Systematization of Species-Speci c Diversity of Genes in Codon Usage: Comparison of the Diversity Among Bacteria and Prediction of the Protein Production Levels in Cells

In the present study, we have developed the procedure for estimating species-speci c heterogeneous codon usage among intraspeci c genes called diversity in codon usage and for systematizing species by the species-speci c diversity on the basis of principal component analysis. We tried to quantify di erences of the diversity among ve species, Escherichia coli (Ec), Salmonella typhimurium (St), Haemophilus in uenzae (Hi), Bacillus subtilis (Bs), and Synechocystis sp. (Ss). In the ve species, many of genes involved in the translation process and energy metabolism had positive values (Z1 > 0) on the rst principal component (PC1). In Ss, many of genes involved in photosynthetic system had also postive Z1-values. These genes are thought to be highly expressed. By the direction of PC1, the ve species were roughly classi ed into three categories, [Ec, St, Hi], [Ss], [Bs]. The dendrogram constructed was roughly consistent with the rRNA-based phylogeny, but interesting di erences were also observed between the two phylogenic trees.