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Genus specific evolution of codon usage and nucleotide compositional traits of poxviruses

Abstract

Poxviruses are complex in their nucleotide compositional features of the coding regions. The codon usages in Poxviruses are in accordance with their compositional bias. In the Poxviridae family, codon usage patterns and nucleotide compositional traits are widely divergent across species but some conservation was observed within a genus. Viruses from six Chordopox genera, i.e., Avipoxvirus, Capripoxvirus, Cervidpoxvirus, Orthopoxvirus, Suipoxvirus, Yatapoxvirus, and one Entomopox genus- Betaentomopoxvirus, and some unclassified Entomopoxvirus are significantly rich in AT composition. Four other Chordopox genera- Molluscipoxvirus, Orthopoxvirus, Parapoxvirus, and some unclassified Chordopoxvirus are dominated by the GC rich viruses. Poxviruses from these AT rich and GC rich genera preferred AT or GC ending codons owing to their respective nucleotide compositional bias. For example, viruses from AT rich Orthopoxvirus, or GC rich Parapoxvirus have evolved with mutually exclusive type codon preferences following their genus-specific nucleotide compositions. Additional factors like gene length and expression level also influenced their codon usage patterns to some extent in some Poxvirus genera. Evidences from correspondence analysis and cluster analysis on the extent of divergence in codon usage also support this genus specific evolution of Poxvirus codon usage. Analyzes suggest that most of the Poxviruses from different genera, have evolved in almost two different evolutionary trajectory in context of their nucleotide composition and codon usage.

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Abbreviations

ORF:

Open reading frame

ENC:

Effective number of codons

RSCU:

Relative synonymous codon usage

CAI:

Codon adaptation index

COA:

Correspondence analysis

References

  1. 1.

    Y. Li, D.S. Carroll, S.N. Gardner, M.C. Walsh, E.A. Vitalis, I.K. Damon, Proc. Natl. Acad. Sci. 104, 15787–15792 (2007)

  2. 2.

    G.L. Smith, G. McFadden, Nature Rev. Immunol. 2, 521–528 (2002)

  3. 3.

    G. McFadden, Nat. Rev. Microbiol. 3, 201–213 (2005)

  4. 4.

    S.E. Frey, R.B. Belshe, N. Engl. J. Med. 650, 324–327 (2004)

  5. 5.

    J.W. Barrett, Y. Sun, S.H. Nazarian, T.A. Belsito, C.R. Brunetti, G. McFadden, Virus Genes 33, 15–26 (2006)

  6. 6.

    M.M. Stanford, G. McFadden, Expert. Opin. Biol. Ther. 7, 1415–1425 (2007)

  7. 7.

    F. Wright, Gene 87, 23–29 (1990)

  8. 8.

    S. RoyChoudhury, D. Mukherjee, Virus Res. 148, 31–43 (2010)

  9. 9.

    R.J. Grocock, P.M. Sharp, Gene 289, 131–139 (2002)

  10. 10.

    S. Karlin, L. Brocchieri, J. Trent, B.E. Blaisdell, J. Mrázek, Theor. Popul. Biol. 61, 367–390 (2002)

  11. 11.

    S. Karlin, C. Burge, Trends Genet. 11, 283–290 (1995)

  12. 12.

    A.T. Lloyd, P.M. Sharp, Nucleic Acids Res. 20, 5289–5295 (1992)

  13. 13.

    P.M. Sharp, W.H. Li, Nucleic Acids Res. 14, 7737–7749 (1986)

  14. 14.

    P. Pavlidis, W.S. Noble, Bioinformatics 19, 295–306 (2003)

  15. 15.

    I. Barrai, C. Scapoli, R. Gambari, F. Brugnoli, J. Theor. Biol. 152, 405–426 (1991)

  16. 16.

    S. Karlin, J. Mrazek, A.M. Campbell, J. Bacteriol. 179, 3899–3913 (1997)

  17. 17.

    E.J. Lefkowitz, C. Wang, C. Upton, Virus Res. 117, 105–118 (2006)

  18. 18.

    B. Moss, B.Y. Ahn, B. Amegadzie, P.D. Gershon, J.G. Keck, J. Biol. Chem. 266, 1355–1358 (1991)

  19. 19.

    B. Moss, in Fundamental Virology, 3rd ed. by B.N. Fields, D.M. Knipe, P.M. Howley (Lippincott-Raven Publishers, Philadelphia, 1996), pp. 1163–1197

  20. 20.

    N. Stoletzki, A. Eyre-Walker, Mol. Biol. Evol. 24, 374–381 (2007)

  21. 21.

    M. Bulmer, Genetics 129, 897–907 (1991)

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Correspondence to Debaprasad Mukherjee.

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RoyChoudhury, S., Pan, A. & Mukherjee, D. Genus specific evolution of codon usage and nucleotide compositional traits of poxviruses. Virus Genes 42, 189–199 (2011). https://doi.org/10.1007/s11262-010-0568-2

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Keywords

  • Codon usage bias
  • Nucleotide composition
  • Correspondence analysis
  • Cluster analysis
  • Poxvirus
  • Evolution