Dinucleotide frequencies and codon usage in jawless and cartilaginous fishes

Dinucleotide frequencies and codon usage in terms of strong-weak codon choices were examined in gene coding regions of 5 jawless and cartilaginous fish species. These dinucleotide frequencies were then compared to gene-coding regions from a vertebrate and an invertebrate species. These primitive vertebrate fishes exhibited species specificity in the hierarchy of dinucleotide frequencies. The most frequently occurring dinucleotide varied among coding regions of jawless and cartilaginous fishes, but it always contained G. Of the 16 dinucleotides, TA had the lowest frequency of occurrence in all species, and it had considerably lower frequencies in jawless fish genes than in cartilaginous fish genes. Dinucleotide frequency analysis suggested CpG conversion to TG in ray genes. Strong-weak codon usage analysis indicated that all 5 fish species used strong-weak-strong bonding codons most frequently; furthermore, each species used any-weak-strong codons in greater than expected levels. Gene coding regions from all 5 species exhibited a bias toward strong bonding nucleotides at codon position 3, with the greatest bias in sea lamprey genes. This bias may reflect the overall G+C content of localized regions of chromosomal DNA in which these genes reside.