title: Variable frequency of plastid RNA editing among ferns and repeated loss of uridine-to-cytidine editing from vascular plants.
abstract: The distinct distribution and abundance of C-to-U and U-to-C RNA editing among land plants suggest that these two processes originated and evolve independently, but the paucity of information from several key lineages limits our understanding of their evolution. To examine the evolutionary diversity of RNA editing among ferns, we sequenced the plastid transcriptomes from two early diverging species, Ophioglossum californicum and Psilotum nudum. Using a relaxed automated approach to minimize false negatives combined with manual inspection to eliminate false positives, we identified 297 C-to-U and three U-to-C edit sites in the O. californicum plastid transcriptome but only 27 C-to-U and no U-to-C edit sites in the P. nudum plastid transcriptome. A broader comparison of editing content with the leptosporangiate fern Adiantum capillus-veneris and the hornwort Anthoceros formosae uncovered large variance in the abundance of plastid editing, indicating that the frequency and type of RNA editing is highly labile in ferns. Edit sites that increase protein conservation among species are more abundant and more efficiently edited than silent and non-conservative sites, suggesting that selection maintains functionally important editing. The absence of U-to-C editing from P. nudum plastid transcripts and other vascular plants demonstrates that U-to-C editing loss is a recurrent phenomenon in vascular plant evolution.
authors.affiliation: Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska, United States of America; School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America; ACGT, Inc., Wheeling, Illinois, United States of America.
authors.forename: Wenhu
authors.initials: W
authors.lastname: Guo
authors.affiliation: Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska, United States of America; Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska, United States of America.
authors.forename: Felix
authors.initials: F
authors.lastname: Grewe
authors.affiliation: Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska, United States of America; Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska, United States of America.
authors.forename: Jeffrey P
authors.initials: JP
authors.lastname: Mower
mesh_terms: D000595:Amino Acid Sequence; D020137:Base Pair Mismatch; D003562:Cytidine / Q000378:metabolism*; D029624:Ferns / Q000235:genetics* / Q000378:metabolism; D017343:Genes, Plant; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics; D018087:Plastids / Q000235:genetics; D017393:RNA Editing; D018749:RNA, Plant / Q000737:chemistry / Q000378:metabolism*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D014529:Uridine / Q000378:metabolism*
chemical_list: D010940:Plant Proteins; D018749:RNA, Plant; D003562:Cytidine; D014529:Uridine