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CLC number: Q939.46; S432.1

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Received: 2008-01-06

Revision Accepted: 2008-05-30

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Journal of Zhejiang University SCIENCE B 2008 Vol.9 No.9 P.667~674

10.1631/jzus.B0820005


Analysis of synonymous codon usage and evolution of begomoviruses


Author(s):  Xiao-zhong XU, Qing-po LIU, Long-jiang FAN, Xiao-feng CUI, Xue-ping ZHOU

Affiliation(s):  College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, China; more

Corresponding email(s):   zzhou@zju.edu.cn

Key Words:  Begomovirus, Synonymous codon usage, Evolution, Bioinformatics


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Xiao-zhong XU, Qing-po LIU, Long-jiang FAN, Xiao-feng CUI, Xue-ping ZHOU. Analysis of synonymous codon usage and evolution of begomoviruses[J]. Journal of Zhejiang University Science B, 2008, 9(1): 667~674.

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author="Xiao-zhong XU, Qing-po LIU, Long-jiang FAN, Xiao-feng CUI, Xue-ping ZHOU",
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pages="667~674",
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doi="10.1631/jzus.B0820005"
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%A Xiao-zhong XU
%A Qing-po LIU
%A Long-jiang FAN
%A Xiao-feng CUI
%A Xue-ping ZHOU
%J Journal of Zhejiang University SCIENCE B
%V 9
%N 9
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%@ 1673-1581
%D 2008
%I Zhejiang University Press & Springer

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T1 - Analysis of synonymous codon usage and evolution of begomoviruses
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A1 - Xue-ping ZHOU
J0 - Journal of Zhejiang University Science B
VL - 9
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SP - 667
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Y1 - 2008
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Abstract: 
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.

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article

Reference

[1] Adams, M.J., Antoniw, J.F., 2004. Codon usage bias amongst plant viruses. Archives of Virology, 149(1):113-135.

[2] Duret, L., Mouchiroud, D., 1999. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proceedings of the National Academy of Sciences of the USA, 96(8):4482-4487.

[3] 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.

[4] Greenacre, M.J., 1984. Theory and Applications of Correspondence Analysis. Academic Press, London, p.1-364.

[5] Gu, W., Zhou, T., Ma, J., Sun, X., Lu, Z., 2004. Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales. Virus Research, 101(2):155-161.

[6] Guo, X.Y., Bao, J.D., Fan, L.J., 2007. Evidence of selectively driven codon usage in rice: implications for GC content evolution of Gramineae genes. FEBS Letters, 581(5):1015-1021.

[7] Gupta, S.K., Bhattacharyya, T.K., Ghosh, T.C., 2004. Synonymous codon usage in Lactococcus lactis: mutational bias versus translational selection. Journal of Biomolecular Structure and Dynamics, 21(4):527-536.

[8] Ha, C., Coombs, S., Revill, P., Harding, R., Vu, M., Dale, J., 2006. Corchorus yellow vein virus, a New World geminivirus from the Old World. Journal of General Virology, 87(4):997-1003.

[9] Harrison, B.D., Robinson, D.J., 1999. Natural genomic and antigenic variation in whitefly-transmitted geminiviruses (Begomoviruses). Annual Review of Phytopathology, 37(1):369-398.

[10] Jenkins, G.M., Holmes, E.C., 2003. The extent of codon usage bias in human RNA viruses and its evolutionary origin. Virus Research, 92(1):1-7.

[11] Mansoor, S., Zafar, Y., Briddon, R.W., 2006. Geminivirus disease complexes: the threat is spreading. Trends in Plant Science, 11(5):209-212.

[12] Moffat, A.S., 1999. Plant pathology: geminiviruses emerges as serious crop threat. Science, 286(5446):1835.

[13] Moriones, E., Navas-Castillo, J., 2000. Tomato yellow leaf curl virus, an emerging virus complex causing epidemics worldwide. Virus Research, 71(1-2):123-134.

[14] Naya, H., Romero, H., Carels, N., Zavala, A., Musto, H., 2001. Translational selection shapes codon usage in the GC-rich genomes of Chlamydomonas reinhardtii. FEBS Letters, 501(2-3):127-130.

[15] Rybicki, E.P., 1994. A phylogenetic and evolutionary justification for three genera of Geminiviridae. Archives of Virology, 139(1-2):49-77.

[16] Sau, K., Gupta, S.K., Sau, S., Ghosh, T.C., 2005a. Synonymous codon usage bias in 16 Staphylococcus aureus phages: implication in phage therapy. Virus Research, 113(2):123-131.

[17] Sau, K., Gupta, S.K., Sau, S., Ghosh, T.C., 2005b. Comparative analysis of the base composition and codon usages in fourteen mycobacteriophage genomes. Journal of Biomolecular Structure and Dynamics, 23(1):63-71.

[18] Sau, K., Sau, S., Mandal, C.S., Ghosh, T.C., 2005c. Factors influencing the synonymous codon and amino acid usage bias in AT-rich Pseudomonas aeruginosa phage PhiKZ. Acta Biochimica et Biophysica Sinica, 37(9):625-633.

[19] Shackelton, L.A., Parrish, C.R., Holmes, E.C., 2006. Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses. Journal of Molecular Evolution, 62(5):551-563.

[20] Sharp, P.M., Li, W.H., 1986. An evolutionary perspective on synonymous codon usage in unicellular organisms. Journal of Molecular Evolution, 24(1-2):28-38.

[21] Sharp, P.M., Li, W.H., 1987. The codon adaptation index—a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Research, 15(3):1281-1295.

[22] 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.

[23] 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).

[24] Wright, F., 1990. The ‘effective number of codons’ used in a gene. Gene, 87(1):23-29.

[25] Zhou, T., Gu, W.J., Ma, J.M., Sun, X., Lu, Z.H., 2005. Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses. Biosystems, 81(1):77-86.

[26] 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.

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