Fig. 3: Developmental and evolutionary features of CDS-recoding events in mitochondria.

A Editing frequencies of 247 C-to-U sites (outside of overlapped genes) in CDS (179 for CDS-recoding and 31 for CDS-synonymous), intronic (25) and intergenic (12) regions during five rice endosperm development stages. In addition, editing frequency of three sites in pseudogenic regions are not compared with that of CDS-recoding sites because of few sites. The Wilcoxon test was used to calculate the statistical significance (p-value, with ***<0.001, and ****<0.0001). Components of the box plot are: center line, median value; box limits, upper and lower quartiles; whiskers, 1.5x interquartile range; error bars: the highest and lowest values excluding outliers. B Editing variabilities of these 247 C-to-U sites across five stages during rice endosperm development. The Wilcoxon test was used to calculate the statistical significance (p-value, with **<0.01, and ***<0.001). Components of the box plot are: center line, median value; box limits, upper and lower quartiles; whiskers, 1.5x interquartile range; error bars: the highest and lowest values excluding outliers. C Correlation between editing frequency of CDS-recoding sites and evolutionary conservation of amino acids corresponding to these CDS-recoding sites. Spearman’s correlation coefficient is calculated for the correlation. The fitted curve is implemented by the generalized linear model. Points in different colors denote CDS-recoding sites in mitochondrial genes encoding different proteins or complexes. Based on the density distribution of conservation of amino acids (Supplementary Fig. 7), thresholds of high and low conservation were set at 0.50 and 0.15, respectively. Similarly, thresholds of high and low editing frequencies were set at 0.89 and 0.10, respectively, according to the density distribution of editing frequencies of these CDS-recoding sites (Supplementary Fig. 8).