Analysis of synonymous codon usage and evolution of begomoviruses
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Begomoviruses are single-stranded DNA viruses and cause severe diseases in major crop plants worldwide. Based on current genome sequence analyses, we found that synonymous codon usage variations in the protein-coding genes of begomoviruses are mainly influenced by mutation bias. Base composition analysis suggested that the codon usage bias of AV1 and BV1 genes is significant and their expressions are high. Fourteen codons were determined as translational optimal ones according to the comparison of codon usage patterns between highly and lowly expressed genes. Interestingly the codon usages between begomoviruses from the Old and the New Worlds are apparently different, which supports the idea that the bipartite begomoviruses of the New World might originate from bipartite ones of the Old World, whereas the latter evolve from the Old World monopartite begomoviruses.
Key wordsBegomovirus Synonymous codon usage Evolution Bioinformatics
CLC numberQ939.46 S432.1
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- Fauquet, C.M., Bisaro, D.M., Briddon, R.W., Brown, J.K., Harrison, B.D., Rybicki, E.P., Stenger, D.C., Stanley, J., 2003. Revision of taxonomic criteria for species demarcation in the family Geminiviridae, and an updated list of begomovirus species. Archives of Virology, 148(2): 405–421. [doi:10.1007/s00705-002-0957-5]PubMedCrossRefGoogle Scholar
- Greenacre, M.J., 1984. Theory and Applications of Correspondence Analysis. Academic Press, London, p.1–364.Google Scholar
- Sharp, P.M., Cowe, E., Higgins, D.G., Shields, D.C., Wolfe, K.H., Wright, F., 1988. Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens: a review of the considerable within-species diversity. Nucleic Acids Research, 16(17):8207–8211. [doi:10.1093/nar/16.17.8207]PubMedCrossRefGoogle Scholar
- Wang, S.F., Xu, H.L., Lu, R.J., Meng, X., Wang, W.L., Wang, Z.Y., Guo, W., Ruan, L., 2002. Analysis of codon usage of vaccinia virus genome. Chinese Journal of Virology, 18(3):227–234 (in Chinese).Google Scholar
- Zhou, X.P., Xie, Y., Tao, X.R., Zhang, Z.K., Li, Z.H., Fauquet, C.M., 2003. Characterization of DNAβ associated with begomoviruses in China and evidence for co-evolution with their cognate viral DNA-A. Journal of General Virology, 84(1):237–247. [doi:10.1099/vir.0.18608-0]PubMedCrossRefGoogle Scholar