Genome-wide analysis of codon usage in Mycobacteriophage and S. aureus
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The molecular genetics of microbial life, including viruses and bacteria, is of great relevance to medicine, evolutionary theory, and other areas of science. Here, we study the implications of codon bias, the non-random usage of synonymous codons, and GC3, the frequency of codons with guanine or cytosine in the third nucleotide position. Biased codon usage frequently is the result of adaptation for optimal expression, reflecting tRNA abundance. It has previously been suggested that GC3 is similarly of functional significance, with implications for transcription and translation. We make use of the HHMI’s mycobacteriophage genome database to analyze trends in codon bias and GC3 content in a diverse set of viruses with a common host. To this end we utilize genome landscapes to observe trends in genome-wide GC3 usage, and find that patterns in GC3 content can be informative in the difficult process of unraveling the complex relationships between mycobacteriophages. Similarly, we show that codon bias is likewise informative, though it in some instances contradicts the evidence provided by GC3 analysis. In a second portion of the study, we investigate the relationship between codon bias, GC3 content, and gene expression in S. aureus BUSA 2288. We find that codon bias is correlated with gene expression in S. aureus, suggesting that it does indeed reflect selection for expression. GC3 is, however, not tied to any trend in expression.