Site to site detection and analysis of C-to-U RNA editing in rice mitochondria-encoded ORFs

Abstract Background Cytidine to uridine (C-to-U) RNA editing is an important type of substitutional RNA editing. In plants, C-to-U modification is almost omnipresent in chloroplasts and mitochondria, where it mainly serves to restore evolutionarily conserved amino acids by changing the codon information. The important roles that C-to-U RNA editing plays in organelle biogenesis, adaptation to environmental changes, and signal transduction have been confirmed in different plant species. In rice mitochondria, 491 C-to-U editing sites have been identified previously, and case studies have elucidated the function of several C-to-U editing sites in rice, but the functional consequence of most C-to-U alteration need to be investigated further. Results Here, we totally identified 539 C-to-U editing sites in rice mitochondria-encoded ORFs, 87.2% of these editing sites were observed on the first or the second base of a codon, resulting in the alteration of encoded amino acid. Moreover, we found some novel editing sites and several inaccurately annotated sites which may be functionally important, with the support of the highly conserved amino acids encoded by these edited codons. Finally, we annotated all 539 C-to-U RNA editing sites in their biological context. Conclusions We detected 539 C-to-U editing sites in rice mitochondria-encoded ORFs and annotated them with more precise information, which will facilitate our investigation on the function of C-to-U editing events in rice.