High levels of RNA editing in a vascular plant chloroplast genome: analysis of transcripts from the fern Adiantum capillus-veneris

Abstract

We sequenced transcripts from all putative genes for proteins, rRNAs, and a selection of gene-encoding tRNAs in the chloroplast genome of the fern Adiantum capillus-veneris. We detected 350 RNA editing sites when the cDNA sequence was compared to that of the genomic DNA. Of these sites, 10% were U-to-C edits and 90% were C-to-U edits. RNA editing created 19 new start codons, three new stop codons, and “repaired” 26 internal stop codons. Of the 332 editing sites that altered a codon, 26% were in the first codon position, 68% in the second, and 6% in the third. We also detected 21 silent edits, as well as 19 edits that were in untranslated regions, including introns and the anticodon of tRNA Leu. The latter edit provided a tRNA that is not otherwise encoded in this genome and accounts for a heavily used leucine codon. The level of RNA editing in this fern is more than ten times that of any other vascular plant examined across an entire chloroplast genome. A previous study found even higher levels of editing in a hornwort (942 sites). This suggests that the relatively low levels of editing in seed plants (less than 0.05%) may not be typical for land plants, and that RNA editing may play a major role in chloroplast genome processing. Additionally, we found that 53 editing sites in A. capillus-veneris are homologous to editing sites in the hornwort, and some other land plants. This implies that a major component of RNA editing sites have been conserved for hundreds of millions of years.