As the AC4 gene is always embedded in the AC1 gene, the codon usage pattern of the AC4 gene might be influenced by the AC1 gene. The sequences of AC1 and AC4 genes were aligned. It was found that the synonymous third codon position of the AC1 gene corresponded to the second codon position of the AC4 gene for all the begomoviruses. Thus the base compositional environment of the AC1 gene might also influence the codon usage pattern of the AC4 gene. It could be postulated that the second codon position of the AC4 gene that tended to use G or C should be influenced by compositional constraints other than translational selection.