An N c plot (a plot of N c vs GC3 content) was widely used to investigate the determinants of the codon usage variations among genes in different organisms. It was suggested that if GC3 content was the only determinant of the codon usage variation among the genes, then the N c value would fall on the continuous curve between N c value and GC3 content (Wright, 1990 ). In general, if genes are distributed in N c plots approaching the expected continuous curve with no selection, then codon usage bias of genes is mainly influenced by compositional constraints. Otherwise the codon usage bias of genes is more affected by other factors such as translational selection, etc. The N c plot for genes of the 147 begomoviruses showed that although a small number of genes were located on the expected curve, most points lay far below the expected curve ( Fig.1) , suggesting that apart from mutation bias, other factors might also play a role in shaping the codon usage bias of begomoviruses (Guo et al., 2007) . Table 1 The GC content at the different codon positions and the A, T, G and C contents at the third position of begomovirus genes Base composition analysis suggested that the codon usage of the AC4 gene, which is always embedded in the AC1 gene, might differentiate from other genes. In addition, strong codon bias was observed in AV1 gene. Because of the special characteristics of the abovementioned genes, we selected them for examining the influence factors in shaping the codon usage (Fig.2a) . The N c plots of AV1, AC1 and AC4 genes suggested that apart from compositional constraints, other factors might play important roles in shaping their codon usage, although high translational selection seems to lay stress on the AC4 gene because of the wide range of N c values for the same GC3 content.