Figure 3

Duplication and loss of Argonaute genes and variation of the catalytic motif. Gene duplication and loss events were estimated by reconciliation analysis. Red and blues dots are shown at internal nodes if duplication and loss were predicted, respectively. Black dots indicate nodes where both duplication and loss were discovered. Numbers of species-level duplication and loss events, and the number of putative genes encoding Argonaute, are shown between the tree and species name. In the rightmost column, amino acid variation of the DDH motif is shown with symbols: i) filled squares indicate that all the genes in the corresponding species had the conserved reference residue; ii) shaded squares indicate existence of the conserved residue and variants; iii) empty squares indicate variants without the conserved residue; and iv) single-letter amino acid codes indicate conserved residues, but not the reference amino acid. For the complete list of partial alignments near each amino acid, see Additional file 2. Pie charts shown in the internal nodes display the distribution of DDH motif variants for each taxon specified. The proportion of genes containing the conserved DDH motif is shown in green; H substituted by D, E, or K is shown in red; H substituted by another amino acid is shown in blue; and other variants are shown in orange.