Abstract
BackgroundCodon bias is a phenomenon of non-uniform usage of codons whereas codon context generally refers to sequential pair of codons in a gene. Although genome sequencing of multiple species of dipteran and hymenopteran insects have been completed only a few of these species have been analyzed for codon usage bias.Methods and Principal FindingsHere, we use bioinformatics approaches to analyze codon usage bias and codon context patterns in a genome-wide manner among 15 dipteran and 7 hymenopteran insect species. Results show that GAA is the most frequent codon in the dipteran species whereas GAG is the most frequent codon in the hymenopteran species. Data reveals that codons ending with C or G are frequently used in the dipteran genomes whereas codons ending with A or T are frequently used in the hymenopteran genomes. Synonymous codon usage orders (SCUO) vary within genomes in a pattern that seems to be distinct for each species. Based on comparison of 30 one-to-one orthologous genes among 17 species, the fruit fly Drosophila willistoni shows the least codon usage bias whereas the honey bee (Apis mellifera) shows the highest bias. Analysis of codon context patterns of these insects shows that specific codons are frequently used as the 3′- and 5′-context of start and stop codons, respectively.ConclusionsCodon bias pattern is distinct between dipteran and hymenopteran insects. While codon bias is favored by high GC content of dipteran genomes, high AT content of genes favors biased usage of synonymous codons in the hymenopteran insects. Also, codon context patterns vary among these species largely according to their phylogeny.
Highlights
Codon usage bias is a phenomenon of non-uniform usage of codons during translation of genes to proteins
While codon bias is favored by high GC content of dipteran genomes, high AT content of genes favors biased usage of synonymous codons in the hymenopteran insects
To understand the pattern of non-random usage of synonymous codons in these insects, relative synonymous codon usage (RSCU) of individual codons were compared between the two groups of species
Summary
Codon usage bias (or codon bias) is a phenomenon of non-uniform usage of codons during translation of genes to proteins. Specific codons are used more often than alternate synonymous codons in genes where such bias exists. Such codons are often referred to as optimized codons or preferred codons. The extent of codon bias is manifested by balance between mutation and translational selection [1], [2], [3], [4]. Variation of codon optimization among genes provides differential efficiency as well as accuracy in the translation of genes [5], [6], [7]. Codon bias is a phenomenon of non-uniform usage of codons whereas codon context generally refers to sequential pair of codons in a gene. Genome sequencing of multiple species of dipteran and hymenopteran insects have been completed only a few of these species have been analyzed for codon usage bias
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