Skip to main content
SpringerLink
Log in

Complete genomic sequence analyses of Apple stem pitting virus isolates from China

  • Published:
Virus Genes Aims and scope Submit manuscript

Abstract

The complete genomic sequences of a Chinese ASPV isolates KL1 and KL9 were determined from ten overlapping cDNA clones. The genomes of both isolates were 9265 nucleotides excluding the poly (A) tail and contained five open reading frames (ORFs). The identities between two complete genomes were 92.5% at nt level. Multiple alignment of the amino acid sequences showed that 110 aa variations between two genomic sequences and the variable domains mainly distributed in 5′-terminal of ORF1, ORF3, and ORF5, respectively. Two complete genomic sequences shared 71.4–77.3% identities with other ASPV isolates at nt level. Phylogenetic relationship analysis of the coat protein genes revealed that ASPV isolates had high variables and formed three groups. All ASPV isolates from apples were clustered to group I, whereas pear were clustered to groups II (except NC_003462) and both KL1 and KL9 were clustered to group III. Nucleotide sequences diversity analysis showed that the between-population d NS /d S ratio 0.092 was similar to these for within-group (0.092–0.095); there was no geographic differentiation between ASPV isolates.

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

Similar content being viewed by others

References

  1. G.P. Martelli, W. Jelkmann, Arch. Virol. 143, 1245–1249 (1998)

    Article  PubMed  CAS  Google Scholar 

  2. W. Jelkmann, Apple stem pitting virus, in Filamentous viruses of woody plants, ed. by P.L. Monette (Research Signpost, Trivandrum, 1997), pp. 133–142

    Google Scholar 

  3. R.F. Stouffer, Apple stem pitting virus, in Virus and virus-like diseases of pome fruit and simulating noninfectious disorders, ed. by P.L. Fridlund (Washington State University, Pullman, 1989), pp. 138–144

    Google Scholar 

  4. G. Leone, J.L. Lindner, F.A. van der Meer, C.D. Schoen, G. Jongedijk, Acta Hortic. 472, 61–65 (1998)

    Google Scholar 

  5. W. Jelkmann, J. Gen. Virol. 75, 1535–1542 (1994)

    Article  PubMed  CAS  Google Scholar 

  6. H. Koganezawa, H. Yanase, Plant Dis. 74, 610–614 (1990)

    Article  CAS  Google Scholar 

  7. N. Galiakparov, D.E. Goszczynski, X. Che, O. Batuman, M. Bar-Joseph, M. Mawassi, Virology 312, 434–448 (2003)

    Article  PubMed  CAS  Google Scholar 

  8. L. Nemchinov, A. Hadidi, F. Faggioli, Acta Hortic. 472, 67–73 (1998)

    CAS  Google Scholar 

  9. K. Schwarz, W. Jelkmann, Acta Hortic. 472, 75–85 (1998)

    CAS  Google Scholar 

  10. N. Yoshikawa, H. Matsuda, Y. Oda, M. Isogai, T. Takahashi, T. Takahasi, T. Ito, K. Yoshida, Acta Hortic. 550, 285–290 (2001)

    CAS  Google Scholar 

  11. F. García-Arenal, A. Fraile, J.M. Malpica, Annu. Rev. Phytopathol. 39, 157–186 (2001)

    Article  PubMed  Google Scholar 

  12. M. Tsompana, J. Abad, M. Purgganan, W. Moyer, J. Mol. Ecol. 14, 53–66 (2005)

    Article  CAS  Google Scholar 

  13. I.M. Moreno, J.M. Malpica, J.A. Díaz-Pendόn, E. Moriones, A. Fraile, F. García-Arenal, Virology 318, 451–460 (2004)

    Article  PubMed  CAS  Google Scholar 

  14. Y. Tomitaka, K. Ohshima, J. Mol. Ecol. 15, 4437–4457 (2006)

    Article  CAS  Google Scholar 

  15. R. Biek, A.J. Drummond, M. Poss, Science 311, 538–541 (2006)

    Article  PubMed  CAS  Google Scholar 

  16. M. He, H.S. Li, Y. Zhao, J.X. Niu, B.G. Ma, J. Shihezi Univ. 22, 474–476 (2004)

    CAS  Google Scholar 

  17. A.R. Mushegian, E.V. Koonin, Arch. Virol. 133, 239–257 (1993)

    Article  PubMed  CAS  Google Scholar 

  18. P. Pomilo, N.O. Bianchi, Mol. Biol. Evol. 10, 271–281 (1993)

    Google Scholar 

  19. W.H. Li, J. Mol. Ecol. 36, 96–99 (1993)

    Article  CAS  Google Scholar 

  20. S.Y. Morozov, A.G. Solovyev, J. Gen. Virol. 84, 1351–1366 (2003)

    Article  PubMed  CAS  Google Scholar 

  21. J. Verchot-Lubicz, Mol. Plant Microbe Interact. 18, 283–290 (2005)

    Article  PubMed  CAS  Google Scholar 

  22. B.Z. Meng, S.Z. Pang, P.L. Forsline, J.R. McFerson, D. Gonsalves, J. Gen. Virol. 79, 2059–2069 (1998)

    PubMed  CAS  Google Scholar 

  23. M.H. Rozanov, E.V. Koonin, A.E. Gorbalenya, J. Gen. Virol. 73, 2129–2134 (1992)

    Article  PubMed  CAS  Google Scholar 

  24. A.E. Gorbalenya, E.V. Koonin, A.P. Donchenko, V.M. Blinov, FEBS Lett. 235, 16–24 (1988)

    Article  PubMed  CAS  Google Scholar 

  25. E.V. Koonin, J. Gen. Virol. 72, 2197–2206 (1991)

    Article  PubMed  Google Scholar 

  26. A.E. Gorbalenya, V.M. Blinov, A.P. Donchenko, E.V. Koonin, J. Mol. Evol. 28, 256–268 (1989)

    Article  PubMed  CAS  Google Scholar 

  27. V.V. Dolja, V.P. Boyko, A.A. Agranovsky, E.V. Koonin, Virology 184, 79–86 (1991)

    Article  PubMed  CAS  Google Scholar 

  28. L. Giunchedi, C. Poggi Pollini, J. Phytopathol. 134, 329–335 (1992)

    Article  Google Scholar 

  29. W. Jelkmann, L. Kunze, H.J. Vetten, D.E. Lesemann, Acta Hortic. 309, 55–62 (1992)

    Google Scholar 

  30. A. Michel, V. Salmon Marina, J. Plant Pathol. (European) 108, 755–762 (2002)

    Article  Google Scholar 

  31. L.L. Li, Y.F. Dong, Z.P. Zhang, Z.H. Zhang, X.D. Fan, G.Q. Pei, Acta Hortic. Sinica (China) 37, 9–16 (2010)

    Google Scholar 

  32. C.K. Hjulsager, B.S. Olsen, D.M.K. Jensen, M.I. Cordea, B.N. Krath, I.E. Johansen, O.S. Lund, Virology 355, 52–61 (2006)

    Article  PubMed  CAS  Google Scholar 

  33. P. Saénz, M.T. Cervera, S. Dallot, L. Quiot, J.-B. Quiot, J.L. Riechmann, J.A. García, J. Gen. Virol. 81, 557–566 (2000)

    PubMed  Google Scholar 

  34. V. Decroocq, B. Salvador, O. Sicard, M. Glasa, P. Cosson, L. Svanella-Dumas, F. Revers, J.A. Garcia, T. Candresse, Mol. Plant Microbe Interact. 22, 1311–1320 (2009)

    Article  Google Scholar 

  35. B. Salvador, M.O. Delgadillo, P. Saenz, J.A. Garcia, C. Simon-Mateo, Mol. Plant Microbe Interact. 21, 20–29 (2003)

    Article  Google Scholar 

Download references

Acknowledgments

This study was supported by National Natural Science Foundation of China (30360066), the National Key Technologies R&D Program of China (2003BA546C), the Foundation Science and Technology Commission Xinjiang Production and Construction Crops, China (NKB02SDXNK01SW), and Natural Science and Technology Innovation of Shihezi University, China (ZRKX200707).

Author information

Authors and Affiliations

  1. Department of Horticultural, Agricultural College of Shihezi University, 832000, Shihezi, People’s Republic of China

    Na Liu, Jianxin Niu & Ying Zhao

Authors
  1. Na Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jianxin Niu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ying Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jianxin Niu.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Liu, N., Niu, J. & Zhao, Y. Complete genomic sequence analyses of Apple stem pitting virus isolates from China. Virus Genes 44, 124–130 (2012). https://doi.org/10.1007/s11262-011-0666-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11262-011-0666-9

Keywords

Search

Navigation