Sequence and structure preferences of the A-to-I editing sites in F. graminearum. (A) Two Sample Logo showing the enriched (above the top line) and depleted (below the bottom line) nucleotides nearby the A's targeted for RNA editing (P < 0.01, t-test), with the level of preference or depletion proportional to the scale. A total of 30,000 adenosine sites randomly chosen from predicted cDNA sequences were used as the negative control. (B) The percentage of marked triplet sequences with A-to-I editing events. For each of the 16 possible triplets centered on the edited adenosine (NAN), the number of observed editing events was divided by its total occurrence in cDNA sequences. The horizontal dotted line marks the average percentage (0.56%) of editing events observed in these 16 NAN triplets. (C) Box plot comparing the editing levels of editing sites in different triplets: (****) P < 0.0001, t-test; (ns) not significant. (D) Stacked column showing the ratio of RNA editing events of marked editing levels in the five types of RNA secondary structure elements diagrammed on the right. The predicted RNA secondary structure is based on 30-nt upstream and 30-nt downstream sequences surrounding the edited A's. The statistical significance for hairpin loop ratio comparison is indicated: (****) P < 0.0001, χ2-test; (ns) not significant. (E) Box plot showing the minimum free energy (MFE) of predicted hairpin loops with A-to-I editing events of different editing levels. The statistical significance for each comparison is indicated: (****) P < 0.0001, t-test; (ns) not significant.
