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Figure 5 | BMC Evolutionary Biology

Figure 5

From: Molecular evolution of pentatricopeptide repeat genes reveals truncation in species lacking an editing target and structural domains under distinct selective pressures

Figure 5

Rate of evolution for individual PPR domains illustrated with OTP82 . Comparable data for CRR4 and CRR21 are shown in Additional file 4. ( A) dN/dS calculated for OTP82 for each PPR domain, E, E+, and DYW domains. ( A, B) Each repeat is labeled 1 through 13 from the N terminus and P, L, and S domains are indicated [1]. (B) dN/dS versus the aligned PPR and each predicted helix. Black bars indicate values calculated from sequences encoding the entire gene, A helices, a single predicted helix for a PPR, and predicted helices 1 and 3 of the E domain. Grey bars indicate dN/dS values of predicted B-helices and helix 2 and 4 of the E domain. ( A and B) P-values were calculated to determine if computed dN/dS values are significantly different from the mean value for the entire aligned gene. The symbols * and ** indicate data points with p-values <0.05 and <0.005 respectively. C) Values for dN/dS are plotted calculated from 7 PPR genes. For each gene estimated dN/dS is shown for the entire aligned gene, concatenated A helices, and concatenated B-helices. P-values indicate the likelihood that predicted dN/dS values for one concatenated helix differs from the other. Symbols * and ** mark dN/dS estimates that have associated p-values <0.05 and <0.005 respectively. D) A structural prediction for a segment of the OTP82 protein. The image illustrates the inner and outer facing surfaces of the superhelical structure that are predicted to be created by the antiparallel helices of three PPR repeats. The region imaged corresponds to 3 repeats between residues N98 to S202 of OTP82.

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