title: Reverse U-to-C editing exceeds C-to-U RNA editing in some ferns - a monilophyte-wide comparison of chloroplast and mitochondrial RNA editing suggests independent evolution of the two processes in both organelles.
abstract: RNA editing by C-to-U conversions is nearly omnipresent in land plant chloroplasts and mitochondria, where it mainly serves to reconstitute conserved codon identities in the organelle mRNAs. Reverse U-to-C RNA editing in contrast appears to be restricted to hornworts, some lycophytes, and ferns (monilophytes). A well-resolved monilophyte phylogeny has recently emerged and now allows to trace the side-by-side evolution of both types of pyrimidine exchange editing in the two endosymbiotic organelles.
  
  
  
  Our study of RNA editing in four selected mitochondrial genes show a wide spectrum of divergent RNA editing frequencies including a dominance of U-to-C over the canonical C-to-U editing in some taxa like the order Schizaeales. We find that silent RNA editing leaving encoded amino acids unchanged is highly biased with more than ten-fold amounts of silent C-to-U over U-to-C edits. In full contrast to flowering plants, RNA editing frequencies are low in early-branching monilophyte lineages but increase in later emerging clades. Moreover, while editing rates in the two organelles are usually correlated, we observe uncoupled evolution of editing frequencies in fern mitochondria and chloroplasts. Most mitochondrial RNA editing sites are shared between the recently emerging fern orders whereas chloroplast editing sites are mostly clade-specific. Finally, we observe that chloroplast RNA editing appears to be completely absent in horsetails (Equisetales), the sister clade of all other monilophytes.
  
  
  
  C-to-U and U-to-C RNA editing in fern chloroplasts and mitochondria follow disinct evolutionary pathways that are surprisingly different from what has previously been found in flowering plants. The results call for careful differentiation of the two types of RNA editing in the two endosymbiotic organelles in comparative evolutionary studies.
authors.affiliation: Abteilung Molekulare Evolution, IZMB - Institut für Zelluläre und Molekulare Botanik, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany.
authors.forename: Nils
authors.initials: N
authors.lastname: Knie
authors.affiliation: Present address: Department of Science and Education, Field Museum of Natural History, Integrative Research Center, 1400 South Lake Shore Drive, Chicago, IL, 60605, USA.
authors.forename: Felix
authors.initials: F
authors.lastname: Grewe
authors.affiliation: Present address: Protrans medizinisch diagnostische Produkte GmbH, Ketschau 2, D-68766, Hockenheim, Germany.
authors.forename: Simon
authors.initials: S
authors.lastname: Fischer
authors.affiliation: Abteilung Molekulare Evolution, IZMB - Institut für Zelluläre und Molekulare Botanik, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany. volker.knoop@uni-bonn.de.
authors.forename: Volker
authors.identifier: 0000-0002-8485-9423
authors.initials: V
authors.lastname: Knoop
mesh_terms: D005075:Biological Evolution; D002736:Chloroplasts / Q000235:genetics*; D003596:Cytosine; D020829:Equisetum / Q000145:classification; D029624:Ferns / Q000235:genetics*; D019684:Magnoliopsida / Q000235:genetics; D008928:Mitochondria / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D012313:RNA / Q000378:metabolism; D017393:RNA Editing; D018747:RNA, Chloroplast / Q000235:genetics; D000077278:RNA, Mitochondrial; D018749:RNA, Plant / Q000378:metabolism*; D012342:RNA, Small Nuclear / Q000378:metabolism; D014498:Uracil
chemical_list: D018747:RNA, Chloroplast; D000077278:RNA, Mitochondrial; D018749:RNA, Plant; D012342:RNA, Small Nuclear; D014498:Uracil; D012313:RNA; D003596:Cytosine
keywords: Chloroplasts; Editing loss; Equisetum; Ferns; Mitochondria; Monilophytes; PPR proteins; RNA editing; Reverse editing