The chloroplast genome of Pellia endiviifolia: gene content, RNA-editing pattern, and the origin of chloroplast editing

Abstract

RNA editing is a post-transcriptional process that can act upon transcripts from mitochondrial, nuclear, and chloroplast genomes. In chloroplasts, single-nucleotide conversions in mRNAs via RNA editing occur at different frequencies across the plant kingdom. These range from several hundred edited sites in some mosses and ferns to lower frequencies in seed plants and the complete lack of RNA editing in the liverwort Marchantia polymorpha. Here, we report the sequence and edited sites of the chloroplast genome from the liverwort Pellia endiviifolia. The type and frequency of chloroplast RNA editing display a pattern highly similar to that in seed plants. Analyses of the C to U conversions and the genomic context in which the editing sites are embedded provide evidence in favor of the hypothesis that chloroplast RNA editing evolved to compensate mutations in the first land plants.

Fig. 1.—

The chloroplast genome of Pellia endiviifolia. The plastome of the liverwort is displayed in a circular pattern. LSC, large single copy region; SSC, small single region; IR_A/B, inverted repeat A/B. Color code see legend on the left. Drawing was made with OGDraw (Lohse et al. 2007).

Fig. 2.—

Nucleotide context of editing sites in Pellia endiviifolia. The diagram shows the direct upstream (pos −1) and downstream (pos +1) nucleotide context of the identified editing sites (Ed) independent of position within the codon. Editing sites are embedded in a context of known low mutation rate in plastid DNA with predominantly 5′-pyrimidine (T or C) and 3′-purine bases (A or G) (see text for a detailed description).

Fig. 3.—

Amino acid exchanges resulting from plastid RNA editing. The types (y axis) and quantities (x axis) of all amino acid exchanges as a result of plastid RNA editing in Pellia endiviifolia are shown. Editing leads to amino acid exchanges, which should have an impact on protein function because affected amino acids have differing biochemical properties or restore a start codon.