The correlation between recombination rate and codon bias in yeast mainly results from mutational bias associated with recombination rather than hill-robertson interference

Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings

Volumn 7 VOLS, Issue , 2005, Pages 4787-4790

  Zhou, T ^a   Lu, Z H ^a   Sun, X ^a  

^a SOUTHEAST UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BYPRODUCTS; CORRELATION METHODS; GENES; MATHEMATICAL MODELS; YEAST;

HILL-ROBERTSON INTERFERENCE; RECOMBINATION RATE;

GENETIC ENGINEERING;

EID: 33846921299     PISSN: 05891019     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/iembs.2005.1615542     Document Type: Conference Paper

References (20)

1. A. Martin, J. Bertranpetit, J.L. Oliver, and J.R. Medina, "Variation in G+C content and codon choice: differences among synonymous codon groups in vertebrate genes," Nucleic Acids Res., vol. 17, pp. 6181-6189, August 1989.
2. A.T. Lloyd and P.M. Sharp, "Evolution of codon usage patterns: The extent and nature of divergence between Candida albicans and Saccharomyces cerevisiae," Nucleic Acids Res., vol. 20, pp. 5289-5295, October 1992.
3. S. Karlin and J. Mrazek, "What drives codon choices in human genes?" J. Mol. Biol., vol. 262, pp. 459-472, October 1996.
4. S.G. Andersson and P.M. Sharp, "Codon usage and base composition in Rickettsia prowazekii," J. Mol. Evol., vol. 42, pp. 525-536, May 1996.
5. W.J. Gu, T. Zhou, J.M. Ma, X. Sun, and Z.H. Lu, "Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales," Virus Res., vol. 101, pp. 155-161, May 2004.
6. 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," J. Mol. Biol., vol. 151, pp. 389-409, September 1981.
7. P.M. Sharp, T. Tuohy, and K. Mosurski, "Codon usage in yeast: Cluster analysis clearly differentiates highly and lowly expressed genes," Nucleic Acids Res., vol. 14, pp. 5125-5143, July 1986.
8. E.N. Moriyama and J.R. Powell, "Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli" Nucleic Acids Res., vol. 26, pp. 3188-3193, July 1998.
9. R.M. Kliman, N. Irving, and M. Santiago, "Selection conflicts, gene expression, and codon usage trends in yeast," J. Mol. Evol., vol. 57, pp. 98-109, July 2003.
10. R.M. Kliman and J. Hey, "Reduced natural selection associated with low recombination in Drosophila melanogaster," Mol. Biol. Evol., vol. 10, pp. 1239-1258, November 1993.
11. G. Marais, D. Mouchiroud, and L. Duret, "Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes," Proc. Natl. Acad. Sci. USA, vol. 98, pp. 5688-5692, April 2001.
12. G. Marais and G. Piganeau, "Hill-Robertson interference is a minor determinant of variations in codon bias across Drosophila melanogaster and Caenorhabditis elegans genome," Mol. Biol. Evol., vol. 19, pp. 1399-1406, September 2002.
13. J.M. Comeron, M. Kreitman, and M. Aguade, "Natural selection on synonymous sites is correlated with gene length and recombination rate in Drosophila," Genetics, vol. 151, pp. 239-249, January 1999.
14. G.A.T. McVean and B. Charlesworth, "The effects of Hill-Robertson interference between weakly selected mutations on patterns of molecular evolution and variation," Genetics, vol. 155, pp. 929-944, June 2000.
15. J.L. Gerton and et al., "Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae," Proc. Natl. Acad. Sci. USA, vol. 97, pp. 11383-11390, October 2000.
16. J. Perry and A. Ashworth, "Evolutionary rate of a gene affected by chromosomal position," Curr. Biol., vol. 9, pp. 987-989, September 1999.
17. S.M. Fullerton, A. Bernardo Carvalho, and A.G. Clark, "Local rates of recombination are positively correlated with GC content in the human genome," Mol. Biol. Evol., vol. 18, pp. 1139-1142, June 2001.
18. P.M. Sharp and W.H. Li, "Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons," Nucleic Acids Res., vol. 14, pp. 7737-7749, October 1986.
19. 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 Res., vol. 15, pp. 1281-1295, February 1987.
20. S. Kanaya, Y. Yamada, Y. Kudo, and T. Ikemura, "Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis," Gene, vol. 238, pp. 143-155, September 1999.