Figure 3

Duplication events in Arabidopsis kinases. (A) Phylogenetic tree of kinase families indicating gene duplication events. Small subfamilies were collapsed into artificial monophyletic clades as discussed earlier and indicated in the figure. Duplications are marked by asterisks at branching points corresponding to the most recent common ancestor of duplicates. The different types of duplication events are color-coded. red: segmental, blue: tandem, green: proximal, and orange: transposed. (B) Box plot of ratios of observed to expected tandem and segmental duplication frequencies for each family. The boxed region is centred on the median ratios (indicated by a black square) for tandem and segmental duplications. The mean of ratios is marked by a black triangle. The boxed region and additional lines refer to one and two standard deviations above and below the median ratios. Pie charts for each family indicate the localization of genes according to SUBA3 as the proportion of all genes in that family. (C) Results of the enrichment analysis. For each family and duplication type, the Pearson residuals from Chi-square tests are plotted together with the corresponding significance levels from Fisher’s exact tests. Duplication types are coded as W/D (whole-genome or segmental duplication), D (dispersed), T (tandem), P (proximal) and S (singleton). Red and green color gradients correspond to negative and positive Pearson residuals indicating depleted and enriched counts for each type of duplication. The significance is coded as follows: *corresponds to p < 0.05, ***corresponds to p < 0.001. P-values were adjusted for multiple testing by applying the Benjamini-Hochberg correction.