The Frequencies of Amino Acids Encoded by Genomes that Utilize Standard and Nonstandard Genetic Codes

Abstract

A number of genomes use genetic codes that are different from the standard genetic code. Since many of these genomes have recently been sequenced, we can now study the evolution of the genetic codes by examining the amino acid frequencies encoded by these genomes. We calculated the amino acid frequencies encoded by twenty-two genomes using codon usage frequencies tabulated from GenBank. By chi-square analysis, no significant differences were observed in the amino acid frequencies encoded by fourteen different genomes that use the standard genetic code. However, among eight genomes that employ nonstandard genetic codes, we found differences between three animal mitochondrial genomes (Fasciola hepatica, Drosophila melanogaster, and Homo sapiens) and the remaining 19 genomes. Of the genomes that were studied, we also observed a trend between the usage of an amino acid and its occurrence in the genetic code. Taken together, our study supports the hypothesis that the standard genetic code formed early in the development of modern life and evolved in different lineages to form several nonstandard genetic codes.