In addition we found that AV1 and BV1 genes had a tendency to usage bias at the synonymous third codon position. The AV1 gene does not tend to use A(T)-ending or G(C)-ending codons but tends to use T-ending codons relative to A-ending codons. However, BV1 gene apparently uses T-ending codons and seldom used C-ending codons. Therefore, AV1 and BV1 genes should show a stronger codon usage bias among the begomovirus genes.