Codon usage in bony fishes

Bony fishes are excellent experimental models that have been used extensively in biochemical and molecular genetic studies. As proteins are isolated and characterized from these organisms, information on codon usage by bony fishes can be used for subsequent recombinant DNA studies. Codon usage and nucleotide bias within codons from three species of bony fishes and two composites of 14 and 15 bony-fish species were analyzed. Although differences in codon usage increased from seven amino acids between fish species to eight amino acids between fish genera, the small number of differences (3 amino acids) between a single species and a fish composite minus that species suggests that codon usage tables constructed from large numbers of fish species are representative of bony fish in general. Furthermore, we found few differences in codon usage between two vertebrate phyla (fish and rat). Codons in fish DNA sequences end predominantly in G or C, even though the coding sequences are not enriched in these nucleotides. This positional base bias can be used to locate putative protein coding regions in fish DNA sequences.