According to the variation analysis of base composition for the genes of begomoviruses, the AV1 gene was selected as a reference dataset to calculate the CAI values of all genes. The correlation analysis between CAI value and the positions of the genes along the first two major axes (generated by correspondence analysis), as well as other indices, was then calculated. It was observed that the CAI values were negatively correlated with the GC3 and GC contents (r=−0.234 and r=−0.535 respectively, P<0.01), while significantly positively correlated with axis 1 (r=0.587, P<0.01). Moreover the CAI value was also significantly negatively correlated with the N c value, indicating a tendency to a higher CAI value or a lower N c value and a higher expression level for begomovirus genes. Thus it is feasible to use the AV1 gene as a reference dataset for our estimation of the CAI value of begomovirus genes.