaborone, Botswana

Authors and Affiliations

  1. Department of Plant Pathology, Washington State University, IAREC, 24106 North Bunn Road, Prosser, WA, 99350, USA

    A. T. Segwagwe & K. C. Eastwell

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

    M. L. Putnam

  3. Department of Plant Pathology, Washington State University, Pullman, WA, USA

    K. L. Druffel & H. R. Pappu

Authors
  1. A. T. Segwagwe
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  2. M. L. Putnam
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  3. K. L. Druffel
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  4. H. R. Pappu
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  5. K. C. Eastwell
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Corresponding author

Correspondence to K. C. Eastwell.

Additional information

Sequences reported here are available in GenBank as DiaYMV: accession number EU684141 and NeRNV-WA: accession number EU684142.

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Segwagwe, A.T., Putnam, M.L., Druffel, K.L. et al. Molecular characterization of a new tymovirus from Diascia ornamental plants. Arch Virol 153, 1495–1503 (2008). https://doi.org/10.1007/s00705-008-0149-z

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  • DOI: https://doi.org/10.1007/s00705-008-0149-z

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