Previous Article |
Table of Contents
| Next Article 
Evolution
Codon usage between genomes is constrained by genome-wide mutational processes
Department of Developmental Biology, Stanford University School of Medicine, Beckman Center, B300, Stanford, CA 94304
Contributed by Lucy Shapiro, December 9, 2003
Analysis of genome-wide codon bias shows that only two parameters effectively differentiate the genome-wide codon bias of 100 eubacterial and archaeal organisms. The first parameter correlates with genome GC content, and the second parameter correlates with context-dependent nucleotide bias. Both of these parameters may be calculated from intergenic sequences. Therefore, genome-wide codon bias in eubacteria and archaea may be predicted from intergenic sequences that are not translated. When these two parameters are calculated for genes from nonmammalian eukaryotic organisms, genes from the same organism again have similar values, and genome-wide codon bias may also be predicted from intergenic sequences. In mammals, genes from the same organism are similar only in the second parameter, because GC content varies widely among isochores. Our results suggest that, in general, genome-wide codon bias is determined primarily by mutational processes that act throughout the genome, and only secondarily by selective forces acting on translated sequences.
Present address: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305.
* To whom correspondence should be addressed. E-mail: slchen{at}stanford.edu.
CiteULike 
Complore 
Connotea 
Del.icio.us 
Digg What's this?
This article has been cited by other articles in HighWire Press-hosted journals:
|
|
 |
|
  P. Puigbo, A. Romeu, and S. Garcia-Vallve HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection Nucleic Acids Res., January 11, 2008; 36(suppl_1): D524 - D527. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Molina and E. van Nimwegen Universal patterns of purifying selection at noncoding positions in bacteria Genome Res., January 1, 2008; 18(1): 148 - 160. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Dethlefsen and T. M. Schmidt Performance of the Translational Apparatus Varies with the Ecological Strategies of Bacteria J. Bacteriol., April 15, 2007; 189(8): 3237 - 3245. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. D. Cutter, J. D. Wasmuth, and M. L. Blaxter The Evolution of Biased Codon and Amino Acid Usage in Nematode Genomes Mol. Biol. Evol., December 1, 2006; 23(12): 2303 - 2315. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Palmeira, L. Gueguen, and J. R. Lobry UV-Targeted Dinucleotides Are Not Depleted in Light-Exposed Prokaryotic Genomes Mol. Biol. Evol., November 1, 2006; 23(11): 2214 - 2219. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y.-S. Lin, J. K. Byrnes, J.-K. Hwang, and W.-H. Li Codon-usage bias versus gene conversion in the evolution of yeast duplicate genes PNAS, September 26, 2006; 103(39): 14412 - 14416. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W.-Y. Ko, S. Piao, and H. Akashi Strong Regional Heterogeneity in Base Composition Evolution on the Drosophila X Chromosome Genetics, September 1, 2006; 174(1): 349 - 362. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Comeron and T. B. Guthrie Intragenic Hill-Robertson Interference Influences Selection Intensity on Synonymous Mutations in Drosophila Mol. Biol. Evol., December 1, 2005; 22(12): 2519 - 2530. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. P.C. Rocha Codon usage bias from tRNA's point of view: Redundancy, specialization, and efficient decoding for translation optimization Genome Res., November 1, 2004; 14(11): 2279 - 2286. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. d. Reis, R. Savva, and L. Wernisch Solving the riddle of codon usage preferences: a test for translational selection Nucleic Acids Res., September 24, 2004; 32(17): 5036 - 5044. [Abstract] [Full Text] [PDF]
|
|
