As to the gene itself, the selection pressures from the external environment always act as effective factors in promoting the gene to adapt to the change in the external environment. On the other hand, direct changes to a gene will interfere with or be harmful to the gene. Therefore, the base mutation at the synonymous third codon position may not affect the protein expression for AC1 gene because of the degeneration of genetic codons. But for the embedded AC4 gene, the corresponding base mutation occurs at the second codon position, which probably results in the loss of function of the translated protein. Thus we suggested that AC4 gene might degenerate step by step during the long period of evolution, which might be an important reason for explaining the loss of function for the AC4 gene in the bipartite begomoviruses with DNA B.