Analysis of synonymous codon usage and evolution of begomoviruses

Journal of Zhejiang University: Science B

Volumn 9, Issue 9, 2008, Pages 667-674

  Xu, Xiao Zhong ^a   Liu, Qing Po ^b   Fan, Long Jiang ^a   Cui, Xiao Feng ^a   Zhou, Xue Ping ^a,b  

^a ZHEJIANG UNIVERSITY   (China)

^b ZHEJIANG A F UNIVERSITY   (China)

Author keywords

Begomovirus; Bioinformatics; Evolution; Synonymous codon usage

Indexed keywords

COAT PROTEIN; DNA A; DNA B; NUCLEAR PROTEIN; PROTEIN AV1; PROTEIN BV1; UNCLASSIFIED DRUG; VIRUS PROTEIN;

AMINO ACID ANALYSIS; ARTICLE; BEGOMOVIRUS; CODON USAGE; CODON USAGE BIAS; CONTROLLED STUDY; DNA BASE COMPOSITION; GENE EXPRESSION; GENE MUTATION; GENE SEQUENCE; MOLECULAR EVOLUTION; NONHUMAN; NUCLEIC ACID ANALYSIS; PRIORITY JOURNAL; TRANSLATION INITIATION; VIRUS GENE;

BEGOMOVIRUS; CHROMOSOME MAPPING; CODON; DNA MUTATIONAL ANALYSIS; DNA, VIRAL; EVOLUTION; EVOLUTION, MOLECULAR;

BEGOMOVIRUS; DNA VIRUSES;

EID: 51649090950     PISSN: 16731581     EISSN: 18621783     Source Type: Journal    
DOI: 10.1631/jzus.B0820005     Document Type: Article

References (26)

1. Adams, M.J., Antoniw, J.F., 2004. Codon usage bias amongst plant viruses. Archives of Virology, 149(1):113-135. [doi:10.1007/ s00705-003-0186-6]
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. [doi:10.1073/pnas.96.8.4482]
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. [doi:10.1007/s00705-002-0957-5]
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. [doi:10.1016/j.virusres.2004.01.006]
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. [doi:10.1016/ j.febslet.2007.01.088]
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. [doi:10.1099/vir.0.81631-0]
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. [doi:10.1146/ annurev.phyto.37.1.369]
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. [doi:10.1016/S0168-1702(02) 00309-X]
11. Mansoor, S., Zafar, Y., Briddon, R.W., 2006. Geminivirus disease complexes: The threat is spreading. Trends in Plant Science, 11(5):209-212. [doi:10.1016/j.tplants.2006. 03.003]
12. Moffat, A.S., 1999. Plant pathology: Geminiviruses emerges as serious crop threat. Science, 286 (5446):1835. [doi:10. 1126/ 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. [doi:10. 1016/S0168-1702(00)00193-3]
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. [doi:10.1016/ S0014-5793(01)02644-8]
15. Rybicki, E.P., 1994. A phylogenetic and evolutionary justification for three genera of Geminiviridae. Archives of Virology, 139(1-2):49-77. [doi:10.1007/BF01309454]
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. [doi:10.1016/ j.virusres.2005.05.001]
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. [doi:10.1111/j.1745-7270.2005.00089.x]
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. [doi:10.1007/ s00239-005-0221-1]
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. [doi:10.1007/BF02099948]
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. [doi:10.1093/nar/15.3.1281]
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. [doi:10.1093/nar/16.17.8207]
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. [doi:10.1016/0378-1119(90)90 491-9]
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. [doi:10.1016/j.biosystems.2005.03.002]
26. Zhou, X.P., Xie, Y., Tao, X.R., Zhang, Z.K., Li, Z.H., Fauquet, C.M., 2003. Characterization of DNAα 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]