Variable frequency of plastid RNA editing among ferns and repeated loss of uridine-to-cytidine editing from vascular plants.

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  • Author(s): Guo W;Guo W;Guo W;Guo W; Grewe F; Grewe F; Grewe F; Mower JP; Mower JP; Mower JP
  • Source:
    PloS one [PLoS One] 2015 Jan 08; Vol. 10 (1), pp. e0117075. Date of Electronic Publication: 2015 Jan 08 (Print Publication: 2015).
  • Publication Type:
    Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
  • Language:
    English
  • Additional Information
    • Source:
      Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE
    • Publication Information:
      Original Publication: San Francisco, CA : Public Library of Science
    • Subject Terms:
      Genes, Plant*; Cytidine/*metabolism ; Ferns/*genetics ; RNA, Plant/*metabolism ; Uridine/*metabolism; Amino Acid Sequence ; Base Pair Mismatch ; Ferns/metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; Plant Proteins/chemistry ; Plant Proteins/genetics ; Plastids/genetics ; RNA Editing ; RNA, Plant/chemistry ; Sequence Alignment ; Sequence Analysis, RNA
    • 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.
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    • Accession Number:
      0 (Plant Proteins)
      0 (RNA, Plant)
      5CSZ8459RP (Cytidine)
      WHI7HQ7H85 (Uridine)
    • Publication Date:
      Date Created: 20150109 Date Completed: 20151229 Latest Revision: 20190223
    • Publication Date:
      20231215
    • Accession Number:
      PMC4287625
    • Accession Number:
      10.1371/journal.pone.0117075
    • Accession Number:
      25568947