Date of this Version
Guo W, Grewe F, Mower JP (2015) Variable Frequency of Plastid RNA Editing among Ferns and Repeated Loss of Uridine-to-Cytidine Editing from Vascular Plants. PLoS ONE 10(1): e0117075. doi:10.1371/journal.pone.0117075
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.
S1 Fig. False positive signals of RNA editing due to DNA heteroplasmy.
Guo PLOS1 2015 Suppl 02.PDF (32 kB)
S2 Fig. False positive signals of RNA editing due to imperfect binding of random hexamers during cDNA preparation.
Guo PLOS1 2015 Suppl 03.PDF (18 kB)
S3 Fig. False positive signals of RNA editing due to mapping artifacts at exon/intron junction sites.
Guo PLOS1 2015 Suppl 04.PDF (24 kB)
S4 Fig. False positive signals of RNA editing due to errors in the reference genome sequence.
Guo PLOS1 2015 Suppl 05.XLS (171 kB)
S1 Table. Transcription read counts for different genomic locations in O. californicum and P. nudum.
Guo PLOS1 2015 Suppl 06.PDF (17 kB)
S2 Table. Inferred false positive locations in (A) O. californicum and (B) P. nudum.
Guo PLOS1 2015 Suppl 07.PDF (76 kB)
S3 Table. Edit site locations in (A) O. californicum and (B) P. nudum.