Skip to main content
SpringerLink
Log in

Nucleotide sequence and genomic organization of a newly identified member of the genus Carmovirus, soybean yellow mottle mosaic virus, from soybean

  • Brief Report
  • Published:
Archives of Virology Aims and scope Submit manuscript

Abstract

The viral genome of soybean yellow mottle mosaic virus (SYMMV) from infected soybean (Glycine max) in Korea was cloned and sequenced. The complete monopartite single-stranded RNA genome of SYMMV consists of 4009 base pairs with six putative open reading frames and includes 5′- and 3′-untranslated regions of 39 and 229 nucleotides, respectively. The nucleotide and coat protein sequences of SYMMV share the highest sequence identity with those of cowpea mottle virus. Based on its genomic organization, its predicted amino acid sequence, and its phylogenetic relatedness to known carmoviruses, we report that SYMMV is a new member of the genus Carmovirus in the family Tombusviridae.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

References

  1. Argos P (1988) A sequence motif in many polymerases. Nucleic Acids Res 16:9909–9916

    Article  PubMed  CAS  Google Scholar 

  2. Boonham N, Henry CM, Wood KR (1998) The characterization of a subgenomic RNA and in vitro translation products of Oat chlorotic stunt virus. Virus Genes 16:141–145

    Article  PubMed  CAS  Google Scholar 

  3. Carrington JC, Heaton LA, Zuidema D, Hillman BI, Morris TJ (1989) The genome structure of Turnip crinkle virus. Virology 170:219–226

    Article  PubMed  CAS  Google Scholar 

  4. Ciuffreda P, Rubino L, Russo M (1998) Molecular cloning and complete nucleotide sequence of Galinsoga mosaic virus genomic RNA. Arch Virol 143:173–180

    Article  PubMed  CAS  Google Scholar 

  5. Cohen Y, Qu F, Gisel A, Morris TJ, Zambryski PC (2000) Nuclear localization of Turnip crinkle virus movement protein p8. Virology 273:276–285

    Article  PubMed  CAS  Google Scholar 

  6. Demski JW, Kuhn CW, Sinclair JB (1989) Virus diseases. In: Sinclair JB, Backman PA (eds) Compendium of soybean disease, 3rd edn. APS Press, St Paul, pp 50–51

    Google Scholar 

  7. Diez J, Marcos JF, Pallas V (1998) Carmovirus isolation and RNA extraction. In: Foster GD, Taylor SC (eds) Methods in molecular biology, vol 81. Plant virology protocols—from virus isolation to transgenic resistance. Humana Press, Totowa, pp 211–217

    Google Scholar 

  8. Guilley H, Carrington JC, Balàzs E, Jonard G, Richards K, Morris TJ (1985) Nucleotide sequence and genome organization of Carnation mottle virus RNA. Nucleic Acids Res 13:6663–6677

    Article  PubMed  CAS  Google Scholar 

  9. Heame PQ, Knorr DA, Hillman BI, Morris TJ (1990) The complete genome structure and synthesis of infectious RNA from clones of Tomato bushy stunt virus. Virology 177:141–151

    Article  Google Scholar 

  10. Huang M, Koh DCY, Weng LJ, Chang ML, Yap YK, Zhang L, Wong SM (2000) Complete nucleotide sequence and genome organization of Hibiscus chlorotic ringspot virus, a new member of the genus Carmovirus: evidence for the presence and expression of two novel open reading frames. J Virol 74:3149–3155

    Article  PubMed  CAS  Google Scholar 

  11. Navarro JA, Genoves A, Climent J, Sauri A, Martinez-Gil L, Mingarro I, Pallas V (2006) RNA-binding properties and membrane insertion of Melon necrotic spot virus (MNSV) double gene block movement proteins. Virology 356:57–67

    Article  PubMed  CAS  Google Scholar 

  12. Nutter RC, Scheets K, Panganiban LC, Lommel SA (1989) The complete nucleotide sequence of the Maize chlorotic mottle virus genome. Nucleic Acids Res 17:3163–3177

    Article  PubMed  CAS  Google Scholar 

  13. Page RDM (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358

    PubMed  CAS  Google Scholar 

  14. Rico P, Hernandez C (2004) Complete nucleotide sequence and genome organization of Pelargonium flower break virus. Arch Virol 149:641–651

    Article  PubMed  CAS  Google Scholar 

  15. Riviere CJ, Rochon KM (1990) Nucleotide sequence and genomic organization of Melon necrotic spot virus. J Gen Virol 71:1887–1896

    Article  PubMed  CAS  Google Scholar 

  16. Rochon DM, Tremaine JH (1989) Complete nucleotide sequence of the Cucumber necrosis virus genome. Virology 169:251–259

    Article  PubMed  CAS  Google Scholar 

  17. Rubino L, Russo M (1997) Molecular analysis of the Pothos latent virus genome. J Gen Virol 78:1219–1226

    PubMed  CAS  Google Scholar 

  18. Ryabov EV, Generozov EV, Kendall TL, Lommel SA, Zavriev SK (1994) Nucleotide sequence of Carnation ringspot dianthovirus RNA-1. J Gen Virol 75:243–247

    Article  PubMed  CAS  Google Scholar 

  19. Skotnicki ML, Mackenzie AM, Torroen M, Gibbs AJ (1993) The genomic sequence of Cardamine chlorotic fleck carmovirus. J Gen Virol 74:1933–1937

    Article  PubMed  CAS  Google Scholar 

  20. Suzuki S, Hase S, Takahashi H, Ikegami M (2002) The genome organization of Pea stem necrosis virus and its assignment to the genus Carmovirus. Intervirology 45(3):160–163

    Article  PubMed  CAS  Google Scholar 

  21. Takemoto Y, Kanehira T, Shinohara M, Yamashita S, Hibi T (2000) The nucleotide sequence and genome organization of Japanese iris necrotic ring virus, a nep species in the genus Carmovirus. Arch Virol 145:651–657

    Article  PubMed  CAS  Google Scholar 

  22. Turina M, Maruoka M, Monis J, Jackson AO, Scholthof KG (1998) Nucleotide sequence and infectivity of a full-Length cDNA clone of Panicum mosaic virus. Virology 241:141–155

    Article  PubMed  CAS  Google Scholar 

  23. Wang J, Simon AE (1997) Analysis of the two subgenomic RNA promoters for Turnip crinkle virus in vivo and in vitro. Virology 232:174–186

    Article  PubMed  CAS  Google Scholar 

  24. Weng Z, Xiong Z (1997) Genome organization and gene expression of Saguaro cactus carmovirus. J Gen Virol 78:525–534

    PubMed  CAS  Google Scholar 

  25. White KA, Skuzeski JM, Li W, Wei N, Morris TJ (1982) Immunodetection, expression strategy and complementation of turnip crinkle virus p28 and p88 replication components. Virology 211:525–534

    Article  Google Scholar 

  26. Xi D, Li J, Han C, Li D, Yu J, Zhou X (2008) Complete nucleotide sequence of a new strain of Tobacco necrosis virus A infecting soybean in China and infectivity of its full-length cDNA clone. Virus Genes 36:259–266

    Article  PubMed  CAS  Google Scholar 

  27. You XJ, Kim JW, Stuart GW, Bozarth RF (1995) The nucleotide sequence of Cowpea mottle virus and its assignment to the genus Carmovirus. J Gen Virol 76:2841–2845

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by the Crop Functional Genomics Center of the 21st Century Frontier R&D Program (grant no. CG2132), which was funded by the Ministry of Education, Science and Technology of the Republic of Korea, by the BioGreen21 program (grant no. 20080701034002), funded by the Rural Development Administration, Republic of Korea, and by 2009 Post Doctoral Course Program of National Academy of Agricultural Science, RDA, Republic of Korea.

Author information

Authors and Affiliations

  1. Agricultural Microbiology Division, National Academy of Agricultural Science, RDA, Suwon, 441-707, Korea

    Moon Nam, Hong Soo Choi & Su-Heon Lee

  2. Central Post-Entry Quarantine Station, The National Plant Quarantine Service, Suwon, 443-400, Korea

    Sang Mok Kim

  3. Department of Crop Sciences, University of Illinois, USDA-ARS, Urbana, IL, 61801, USA

    Leslie L. Domier

  4. Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Korea

    Serry Koh & Jae Sun Moon

  5. Legume and Oil Crop Research Division, National Institute of Crop Science, RDA, Milyang, 627-803, Korea

    Jung Kyung Moon

  6. Department of Agricultural Biology, Chungnam National University, Daejeon, 305-764, Korea

    Hong Gi Kim

Authors
  1. Moon Nam
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sang Mok Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Leslie L. Domier
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Serry Koh
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jung Kyung Moon
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Hong Soo Choi
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Hong Gi Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Jae Sun Moon
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Su-Heon Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Jae Sun Moon or Su-Heon Lee.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Nam, M., Kim, S.M., Domier, L.L. et al. Nucleotide sequence and genomic organization of a newly identified member of the genus Carmovirus, soybean yellow mottle mosaic virus, from soybean. Arch Virol 154, 1679–1684 (2009). https://doi.org/10.1007/s00705-009-0480-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00705-009-0480-z

Keywords

Search

Navigation