The chloroplast and mitochondrial C-to-U RNA editing in Arabidopsis thaliana shows signals of adaptation

C-to-U RNA editing is the conversion from cytidine to uridine at RNA level. In plants, the genes undergo C-to-U RNA modification are mainly chloroplast and mitochondrial genes. Case studies have identified the roles of C-to-U editing in various biological processes, but the functional consequence of the majority of C-to-U editing events is still undiscovered. We retrieved the deep sequenced transcriptome data in roots and shoots of Arabidopsis thaliana and profiled their C-to-U RNA editomes and gene expression patterns. We investigated the editing level and conservation pattern of these C-to-U editing sites. The levels of nonsynonymous C-to-U editing events are higher than levels of synonymous events. The fraction of nonsynonymous editing sites is higher than neutral expectation. Highly edited cytidines are more conserved at DNA level, and the gene expression levels are correlated with C-to-U editing levels. Our results demonstrate that the global C-to-U editome is shaped by natural selection and that many nonsynonymous C-to-U editing events are adaptive. The editing mechanism might be positively selected and maintained and could have profound effects on the modified RNAs.