The Amount of RNA Editing Sites in Liverwort Organellar Genes Is Correlated with GC Content and Nuclear PPR Protein Diversity

Abstract

RNA editing occurs in the organellar mRNAs of all land plants but the marchantioid liverworts, making liverworts a perfect group for studying the evolution of RNA editing. Here, we profiled the RNA editing of 42 exemplars spanning the ordinal phylogenetic diversity of liverworts, and screened for the nuclear-encoded pentatricopeptide repeat (PPR) proteins in the transcriptome assemblies of these taxa. We identified 7,428 RNA editing sites in 128 organellar genes from 31 non-marchantioid liverwort species, and characterized 25,059 PPR protein sequences. The abundance of organellar RNA editing sites varies greatly among liverwort lineages, genes, and codon positions, and shows strong positive correlations with the GC content of protein-coding genes, and the diversity of the PLS class of nuclear PPR proteins.

Keywords: GC content; PLS PPR proteins; RNA editing; liverworts; organellar genes; phylogeny.

Fig. 1.

—(a) Phylogenetic tree of liverworts based on a concatenated nucleotide data set of 41 mt and 86 pt genes. Branches are maximally supported (i.e., 100% bootstrap frequencies) unless otherwise marked. (b) Heatmap of PPR protein diversity across liverworts. (c) Histogram of RNA editing site abundance in mt (pink) and pt (green) genomes for each liverwort accession.