Plant Molecular Biology (2018) 97:215–231
Towards a comprehensive picture of C-to-U RNA editing sites
in angiosperm mitochondria
Alejandro A. Edera
· Carolina L. Gandini
· M. Virginia Sanchez‑Puerta
Received: 16 November 2017 / Accepted: 2 May 2018 / Published online: 14 May 2018
© Springer Science+Business Media B.V., part of Springer Nature 2018
Key message Our understanding of the dynamic and evolution of RNA editing in angiosperms is in part limited by
the few editing sites identiﬁed to date. This study identiﬁed 10,217 editing sites from 17 diverse angiosperms. Our
analyses conﬁrmed the universality of certain features of RNA editing, and oﬀer new evidence behind the loss of
editing sites in angiosperms.
Abstract RNA editing is a post-transcriptional process that substitutes cytidines (C) for uridines (U) in organellar transcripts
of angiosperms. These substitutions mostly take place in mitochondrial messenger RNAs at speciﬁc positions called editing
sites. By means of publicly available RNA-seq data, this study identiﬁed 10,217 editing sites in mitochondrial protein-coding
genes of 17 diverse angiosperms. Even though other types of mismatches were also identiﬁed, we did not ﬁnd evidence
of non-canonical editing processes. The results showed an uneven distribution of editing sites among species, genes, and
codon positions. The analyses revealed that editing sites were conserved across angiosperms but there were some species-
speciﬁc sites. Non-synonymous editing sites were particularly highly conserved (~ 80%) across the plant species and were
eﬃciently edited (80% editing extent). In contrast, editing sites at third codon positions were poorly conserved (~ 30%) and
only partially edited (~ 40% editing extent). We found that the loss of editing sites along angiosperm evolution is mainly
occurring by replacing editing sites with thymidines, instead of a degradation of the editing recognition motif around edit-
ing sites. Consecutive and highly conserved editing sites had been replaced by thymidines as result of retroprocessing, by
which edited transcripts are reverse transcribed to cDNA and then integrated into the genome by homologous recombination.
This phenomenon was more pronounced in eudicots, and in the gene cox1. These results suggest that retroprocessing is a
widespread driving force underlying the loss of editing sites in angiosperm mitochondria.
Keywords RNA editing · Mitochondrial genome · Angiosperm · Retroprocessing
RNA editing is a post-transcriptional event that alters
the content of plant organellar RNAs. The speciﬁc RNA
positions affected by RNA editing, along with their
corresponding DNA positions, are usually known as edit-
ing sites. In angiosperms, this post-transcriptonal event sub-
stitutes cytidines (C) for uridines (U) mainly in mitochon-
drial transcripts, in which ca. 400 editing sites have been
reported in Arabidopsis (Bentolila et al. 2013; Giegé and
Brennicke 1999), in comparison to the ca. 30 editing sites
found in chloroplasts (Chateigner-Boutin and Small 2007;
Lutz and Maliga 2001; Fujii and Small 2011; Tillich et al.
2006). Most editing sites are located in protein-coding genes
but also in non-coding regions, tRNAs, introns, or UTRs
(Castandet et al. 2010; Grimes et al. 2014).
Editing sites are surrounded by a sequence motif involved
in the binding of the editosome (Cummings and Myers 2004;
Farré et al. 2001; Giegé and Brennicke 1999; Mulligan et al.
2007; Neuwirt et al. 2005). The editosome is composed of
distinct nuclear-encoded proteins with variable speciﬁcity
Electronic supplementary material The online version of this
article (https ://doi.org/10.1007/s1110 3-018-0734-9) contains
supplementary material, which is available to authorized users.
* Alejandro A. Edera
IBAM, Facultad de Ciencias Agrarias,
CONICET, Universidad Nacional de Cuyo,
M5528AHB Chacras de Coria, Argentina
Facultad de Ciencias Exactas y Naturales, Universidad
Nacional de Cuyo, 5500 Mendoza, Argentina