Fig. 2

Lack of concerted evolution at sequence and expression level among two-copy homeolog groups. a Scatter plot comparing divergence in evolutionary rate (dN/dS ratio) and divergence in expression level for two-copy homeolog pairs in T. coremiiforme. Divergences were calculated as the ratios of subgenome A homeolog’s over subgenome B homeolog’s. Black x markers display the data for all two-copy homeolog pairs. Blue and magenta circles indicate homeolog pairs with significant divergence in only evolutionary rate or only expression level, respectively (adjusted p-value ≤ 0.01 and fold-difference ≥ 3, see the “Materials and methods” section). Red asterisks indicate homeolog groups with significant divergence in both evolutionary rate and expression level and the number of these homeolog groups are indicated in each quadrant. Expression levels from log-phase growth condition are shown. b Box plots showing log-phase expression level of two-copy homeolog pairs in T. coremiiforme with divergent evolutionary rates or decelerated evolutionary rates compared to T. asahii’s orthologs (see the “Materials and methods” section). Mann–Whitney U-test p-value for the comparison between homeolog pairs with decelerated evolutionary rates and those without is indicated at the top. The numbers of homeolog pairs belonging to each class are indicated next to the corresponding box plot. Blue boxes designate the 25th–75th percentile ranges. Red bars indicate the medians. Black whiskers designate the approximated 0.35th–99.65th percentile ranges. Red cross markers indicate individual data points lying outside the 0.35th–99.65th percentile ranges. c and d Similar plots for T. ovoides–T. inkin comparison