Difference in Synonymous Polymorphism Related to Codon Degeneracy between Co-Transcribed Genes in the Genome of Escherichia coli

In our study, we compared synonymous polymorphism in co-transcribed gene pairs within five well-known Escherichia coli operons (rpoB/C, lacZ/Y, kdpA/B, araB/A and bcsA/B). Interestingly, the transition to transversion ratio between gene pairs were different due to their compositional differences of two-fold and four-fold degenerate codons. The differences in polymorphism spectra were more pronounced in four-fold and six-fold codons compared to two-fold degenerate codons. Notably, rpoB and rpoC showed significant distinctions in UCC, GUA, CCG, GCU, GGC and CGC codons. Similar trends were observed in other gene pairs, particularly in higher degenerate codons. Notably, two-fold degenerate codons primarily exhibited synonymous polymorphisms through transitions, while higher degenerate codons encompassed both transition and transversion events. This underscores the intriguing role of degenerate codons in molecular evolution.