Abstract
In order to examine differences of preferential usage of synonymous codons among species systematically, principal component analysis is applied to a matrix consisting of relative frequencies in synonymous codons. The first two principal components (PC1 and PC2) account for 66% and 8%, respectively. From the PC projection by the first two components, the following conclusion can be obtained:(1) The base-preference of A and U (G and C) at the third position in synonymous codon contributes negatively (positively) to the PC1: Vertebrates and chloroplasts are clusterized in narrow regions with positive and the most negative PC1, respectively.(2) The PC2 is important to distinguish between prokaryotes and (eukaryotes: Eukaryotes prokaryotes) prefer di-nucleotides GA, AG, CU and CA (CG, GC, and AA) at the second and the third positions in codons.
