Modeling Sites of RNA Editing as a Fifth Nucleotide State Reveals Progressive Loss of Edited Sites from Angiosperm Mitochondria

Abstract

RNA editing is a type of nucleic acid modification found in many eukaryotic lineages. In plants, RNA editing occurs by the site-specific conversion of cytidines to uridines in mitochondrial and plastid transcripts. To quantify the rates of edit site gain and loss in angiosperm mitochondrial genes, a nonreversible maximum likelihood model was developed that treats sites of RNA editing as a fifth nucleotide state. The rate of loss of editing, either by genomic replacement with a thymidine or by loss of recognition by the editing complex, was found to be significantly higher than the rate of gain. Furthermore, the frequency of editing is not at equilibrium in angiosperm mitochondrial sequences; there is a strong tendency for the number of edited sites to decrease over time. These results indicate that selection plays a key role in driving the higher rate of edit site loss relative to gain and suggest that the strength of selection against editing has become increasingly stringent over the course of angiosperm evolution. The model described here should be easily adaptable to other systems that involve nucleic acid modifications.