Virus Genes

, Volume 38, Issue 1, pp 104–112

Analysis of synonymous codon usage in classical swine fever virus

  • Pan Tao
  • Li Dai
  • Mengcheng Luo
  • Fangqiang Tang
  • Po Tien
  • Zishu Pan
Article

Abstract

Using the complete genome sequences of 35 classical swine fever viruses (CSFV) representing all three genotypes and all three kinds of virulence, we analyzed synonymous codon usage and the relative dinucleotide abundance in CSFV. The general correlation between base composition and codon usage bias suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in CSFV. Furthermore, we observed that the relative abundance of dinucleotides in CSFV is independent of the overall base composition but is still the result of differential mutational pressure, which also shapes codon usage. In addition, other factors, such as the subgenotypes and aromaticity, also influence the codon usage variation among the genomes of CSFV. This study represents the most comprehensive analysis to date of CSFV codon usage patterns and provides a basic understanding of the mechanisms for codon usage bias.

Keywords

Classical swine fever virus (CSFV) Synonymous codon usage Mutational bias Dinucleotide bias Subgenotype 

Supplementary material

References

  1. 1.
    S. Karlin, J. Mrazek, J. Mol. Biol. 262, 459–472 (1996). doi:10.1006/jmbi.1996.0528 PubMedCrossRefGoogle Scholar
  2. 2.
    T. Lesnik, J. Solomovici, A. Deana, R. Ehrlich, C. Reiss, J. Theor. Biol. 202, 175–185 (2000). doi:10.1006/jtbi.1999.1047 PubMedCrossRefGoogle Scholar
  3. 3.
    P.M. Sharp, W.H. Li, Nucleic Acids Res. 14, 7737–7749 (1986). doi:10.1093/nar/14.19.7737 PubMedCrossRefGoogle Scholar
  4. 4.
    P.M. Sharp, T.M. Tuohy, K.R. Mosurski, Nucleic Acids Res. 14, 5125–5143 (1986). doi:10.1093/nar/14.13.5125 PubMedCrossRefGoogle Scholar
  5. 5.
    L.A. Shackelton, C.R. Parrish, E.C. Holmes, J. Mol. Evol. 62, 551–563 (2006). doi:10.1007/s00239-005-0221-1 PubMedCrossRefGoogle Scholar
  6. 6.
    A.O. Mooers, E.C. Holmes, Trends Ecol. Evol. 15, 365–369 (2000). doi:10.1016/S0169-5347(00)01934-0 PubMedCrossRefGoogle Scholar
  7. 7.
    G.M. Jenkins, E.C. Holmes, Virus Res. 92, 1–7 (2003). doi:10.1016/S0168-1702(02)00309-X PubMedCrossRefGoogle Scholar
  8. 8.
    J. Zhou, W.J. Liu, S.W. Peng, X.Y. Sun, I. Frazer, J. Virol. 73, 4972–4982 (1999)PubMedGoogle Scholar
  9. 9.
    K.N. Zhao, W.J. Liu, I.H. Frazer, Virus Res. 98, 95–104 (2003). doi:10.1016/j.virusres.2003.08.019 PubMedCrossRefGoogle Scholar
  10. 10.
    S. Karlin, B.E. Blaisdell, G.A. Schachtel, J. Virol. 64, 4264–4273 (1990)PubMedGoogle Scholar
  11. 11.
    J. Sewatanon, S. Srichatrapimuk, P. Auewarakul, Intervirology 50, 123–132 (2007). doi:10.1159/000098238 PubMedCrossRefGoogle Scholar
  12. 12.
    F.J. van Hemert, B. Berkhout, V.V. Lukashov, Virology 361, 447–454 (2007). doi:10.1016/j.virol.2006.11.021 PubMedCrossRefGoogle Scholar
  13. 13.
    S. Edwards, A. Fukusho, P.C. Lefevre, A. Lipowski, Z. Pejsak, P. Roehe, J. Westergaard, Vet. Microbiol. 73, 103–119 (2000). doi:10.1016/S0378-1135(00)00138-3 PubMedCrossRefGoogle Scholar
  14. 14.
    C.M. Rice, Flaviviridae: The Viruses and their Replication (Lippincott Raven, Philadelphia, 1996)Google Scholar
  15. 15.
    D.J. Paton, A. McGoldrick, I. Greiser-Wilke, S. Parchariyanon, J.Y. Song, P.P. Liou, T. Stadejek, J.P. Lowings, H. Bjorklund, S. Belak, Vet. Microbiol. 73, 137–157 (2000). doi:10.1016/S0378-1135(00)00141-3 PubMedCrossRefGoogle Scholar
  16. 16.
    X. Li, Z. Xu, Y. He, Q. Yao, K. Zhang, M. Jin, H. Chen, P. Qian, Virus Genes 33, 133–142 (2006). doi:10.1007/s11262-005-0048-2 PubMedCrossRefGoogle Scholar
  17. 17.
    F. Tang, Z. Pan, C. Zhang, Virus Res. 131, 132–135 (2008). doi:10.1016/j.virusres.2007.08.015 PubMedCrossRefGoogle Scholar
  18. 18.
    H.X. Wu, C.Y. Zhang, C.Y. Zheng, J.Q. Guo, Wuhan Univ. J. Nat. Sci. 6, 864–866 (2001). doi:10.1007/BF02850922 CrossRefGoogle Scholar
  19. 19.
    H.X. Wu, J.F. Wang, C.Y. Zhang, L.Z. Fu, Z.S. Pan, N. Wang, P.W. Zhang, W.G. Zhao, Virus Genes 23, 69–76 (2001). doi:10.1023/A:1011187413930 PubMedCrossRefGoogle Scholar
  20. 20.
    Y. Fan, Q. Zhao, Y. Zhao, Q. Wang, Y. Ning, Z. Zhang, Virus Genes 36, 531–538 (2008). doi:10.1007/s11262-008-0229-x PubMedCrossRefGoogle Scholar
  21. 21.
    T.V. Grebennikova, A.D. Zaberezhnyi, V.A. Sergeev, S.F. Biketov, T.I. Aliper, E.A. Nepoklonov. Mol. Gen. Mikrobiol. Virusol. 2, 34–40 (1999)Google Scholar
  22. 22.
    K. Ishikawa, H. Nagai, K. Katayama, M. Tsutsui, K. Tanabayashi, K. Takeuchi, M. Hishiyama, A. Saitoh, M. Takagi, K. Gotoh et al., Arch. Virol. 140, 1385–1391 (1995). doi:10.1007/BF01322665 PubMedCrossRefGoogle Scholar
  23. 23.
    Y.J. Lin, M.S. Chien, M.C. Deng, C.C. Huang, Virus Genes 35, 737–744 (2007). doi:10.1007/s11262-007-0154-4 PubMedCrossRefGoogle Scholar
  24. 24.
    D. Mayer, T.M. Thayer, M.A. Hofmann, J.D. Tratschin, Virus Res. 98, 105–116 (2003). doi:10.1016/j.virusres.2003.08.020 PubMedCrossRefGoogle Scholar
  25. 25.
    G. Meyers, T. Rumenapf, H.J. Thiel, Virology 171, 555–567 (1989). doi:10.1016/0042-6822(89)90625-9 PubMedCrossRefGoogle Scholar
  26. 26.
    R.J. Moormann, H.G. van Gennip, G.K. Miedema, M.M. Hulst, P.A. van Rijn, J. Virol. 70, 763–770 (1996)PubMedGoogle Scholar
  27. 27.
    R.J. Moormann, P.A. Warmerdam, B. van der Meer, W.M. Schaaper, G. Wensvoort, M.M. Hulst, Virology 177, 184–198 (1990). doi:10.1016/0042-6822(90)90472-4 PubMedCrossRefGoogle Scholar
  28. 28.
    G.R. Risatti, M.V. Borca, G.F. Kutish, Z. Lu, L.G. Holinka, R.A. French, E.R. Tulman, D.L. Rock, J. Virol. 79, 3787–3796 (2005). doi:10.1128/JVI.79.6.3787-3796.2005 PubMedCrossRefGoogle Scholar
  29. 29.
    N. Ruggli, C. Moser, D. Mitchell, M. Hofmann, J.D. Tratschin, Virus Genes 10, 115–126 (1995). doi:10.1007/BF01702592 PubMedCrossRefGoogle Scholar
  30. 30.
    A. Uttenthal, M.F. Le Potier, L. Romero, G.M. De Mia, G. Floegel-Niesmann, Vet. Microbiol. 83, 85–106 (2001). doi:10.1016/S0378-1135(01)00409-6 PubMedCrossRefGoogle Scholar
  31. 31.
    X.S. Wu, T.R. Luo, S.H. Liao, Q.Z. Liu, W.J. Huang, Chin. J. Vet. Sci. 25, 125–128 (2003)Google Scholar
  32. 32.
    Y. Nie, Y. Ke, J. Chen, M. Ding, Wei Sheng Wu Xue Bao 41, 452–456 (2001)PubMedGoogle Scholar
  33. 33.
    J.J. Zhao, D. Cheng, N. Li, Y. Sun, Z. Shi, Q.H. Zhu, C. Tu, G.Z. Tong, H.J. Qiu, Vet. Microbiol. 126, 1–10 (2008). doi:10.1016/j.vetmic.2007.04.046 PubMedCrossRefGoogle Scholar
  34. 34.
    S. Dreier, B. Zimmermann, V. Moennig, I. Greiser-Wilke, J. Virol. Methods 140, 95–99 (2007). doi:10.1016/j.jviromet.2006.11.013 PubMedCrossRefGoogle Scholar
  35. 35.
    P.M. Sharp, W.H. Li, J. Mol. Evol. 24, 28–38 (1986). doi:10.1007/BF02099948 PubMedCrossRefGoogle Scholar
  36. 36.
    F. Wright, Gene 87, 23–29 (1990). doi:10.1016/0378-1119(90)90491-9 PubMedCrossRefGoogle Scholar
  37. 37.
    J.M. Comeron, M. Aguade, J. Mol. Evol. 47, 268–274 (1998). doi:10.1007/PL00006384 PubMedCrossRefGoogle Scholar
  38. 38.
    S. Karlin, C. Burge, Trends Genet. 11, 283–290 (1995). doi:10.1016/S0168-9525(00)89076-9 PubMedCrossRefGoogle Scholar
  39. 39.
    I. Ahn, B.J. Jeong, S.E. Bae, J. Jung, H.S. Son, Eur. J. Epidemiol 21, 511–519 (2006). doi:10.1007/s10654-006-9031-z PubMedCrossRefGoogle Scholar
  40. 40.
    W. Gu, T. Zhou, J. Ma, X. Sun, Z. Lu, Virus Res. 101, 155–161 (2004). doi:10.1016/j.virusres.2004.01.006 PubMedCrossRefGoogle Scholar
  41. 41.
    S. Zhao, Q. Zhang, X. Liu, X. Wang, H. Zhang, Y. Wu, F. Jiang, Biosystems 92, 207–214 (2008). doi:10.1016/j.biosystems.2008.01.006 PubMedCrossRefGoogle Scholar
  42. 42.
    J. Zhong, Y. Li, S. Zhao, S. Liu, Z. Zhang, Virus Genes 35, 767–776 (2007). doi:10.1007/s11262-007-0159-z PubMedCrossRefGoogle Scholar
  43. 43.
    T. Zhou, W. Gu, J. Ma, X. Sun, Z. Lu, Biosystems 81, 77–86 (2005). doi:10.1016/j.biosystems.2005.03.002 PubMedCrossRefGoogle Scholar
  44. 44.
    Y. Wang, Q. Wang, X. Lu, C. Zhang, X. Fan, Z. Pan, L. Xu, G. Wen, Y. Ning, F. Tang, Y. Xia, Virology 374, 390–398 (2008). doi:10.1016/j.virol.2008.01.008 PubMedCrossRefGoogle Scholar
  45. 45.
    M. Bulmer, Genetics 129, 897–907 (1991)PubMedGoogle Scholar
  46. 46.
    J.W. Drake, J.J. Holland, Proc. Natl. Acad. Sci. USA 96, 13910–13913 (1999). doi:10.1073/pnas.96.24.13910 PubMedCrossRefGoogle Scholar
  47. 47.
    C.Q. He, N.Z. Ding, J.G. Chen, Y.L. Li, Virus Res. 126, 179–185 (2007). doi:10.1016/j.virusres.2007.02.019 PubMedCrossRefGoogle Scholar
  48. 48.
    S. Karlin, W. Doerfler, L.R. Cardon, J. Virol. 68, 2889–2897 (1994)PubMedGoogle Scholar
  49. 49.
    P.C. Woo, B.H. Wong, Y. Huang, S.K. Lau, K.Y. Yuen, Virology 369, 431–442 (2007). doi:10.1016/j.virol.2007.08.010 PubMedCrossRefGoogle Scholar
  50. 50.
    H. Wagner, Trends Immunol. 25, 381–386 (2004). doi:10.1016/j.it.2004.04.011 PubMedCrossRefGoogle Scholar
  51. 51.
    T. Sugiyama, M. Gursel, F. Takeshita, C. Coban, J. Conover, T. Kaisho, S. Akira, D.M. Klinman, K.J. Ishii, J. Immunol. 174, 2273–2279 (2005)PubMedGoogle Scholar
  52. 52.
    M.T. Harte, I.R. Haga, G. Maloney, P. Gray, P.C. Reading, N.W. Bartlett, G.L. Smith, A. Bowie, L.A. O’Neill, J. Exp. Med. 197, 343–351 (2003). doi:10.1084/jem.20021652 PubMedCrossRefGoogle Scholar
  53. 53.
    L. Chen, Y.H. Xia, Z.S. Pan, C.Y. Zhang, Protein Expr. Purif. 55, 379–387 (2007). doi:10.1016/j.pep.2007.05.003 PubMedCrossRefGoogle Scholar
  54. 54.
    N. Ruggli, B.H. Bird, L. Liu, O. Bauhofer, J.D. Tratschin, M.A. Hofmann, Virology 340, 265–276 (2005). doi:10.1016/j.virol.2005.06.033 PubMedCrossRefGoogle Scholar
  55. 55.
    N. Ruggli, J.D. Tratschin, M. Schweizer, K.C. McCullough, M.A. Hofmann, A. Summerfield, J. Virol. 77, 7645–7654 (2003). doi:10.1128/JVI.77.13.7645-7654.2003 PubMedCrossRefGoogle Scholar
  56. 56.
    Y.H. Xia, L. Chen, Z.S. Pan, C.Y. Zhang, J. Biochem. Mol. Biol. 40, 611–616 (2007)PubMedGoogle Scholar
  57. 57.
    S.A. La Rocca, R.J. Herbert, H. Crooke, T.W. Drew, T.E. Wileman, P.P. Powell, J. Virol. 79, 7239–7247 (2005). doi:10.1128/JVI.79.11.7239-7247.2005 PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Pan Tao
    • 1
  • Li Dai
    • 2
  • Mengcheng Luo
    • 1
  • Fangqiang Tang
    • 1
  • Po Tien
    • 1
  • Zishu Pan
    • 1
  1. 1.State Key Laboratory of Virology, College of Life SciencesWuhan UniversityWuhanChina
  2. 2.Key Laboratory of MOE for Development Biology, College of Life SciencesWuhan UniversityWuhanChina

Personalised recommendations