The influence of translational selection on codon usage in fishes from the family Cyprinidae

In this paper, the main factors shaping codon usage in three species of fishes that belong to the family Cyprinidae (namely Brachidanio rerio, Cyprinus carpio, and Carassius auratus) are reported. Correspondence analysis (COA), a commonly used multivariate statistical approach, was used to analyze codon usage bias. Our results show that the main trend is strongly correlated with the GC(3) content at silent sites of each sequence. On the other hand, the second axis discriminates between presumed highly and lowly expressed genes, a result that is confirmed by the distribution of matching expressed sequence tags (ESTs) along that axis. Translational selection appears, therefore, to influence synonymous codon usage in these fishes. The comparison of codon usages of the sequences displaying the extreme values on the second axis indicates that several codons are significantly incremented among the heavily expressed sequences. Interestingly, several of these triplets are not only shared by the three fishes but also by Xenopus laevis, another cold-blooded vertebrate in which translational selection influences codon choices. We postulate that natural selection was operative for codon usage in the last common ancestor of these fishes and Xenopus, and will probably be detected in cold-blooded vertebrates in general. Finally, we raise the possibility that the same phenomena will be found among warm-blooded vertebrates.