PMID: 2120453Aug 1, 1990Paper

Codon usage changes and sequence dissimilarity between human and rat

Journal of Molecular Evolution
D Mouchiroud, C Gautier

Abstract

This paper reports on the relationship between the number of silent differences and the codon usage changes in the lineages leading to human and rat. Examination of 102 pairs of homologous genes gives rise to four main conclusions: (1) We have previously demonstrated the existence of a codon usage change (called the minor shift) between human and rat; this was confirmed here with a larger sample. For genes with extreme C & G frequencies, the C & G level in the third codon position is less extreme in rat than in human. (2) Protein similarity and percentage of positive differences are the two main factors that discriminate homologous genes when characterized by differences between rat and human. By definition, positive differences result from silent changes between A or T and C or G with a direction implying a C & G content variation in the same direction as the overall gene variation. (3) For genes showing both codon usage change and low protein similarity, a majority of amino acid replacements contributes to C & G level variation in positions I and II in the same direction as the variation in position III. This is thus a new example of protein evolution due to constraints acting at the DNA level. (4) In heavy isochores (high C ...Continue Reading

References

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Citations

Mar 1, 1995·Journal of Molecular Evolution·S CacciòG Bernardi
Oct 1, 1990·Journal of Molecular Evolution·G Bernardi, G Bernardi
Aug 1, 1993·Journal of Molecular Evolution·G SabeurG Bernardi
Aug 1, 1993·Journal of Molecular Evolution·D Mouchiroud, G Bernardi
Apr 1, 1991·Gene·D MouchiroudG Bernardi
Aug 6, 2000·International Journal for Parasitology·A Hemphill, B Gottstein
Jan 1, 1995·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·M S Gelfand
Jun 25, 1994·Nucleic Acids Research·L DuretM Gouy
Nov 23, 2000·Current Opinion in Genetics & Development·C Gautier
Jan 7, 1998·Molecular Phylogenetics and Evolution·M RobinsonD Mouchiroud
Dec 6, 2002·Nature·UNKNOWN Mouse Genome Sequencing ConsortiumEric S Lander
Dec 2, 1998·Genetics·N Galtier, D Mouchiroud

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