Skip to main content
SpringerLink
Log in

Genetic diversity and phylogenetic analysis of Australian Grapevine Viroid (AGVd) isolated from different grapevines in China

  • Published:
Virus Genes Aims and scope Submit manuscript

Abstract

Australian grapevine viroid (AGVd) is found in only three countries in the world. Here, the genetic diversity and phylogenetic relationships of AGVd isolates from three different grape varieties (Thomson Seedless, Jingchuan and Zaoyu) in China were studied. A hundred of independent cDNA clones from each of the three isolates, in total of 300, were sequenced. We identified 29 sequence variants including two predominant ones in Thomson Seedless, and 48 each including a unique predominant one in Jingchuan and Zaoyu. In silico structure analysis revealed that base changes were clustered in the left terminal domain of the predicted secondary structure in all three isolates. Further, these changes were shown to affect their secondary structures to varying degrees. Genetic diversity and phylogenetic analysis of four predominant sequence variants from this study, plus four others from Australia and Tunisia, revealed obvious regional disparity and variety-specificity in AGVd.

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
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  1. C.M. Fauquet, M.A. Mayo, J. Maniloff, U. Desselberger, L.A. Ball (eds.), Virus Taxonomy. Eighth Report of the International Committee on Taxonomy of Viruses (Elsevier, San Diego, 2005), pp. 1145–1160

  2. M.A. Rezaian, A.M. Koltunow, L.R. Krake, J. Gen. Virol. 69, 413–422 (1988). doi:https://doi.org/10.1099/0022-1317-69-2-413

    Article  CAS  PubMed Central  Google Scholar 

  3. J.A. Szychowski, A.C. Goheen, J.S. Semancik, J. Am. Enol. 39, 213–216 (1988)

    Google Scholar 

  4. A.M. Koltunow, M.A. Rezaian, Intervirology 30, 194–201 (1989)

    Article  CAS  PubMed Central  Google Scholar 

  5. M.A. Rezaian, Nucleic Acids Res. 18, 1813–1818 (1990). doi:https://doi.org/10.1093/nar/18.7.1813

    Article  CAS  PubMed Central  Google Scholar 

  6. A. Elleuch, H. Fakhfakh, M. Pelchat, P. Landry, M. Marrakchi, J.P. Perreault, Eur. J. Plant Pathol. 108, 815–820 (2002). doi:https://doi.org/10.1023/A:1020855405948

    Article  CAS  Google Scholar 

  7. S.F. Li, R. Guo, M. Tsuji, T. Sano, Plant. Pathol. 55, 564–564 (2006). doi:https://doi.org/10.1111/j.1365-3059.2006.01424.x

    Article  Google Scholar 

  8. S.F. Li, S. Onodera, T. Sano, K. Yoshida, G.P. Wang, E. Shikata, Ann. Phytopathological Soc. Jpn. 61, 9 (1995)

    Article  Google Scholar 

  9. A. Iijima, Shokubutsu Boeki 44, 130–132 (1990)

    Google Scholar 

  10. E.J.J.H. Domingo, Annu. Rev. Microbiol. 51, 151–178 (1997). doi:https://doi.org/10.1146/annurev.micro.51.1.151

    Article  CAS  PubMed Central  Google Scholar 

  11. C. Domingo, V. Conejero, P. Vera, Plant Mol. Biol. 24, 725–732 (1994). doi:https://doi.org/10.1007/BF00029854

    Article  CAS  PubMed Central  Google Scholar 

  12. M. Gandia, L. Rubio, A. Palacio, N. Duran-Vila, Arch. Virol. 150, 1945–1957 (2005). doi:https://doi.org/10.1007/s00705-005-0570-5

    Article  CAS  Google Scholar 

  13. S. Ambros, J.C. Desvignes, G. Llacer, R. Flores, J. Gen. Virol. 76, 2625–2629 (1995). doi:https://doi.org/10.1099/0022-1317-76-10-2625

    Article  CAS  PubMed Central  Google Scholar 

  14. S. Ambros, C. Hernandez, J.C. Desvignes, R. Flores, J. Virol. 72, 7397–7406 (1998)

    CAS  PubMed  PubMed Central  Google Scholar 

  15. A. Palacio-Bielsa, J. Romero-Durban, N. Duran-Vila, Arch. Virol. 149, 537–552 (2004). doi:https://doi.org/10.1007/s00705-003-0223-5

    Article  CAS  Google Scholar 

  16. X. Foissac, N. Duran-Vila, Arch. Virol. 145, 1975–1983 (2000). doi:https://doi.org/10.1007/s007050070070

    Article  CAS  Google Scholar 

  17. H. Polivka, U. Staub, H.J. Gross, J. Gen. Virol. 77, 155–161 (1996). doi:https://doi.org/10.1099/0022-1317-77-1-155

    Article  CAS  Google Scholar 

  18. T. Sano, R. Mimura, K. Ohshima, Virus Genes 22, 53 (2001). doi:https://doi.org/10.1023/A:1008182302704

    Article  CAS  Google Scholar 

  19. W.X. Xu, N. Hong, G.P. Wang, X. Fan, J. Phytopathol. 156(9), 565–572 (2008). doi:https://doi.org/10.1111/j.1439-0434.2008.01398.x

    Article  CAS  Google Scholar 

  20. J.E. Visvader, R.H. Symons, Nucleic Acids Res. 13, 2907–2920 (1985). doi:https://doi.org/10.1093/nar/13.8.2907

    Article  CAS  PubMed Central  Google Scholar 

  21. M.A. Bracho, E. Barrio, J. Gen. Virol. 79, 2921–2928 (1998)

    Article  CAS  Google Scholar 

  22. A.J. Dingley, G. Steger, B. Esters, D. Riesner, S. Grzesiek, J. Mol. Biol. 334, 751–767 (2003). doi:https://doi.org/10.1016/j.jmb.2003.10.015

    Article  CAS  Google Scholar 

  23. J.S. Semancik, G. Vidalakis, Arch. Virol. 150, 1059 (2005). doi:https://doi.org/10.1007/s00705-005-0499-8

    Article  CAS  Google Scholar 

  24. P. Keese, R.H. Symons, Proc. Natl Acad. Sci. USA 82, 4582–4586 (1985). doi:https://doi.org/10.1073/pnas.82.14.4582

    Article  CAS  PubMed Central  Google Scholar 

Download references

Acknowledgments

This work was supported by grants from the National Basic Research and Development Program of China (973 Program) (No. 2006CB100203 and No. 2009CB119200), the National Natural Science Foundation of China (No.30771403) and the Beijing Natural Science Foundation of China (No. 6072022), and the Opening Project of State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences. This work was also supported by NSFC-JSPS Joint Research Project between China and Japan (30811140157). We specially thank Prof. Teruo Sano at Hirosaki University of Japan for his valuable comments and the critical reading of this manuscript. We also thank Mr. Lingxiao Mu, graduate student of Shenyang Agricultural University, for his assistance in artwork preparation.

Author information

Authors and Affiliations

  1. Institute of Plant Virology, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, Fujian, 350002, People’s Republic of China

    Dongmei Jiang & Zujian Wu

  2. State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road No2, Haidian District, Beijing, 100193, People’s Republic of China

    Dongmei Jiang, Shan Peng, Zhuomin Cheng & Shifang Li

Authors
  1. Dongmei Jiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Shan Peng
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Zujian Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Zhuomin Cheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Shifang Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Shifang Li.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Jiang, D., Peng, S., Wu, Z. et al. Genetic diversity and phylogenetic analysis of Australian Grapevine Viroid (AGVd) isolated from different grapevines in China. Virus Genes 38, 178–183 (2009). https://doi.org/10.1007/s11262-008-0306-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11262-008-0306-1

Keywords

Search

Navigation