Diversity of RNA editing in chloroplast transcripts across three main plant clades

RNA editing is a post-transcriptional modification of an RNA nucleotide sequence. Until now, different RNA editing systems were found in the major eukaryotic clades. In the plant kingdom, RNA editing was mainly documented in the mitochondria and chloroplast genomes. However, variation among large taxonomic groups and the evolutionary trajectory in terms of intra- and inter-clades remains unclear. To gain a better understanding of RNA editing evolution, in this study, based on publicly available RNA-seq data across three clades (fern, gymnosperm, and angiosperm), we provided a detailed analysis of chloroplast RNA editing events and discussed its evolution in land plants. A total of 5203 editing sites were determined across 21 species after rigorous screening. We found that the clustering relations of RNA editing sites across 21 species agreed with the phylogenetic tree based on protein sequences approximately, and more editing sites occurred in early diverging lineages for all three clades, implying they shared similar evolutionary trajectories of editing loss. We observed that the average RNA editing level varied among species as well as genes, a lowest RNA editing level (similar to 0.42) was detected in Selaginella moellendorffii; the highest editing level (similar to 0.88) was detected in the atpA gene. The reduction of cytosine content with evolution detected in our study further suggested that the substitution of the genomic sequence was the significant driver of loss of editing for later-branching plants. Many of the identified sites in our study have not been previously reported and provided a valuable data set for the future research community. Our findings also provide valuable information for the evolution of RNA editing in plants.

Automated summary

This study provides a detailed analysis of chloroplast RNA editing events and their evolution in land plants based on publicly available RNA-seq data. A total of 5203 editing sites were identified across 21 species, and the clustering of these sites agreed with the phylogenetic tree. The study also identified previously unreported editing sites, providing valuable data for future research.