Skip to main content

Complete genome sequence and organization of a novel virus from the rice false smut fungus Ustilaginoidea virens

Virus Genes volume 48, pages 329–333 (2014)Cite this article

Abstract

In this study, three dsRNA segments from the rice false smut fungus Ustilaginoidea virens, the causal agent of a serious disease in rice, with molecular size ranging from 1.3 to 5 Kb, were isolated and named as dsRNA-L, dsRNA-M, and dsRNA-S. The complete nucleotide sequences of dsRNA-M and dsRNA-S were determined and analyzed. The dsRNA-M putatively encodes an RNA-dependent RNA polymerase, which is similar to that of the partitiviruses in the family Partitiviridae. Although the protein encoded by dsRNA-S showed less similarity to the typical coat protein of the virus in the family Partitiviridae, the structural analysis results indicated that the dsRNA-S might function as the capsid protein. We propose that the virus is Ustilaginoidea virens partitivirus 2-Uv0901, a new member, but distantly related to the newly proposed genus Gammapartitivirus with a distinct sequence pattern of capsid protein.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

43,34 €

Price includes VAT (Finland)
Tax calculation will be finalised during checkout.

Fig. 1
Fig. 2
Fig. 3

References

  1. D.L. Nuss, Hypovirulence: mycoviruses at the fungal-plant interface. Nat. Rev. Microbiol. 3, 632–642 (2005)

    CAS  PubMed  Article  Google Scholar 

  2. S. Chiba, L. Salaipeth, Y.H. Lin, A. Sasaki, S. Kanematsu, N. Suzuki, A novel bipartite double-stranded RNA mycovirus from the white root rot fungus Rosellinia necatrix: molecular and biological biological characterization, taxonomic considerations, and potential for biological control. J. Virol. 83, 12801–12812 (2009)

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  3. N. Aoki, H. Moriyama, M. Kodama, T. Arie, T. Teraoka, T. Fukuhara, A novel mycovirus associated with four double stranded RNAs affects host fungal growth in Alternaria alternata. Virus Res. 140, 179–187 (2009)

    CAS  PubMed  Article  Google Scholar 

  4. L.Y. Zhang, Y.P. Fu, J.T. Xie, D.H. Jiang, G.Q. Li, X.H. Yi, A novel virus that infecting hypovirulent strain XG36-1 of plant fungal pathogen Sclerotinia sclerotiorum. Virol. J. 6, 96 (2009)

    PubMed Central  PubMed  Article  Google Scholar 

  5. J.T. Xie, X.Q. Xiao, Y.P. Fu, H.Q. Liu, J.S. Cheng, S.A. Ghabrial, G.Q. Li, D.H. Jiang, A novel mycovirus closely related to hypoviruses that infects the plant pathogenic fungus Sclerotinia sclerotiorum. Virology 418, 49–56 (2011)

    CAS  PubMed  Article  Google Scholar 

  6. H.Q. Liu, Y.P. Fu, D.H. Jiang, G.Q. Li, J. Xie, Y.L. Peng, X.H. Yi, S.A. Ghabrial, A novel mycovirus that is related to the human pathogen hepatitis E virus and Rubi-like viruses. J. Virol. 83, 1981–1991 (2009)

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  7. N. Herrero, E. Duenas, E.Q. Moraga, I. Zabalgogeazcoa, Prevalence and diversity of viruses in the entomopathogenic fungus Beauveria bassiana. Appl. Environ. Microbiol. 78, 8523–8530 (2012)

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  8. M.C. Cooke, Some extra-European fungi. Grevillea 7, 13–15 (1978)

    Google Scholar 

  9. T.T. Zhang, Y.H. Jiang, J.B. Huang, W.B. Dong, Complete genome sequence of a putative novel victorivirus from Ustilaginoidea virens. Arch. Virol. 158, 1403–1406 (2013)

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  10. T.T. Zhang, Y.H. Jiang, J.B. Huang, W.B. Dong, Genomic organization of a novel partitivirus from the phytopathogenic fungus Ustilaginoidea virens. Arch. Virol. 158, 2415–2419 (2013)

    CAS  PubMed  Article  Google Scholar 

  11. T.J. Morris, J.A. Dodds, Isolation and analysis of double stranded RNA from virus-infected plant and fungal tissue. Phytopathology 69, 854–858 (1979)

    CAS  Article  Google Scholar 

  12. A.C. Potgieter, A.D Steele, A.A. vanDijk, Cloning of complete genome sets of six dsRNA viruses using an improved cloning method for large dsRNA genes. J. Gen. Virol. 83, 2215–2223 (2002)

    CAS  PubMed  Google Scholar 

  13. L. Chen, J.S. Chen, L. Liu, X. Yu, S. Yu, T.Z. Fu, W.H. Liu, Complete nucleotide sequences and genome characterization of double-stranded RNA 1 and RNA 2 in the Raphanus sativus-root cv. Yidianhong [corrected]. Arch. Virol. 151, 849–859 (2006)

    CAS  PubMed  Article  Google Scholar 

  14. M.A. Larkin, G. Blackshields, N.P. Brown, R. Chenna, P.A. McGettigan, H. McWilliam, D.G. Higgins, Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947–2948 (2007)

    CAS  PubMed  Article  Google Scholar 

  15. K. Tamura, J. Dudley, M. Nei, S. Kumar, MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596–1599 (2007)

    CAS  PubMed  Article  Google Scholar 

  16. S. Chiba, H. Kondo, A. Tani, D. Saisho, W. Sakamoto, S. Kanematsu, N. Suzuki, Widespread endogenization of genome sequences of non-retroviral RNA viruses into plant genomes. PLoS Pathog. 7(7), e1002146 (2011)

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  17. R.S.D. Blawid, E. Maiss, Alphacryptovirus and Betacryptovirus, Encyclopedia of Virology, 3rd edn. (Elsevier, Oxford, 2008), pp. 98–104

    Chapter  Google Scholar 

  18. L.J. McGuffin, K. Bryson, D.T. Jones, The PSIPRED protein structure prediction server. Bioinformatics 16, 404–405 (2000)

    CAS  PubMed  Article  Google Scholar 

  19. J. Söding, Protein homology detection by HMM–HMM comparison. Bioinformatics 21, 951–960 (2005)

    PubMed  Article  Google Scholar 

  20. L.A. Kelley, M.J. Sternberg, Protein structure prediction on the Web: a case study using the Phyre server. Nat. Protoc. 4, 363–371 (2009)

    CAS  PubMed  Article  Google Scholar 

  21. S.A. Ghabrial, M.L. Nibert, E. Maiss, T. Lesker, T.S. Baker, Y.J. Tao, Family Partitiviridae, in Virus taxonomy: ninth report of the international committee on taxonomy of viruses, ed. by A.M.Q. King, M.J. Adams, E.B. Carstens, E.J. Lefkowitz (Elsevier, San Diego, 2011), pp. 523–534

    Google Scholar 

  22. W. Liu, G. Duns, J. Chen, Genomic characterization of a novel partitivirus infecting Aspergillus ochraceus. Virus Genes 37, 322–327 (2008)

    CAS  PubMed  Article  Google Scholar 

  23. M.F. Bhatti, E.M. Bignell, RH.A. Coutts, Complete nucleotide sequences of two dsRNAs associated with a new partitivirus infecting Aspergillus fumigatus. Arch. Virol. 156, 1677–1680 (2011)

    CAS  PubMed  Article  Google Scholar 

Download references

Acknowledgments

This study is funded by the National Key Technology R&D Program of China (2012BAD15B04-1) and the Special Fund for Agro-Scientific Research in the Public Interest of China (200903039). The authors thank Xiao-Wen Cheng of the Department of Mycology, Miami University for his assistance and valuable suggestions.

Author information

Affiliations

  1. Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, China

    Jie Zhong, Jun-Zi Zhu, Xiang-Hua Lei, Dan Chen, Hong-Jian Zhu & Bi-Da Gao

Authors
  1. Jie Zhong
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jun-Zi Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xiang-Hua Lei
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Dan Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hong-Jian Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Bi-Da Gao
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Bi-Da Gao.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Zhong, J., Zhu, JZ., Lei, XH. et al. Complete genome sequence and organization of a novel virus from the rice false smut fungus Ustilaginoidea virens . Virus Genes 48, 329–333 (2014). https://doi.org/10.1007/s11262-013-1022-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11262-013-1022-z

Keywords

  • dsRNA
  • Partitiviridae
  • Ustilaginoidea virens
  • Capsid protein