Prokaryotic Genome Evolution as Assessed by Multivariate Analysis of Codon Usage Patterns

Microbial and Comparative Genomics

Volumn 2, Issue 1, 1997, Pages 89-97

  Mcinerney, James O ^a  

^a DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84975862989     PISSN: 10906592     EISSN: None     Source Type: Journal    
DOI: 10.1089/omi.1.1997.2.89     Document Type: Article

References (25)

1. ANDERSSON, S. G. E., and SHARP, P. M. (1996). Codon usage and base composition in Rickettsia prowazekii. J Mol Evol 42, 525–536.
2. BENNETZEN, J. L., and HALL, B. D. (1982). Codon selection in yeast. J Biol Chem 257, 3026–3031.
3. BERNARDI, G. (1993). The isochore organisation of the human genome and its evolutionary history—a review. Gene 135, 57–66.
4. BULT, C. J., WHITE, O., OLSEN, G. J., ZHOU, L., FLEISCHMANN, R. D., SUTTON, G. C., et al. (1996). Complete genome sequence of the methanogenic Archaeon, Methanococcus jannaschii. Science 273, 1058–1073.
5. FELSENSTEIN, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368–376.
6. FLEISCHMANN, R. D., ADAMS, M. D., WHITE, O., CLAYTON, R. A., KIRKNESS, E. F., KERLAVAGE, A. R., et al. (1995). Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496–512.
7. FRASER, C. M., GOCAYNE, J. D., WHITE, O., ADAMS, M. D., CLAYTON, R. A., FLEISCHMANN, R. D., et al. (1995). The minimal gene complement of Mycoplasma genitalium. Science 270, 397–403.
8. GRANTHAM, R., GAUTIER, C., GOUY, M., JACOBZONE, M., and MERCIER, R. (1981). Codon catalog usage is a genome strategy modulated for gene expressivity. Nucleic Acids Res, 9, r43-r74.
9. GREENACRE, M. J. (1984). Theory and Applications of Correspondence Analysis. (Academic Press, London).
10. IKEMURA, T. (1981). Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein sequence: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. I Mol Biol 151, 389–409.
11. IKEMURA, T. (1982). Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. J Mol Biol 158, 573–597.
12. IWABE, N., KUMA, K. L., HASEGAWA, M., OSAWA, S., and MIYATA, T. (1989). Evolutionary relationships of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc Natl Acad Sci USA 86, 9355–9359.
13. LLOYD, A. T., and SHARP, P. M. (1991). Codon usage in Aspergillus nidulans. Mol Gen Genet 230, 288–294.
14. LLOYD, A. T., and SHARP, P. M. (1992). CODONS: a microcomputer program for codon usage analysis. J Hered 83, 239–240.
15. LLOYD, A. T., and SHARP, P. M. (1993). Synonymous codon usage in Kluyveromyces lactis. Yeast 9, 1219–1228.
16. MÉDIGUE, C., ROUXEL, T., VIGIER, P., HÉNAUT, A., and DANCHIN, A. (1991). Evidence for horizontal gene transfer in Escherichia coli speciation. J Mol Biol 222, 851–856.
17. MUTO, A., and OSAWA, S. (1987). The guanine and cytosine content of genomic DNA and bacterial evolution. Proc Natl Acad Sci USA 84, 166–169.
18. SHARP, P. M., and COWE, E. (1991). Synonymous codon usage in Saccharomyces cerevisiae. Yeast 7, 657–678.
19. SHARP, P. M., and DEVINE, K. M. (1989). Codon usage and gene expression level in Dictyostelium discoideum: highly expressed genes do “prefer” optimal codons. Nucleic Acids Res 17, 5029–5039.
20. SHARP, P. M., STENICO, M., PEDEN, J. F., and LLOYD, A. T. (1993). Codon usage: mutational bias, translational selection or both? Biochem Soc Trans 21, 835–841.
21. SHARP, P. M., TUOHY, T. M. F., and MOSURSKI, K. R. (1986). Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res 14, 5125–5143.
22. SRIVASTAVA, A. K., and SCHLESSINGER, D. (1990). Mechanism and regulation of bacterial ribosomal RNA processing. Annu Rev Microbiol 44, 105–129.
23. WOESE, C. R., KANDLER, O., and WHEELIS, M. L. (1990). Towards a natural system of organisms: proposal for the domains Archaea, Bacteria and Eucarya. Proc Natl Acad Sci USA 87, 4587.
24. WOLFE, K. H., SHARP, P. M., and LI, W. H. (1989). Mutation rates differ among regions of the mammalian genome. Nature 337, 283–285.
25. WRIGHT, F. (1990). The “effective number of codons” used in a gene. Gene 87, 23–29.