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Evolutionary Basis of Codon Usage and Nucleotide Composition Bias in Vertebrate DNA Viruses

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Abstract

Understanding the extent and causes of biases in codon usage and nucleotide composition is essential to the study of viral evolution, particularly the interplay between viruses and host cells or immune responses. To understand the common features and differences among viruses we analyzed the genomic characteristics of a representative collection of all sequenced vertebrate-infecting DNA viruses. This revealed that patterns of codon usage bias are strongly correlated with overall genomic GC content, suggesting that genome-wide mutational pressure, rather than natural selection for specific coding triplets, is the main determinant of codon usage. Further, we observed a striking difference in CpG content between DNA viruses with large and small genomes. While the majority of large genome viruses show the expected frequency of CpG, most small genome viruses had CpG contents far below expected values. The exceptions to this generalization, the large gammaherpesviruses and iridoviruses and the small dependoviruses, have sufficiently different life-cycle characteristics that they may help reveal some of the factors shaping the evolution of CpG usage in viruses.

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Acknowledgments

This work was completed under a Howard Hughes Medical Institute Fellowship to L.A.S. and NIH Grant R01AI028385 to C.R.P.

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Authors and Affiliations

  1. Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK

    Laura A. Shackelton

  2. J.A. Baker Institute, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA

    Colin R. Parrish

  3. Center for Infectious Disease Dynamics, Department of Biology, Mueller Laboratory, The Pennsylvania State University, University Park, PA, 16802, USA

    Edward C. Holmes

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  1. Laura A. Shackelton
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  2. Colin R. Parrish
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  3. Edward C. Holmes
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Correspondence to Edward C. Holmes.

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Shackelton, L.A., Parrish, C.R. & Holmes, E.C. Evolutionary Basis of Codon Usage and Nucleotide Composition Bias in Vertebrate DNA Viruses. J Mol Evol 62, 551–563 (2006). https://doi.org/10.1007/s00239-005-0221-1

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