- About this Journal ·
- Abstracting and Indexing ·
- Aims and Scope ·
- Annual Issues ·
- Article Processing Charges ·
- Articles in Press ·
- Author Guidelines ·
- Bibliographic Information ·
- Citations to this Journal ·
- Contact Information ·
- Editorial Board ·
- Editorial Workflow ·
- Free eTOC Alerts ·
- Publication Ethics ·
- Reviewers Acknowledgment ·
- Submit a Manuscript ·
- Subscription Information ·
- Table of Contents
BioMed Research International
Volume 2013 (2013), Article ID 406342, 10 pages
A Comparison of Synonymous Codon Usage Bias Patterns in DNA and RNA Virus Genomes: Quantifying the Relative Importance of Mutational Pressure and Natural Selection
Department of Zoology, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
Received 15 April 2013; Revised 30 June 2013; Accepted 4 August 2013
Academic Editor: Sankar Subramanian
Copyright © 2013 Youhua Chen. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- M. Archetti, “Codon usage bias and mutation constraints reduce the level of error minimization of the genetic code,” Journal of Molecular Evolution, vol. 59, no. 2, pp. 258–266, 2004.
- L. Duret and D. Mouchiroud, “Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 96, no. 8, pp. 4482–4487, 1999.
- P. Tao, L. Dai, M. Luo, F. Tang, P. Tien, and Z. Pan, “Analysis of synonymous codon usage in classical swine fever virus,” Virus Genes, vol. 38, no. 1, pp. 104–112, 2009.
- E. N. Moriyama and J. R. Powell, “Codon usage bias and tRNA abundance in Drosophila,” Journal of Molecular Evolution, vol. 45, no. 5, pp. 514–523, 1997.
- G. P. Holmquist and J. Filipski, “Organization of mutations along the genome: a prime determinant of genome evolution,” Trends in Ecology and Evolution, vol. 9, no. 2, pp. 65–69, 1994.
- X. Liu, C. Wu, and A. Y.-H. Chen, “Codon usage bias and recombination events for neuraminidase and hemagglutinin genes in Chinese isolates of influenza A virus subtype H9N2,” Archives of Virology, vol. 155, no. 5, pp. 685–693, 2010.
- Y. Zhang, Y. Liu, W. Liu et al., “Analysis of synonymous codon usage in Hepatitis A virus,” Virology Journal, vol. 8, article 174, 2011.
- F. P. Lobo, B. E. F. Mota, S. D. J. Pena et al., “Virus-host coevolution: common patterns of nucleotide motif usage in Flaviviridae and their hosts,” PLoS ONE, vol. 4, no. 7, Article ID e6282, 2009.
- A. Lukashev, J. Drexler, I. Belalov, M. Eschbach-Bludau, S. Baumgrate, and C. Drosten, “Genetic variation and recombination in Aichi virus,” Journal of General Virology, vol. 93, pp. 1226–1235, 2012.
- J. Zhang, M. Wang, W.-Q. Liu et al., “Analysis of codon usage and nucleotide composition bias in polioviruses,” Virology Journal, vol. 8, article 146, 2011.
- L. A. Shackelton and E. C. Holmes, “The evolution of large DNA viruses: combining genomic information of viruses and their hosts,” Trends in Microbiology, vol. 12, no. 10, pp. 458–465, 2004.
- G. M. Jenkins and E. C. Holmes, “The extent of codon usage bias in human RNA viruses and its evolutionary origin,” Virus Research, vol. 92, no. 1, pp. 1–7, 2003.
- I. Belalov and A. Lukashev, “Causes and implications of codon usage bias in RNA viruses,” PLoS ONE, vol. 8, Article ID e56642, 2013.
- P. M. Sharp and W.-H. Li, “Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons,” Nucleic Acids Research, vol. 14, no. 19, pp. 7737–7749, 1986.
- F. Wright, “The ‘effective number of codons’ used in a gene’,” Gene, vol. 87, pp. 23–29, 1990.
- P. M. Sharp and W.-H. Li, “The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications,” Nucleic Acids Research, vol. 15, no. 3, pp. 1281–1295, 1987.
- J. Peden, Analysis of codon usage [Ph.D. thesis], Department of Genetics; Unviersity of Norttingham, 1999.
- C. J. F. Ter Braak, “Canonical correspondence analysis: a new eigenvector technique for multivariate direct gradient analysis,” Ecology, vol. 67, no. 5, pp. 1167–1179, 1986.
- P. Legendre and L. Legendre, Numerical Ecology, Elsevier Science BV, Amsterdam, The Netherlands, 1998.
- P. Legendre, J. Oksanen, and C. Ter Braak, “Testing the significance of canonical axes in redundancy analysis,” Methods in Ecology and Evolution, vol. 2, pp. 269–277, 2011.
- P. R. Peres-Neto, P. Legendre, S. Dray, and D. Borcard, “Variation partitioning of species data matrices: estimation and comparison of fractions,” Ecology, vol. 87, no. 10, pp. 2614–2625, 2006.
- H. Liu, R. He, H. Zhang, Y. Huang, M. Tian, and J. Zhang, “Analysis of synonymous codon usage in Zea mays,” Molecular Biology Reports, vol. 37, no. 2, pp. 677–684, 2010.
- P. Legendre, D. Borcard, and P. R. Peres-Neto, “Analyzing beta diversity: partitioning the spatial variation of community composition data,” Ecological Monographs, vol. 75, no. 4, pp. 435–450, 2005.
- D. Borcard, P. Legendre, and P. Drapeau, “Partialling out the spatial component of ecological variation,” Ecology, vol. 73, no. 3, pp. 1045–1055, 1992.
- R. Development Core Team, “R: A Language and Environment for Statistical Computing, Vienna, Austria,” R Foundation for Statistical Computing, Vienna, Austria, 2011, http://www.R-project.org.
- J. Oksanen, G. Blanchet, R. Kindt, et al., “Vegan: Community Ecology Package. R package version 2. 0-4,” 2012.
- J. Peden, “CodonW,” 2005, http://codonw.sourceforge.net/.
- T. Zhou, W. Gu, J. Ma, X. Sun, and Z. Lu, “Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses,” BioSystems, vol. 81, no. 1, pp. 77–86, 2005.
- S. Shi, Y. Jiang, Y. Liu, R. Xia, and L. Qin, “Selective pressure dominates the synonymous codon usage in parvoviridae,” Virus Genes, vol. 40, pp. 10–19, 2013.
- C. Fu, J. Xiong, and W. Miao, “Genome-wide identification and characterization of cytochrome P450 monooxygenase genes in the ciliate Tetrahymena thermophila,” BMC Genomics, vol. 10, article 208, 2009.
- N. Sueoka, “Translation-coupled violation of Parity Rule 2 in human genes is not the cause of heterogeneity of the DNA G+C content of third codon position,” Gene, vol. 238, no. 1, pp. 53–58, 1999.
- N. Sueoka, “Intrastrand parity rules of DNA base composition and usage biases of synonymous codons,” Journal of Molecular Evolution, vol. 40, no. 3, pp. 318–325, 1995.
- M. Wang, J. Zhang, J.-H. Zhou et al., “Analysis of codon usage in bovine viral diarrhea virus,” Archives of Virology, vol. 156, no. 1, pp. 153–160, 2011.
- H. W. Cao, H. Zhang, Y. Liu, and D. S. Li, “Synonymous codon usage bias of spike genes of porcine epidemic diarrhea virus,” African Journal of Microbiology Research, vol. 5, no. 22, pp. 3784–3789, 2011.
- N. Stoletzki, “The surprising negative correlation of gene length and optimal codon use—disentangling translational selection from GC-biased gene conversion in yeast,” BMC Evolutionary Biology, vol. 11, no. 1, article 93, 2011.
- N. Stoletzki and A. Eyre-Walker, “Synonymous codon usage in Escherichia coli: selection for translational accuracy,” Molecular Biology and Evolution, vol. 24, no. 2, pp. 374–381, 2007.
- M. D. Ermolaeva, “Synonymous codon usage in bacteria,” Current Issues in Molecular Biology, vol. 3, no. 4, pp. 91–97, 2001.
- A. Eyre-Walker, “Synonymous codon bias is related to gene length in Escherichia coli: selection for translational accuracy?” Molecular Biology and Evolution, vol. 13, no. 6, pp. 864–872, 1996.
- G. Marais and L. Duret, “Synonymous codon usage, accuracy of translation, and gene length in Caenorhabditis elegans,” Journal of Molecular Evolution, vol. 52, no. 3, pp. 275–280, 2001.
- T. Zhou, X. Sun, and Z. Lu, “Synonymous codon usage in environmental chlamydia UWE25 reflects an evolutional divergence from pathogenic chlamydiae,” Gene, vol. 368, no. 1-2, pp. 117–125, 2006.
- J. W. Drake and J. J. Holland, “Mutation rates among RNA viruses,” Proceedings of the National Academy of Sciences of the United States of America, vol. 96, no. 24, pp. 13910–13913, 1999.
- V. V. Khrustalev and E. V. Barkovsky, “Mutational pressure is a cause of inter- and intragenomic differences in GC-content of simplex and varicello viruses,” Computational Biology and Chemistry, vol. 33, no. 4, pp. 295–302, 2009.
- W.-Q. Liu, J. Zhang, Y.-Q. Zhang et al., “Compare the differences of synonymous codon usage between the two species within cardiovirus,” Virology Journal, vol. 8, article 325, 2011.
- J. Zhou, Z. Gao, J. Sun et al., “A comparative analysis on the synonymous codon usage pattern in viral functional genes and their translational initiation region of ASFV,” Virus Genes, vol. 46, no. 2, pp. 271–279, 2013.
- T. Ikemura, “Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system,” Journal of Molecular Biology, vol. 151, no. 3, pp. 389–409, 1981.
- T. Zhou, Z. H. Lu, and X. Sun, “The correlation between recombination rate and codon bias in yeast mainly results from mutational bias associated with recombination rather than hill-robertson interference,” in Proceedings of the 27th Annual International Conference of the Engineering in Medicine and Biology Society (IEEE-EMBS '05), pp. 4787–4790, September 2005.
- G. Marais, D. Mouchiroud, and L. Duret, “Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 10, pp. 5688–5692, 2001.
- S. Behura and D. Severson, “Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes,” Biological Reviews, vol. 88, pp. 49–61, 2013.
- M. Worobey, “Extensive homologous recombination among widely divergent TT viruses,” Journal of Virology, vol. 74, no. 16, pp. 7666–7670, 2000.
- E. van der Walt, E. P. Rybicki, A. Varsani et al., “Rapid host adaptation by extensive recombination,” Journal of General Virology, vol. 90, no. 3, pp. 734–746, 2009.
- G.-Z. Han and M. Worobey, “Homologous recombination in negative sense RNA viruses,” Viruses, vol. 3, no. 8, pp. 1358–1373, 2011.
- C.-Q. He, Z.-X. Xie, G.-Z. Han et al., “Homologous recombination as an evolutionary force in the avian influenza A virus,” Molecular Biology and Evolution, vol. 26, no. 1, pp. 177–187, 2009.