The results of the N c -plot and base composition analysis indicated that the codon usage pattern of begomoviruses was influenced by mutation bias as well as other factors such as translational selection. Comparative analysis of AC1 and AC4 genes showed that the compositional environment of the former genes might play a role in dictating the codon usage of the latter gene. Thus, although it seems that strong translational selection might have an influence on shaping the codon usage of AC4 genes, the compositional constraints derived from AC1 genes might be the major determinant in determining codon usage.