Fig. 5

Purifying and positive selection of VQs during evolution. a The selection force of duplicated VQs in 12 species shown by Ka/Ks values. The tandem and segmentally duplicated VQ pairs were used for Ka/Ks calculation. Two Ka/Ks values were displayed and separated by semicolons. The left values were estimated using VQ motif regions and right values were calculated using the full-length VQs. The figure showed the average Ka/Ks ratios among duplicated VQ pairs in each species. The phylogenetic tree was constructed according to the data retrieved from the NCBI Taxonomy database (http://www.ncbi.nlm.nih.gov/taxonomy). b and c Orthologous genes (shown by locus names) with positive selection among 7 species/subspecies from the Oryza genus. These species include O. barthii, O. glumaepatula, O. meridionalis, O. nivara, O. rufipogon, O. sativa Indica, and O. sativa japonica. A pair of orthologous genes from two species was linked by a line and the corresponding Ka/Ks ratio was labelled near the line. d Alignment of amino acid residues from the 5 VQs with positive selection in b. The amino acid residues with positive selection were highlighted by blue color. Their Ka/Ks ratios were shown under the highlighted residues. VQ motif regions were highlighted by white color. The dots “···” represent the omitted amino acid residues with no variation among 6 species. The asterisk “*” indicates positions with fully conserved residues. The colon “:” and the period “.” indicate conservation between groups of strongly and weakly similar properties of residues, respectively