The complete genomic sequences of 147 begomovirus species were downloaded from the GenBank database, from which a total of 932 variants of the 8 known protein-coding genes were extracted. To minimize sampling errors, 915 variants were selected for further analysis by the following sifting standard: (1) the selected genes should be complete coding DNA sequences (CDS) with correct initial and terminal codons; (2) only those CDS including at least 80 codons were selected in the dataset; (3) those CDS with uncertain annotation or annotated as hypothetical protein-coding genes were excluded from this study.