Losing genes, gaining edits: how relaxed selection and inverted repeat expansion shape RNA editing in Schizaeaceae plastomes

Abstract

RNA editing is a post-transcriptional pyrimidine exchange process that alters plastid and mitochondrial transcripts in nearly all land plants. Although confined to organelles, it is directed by nuclear-encoded PLS-type pentatricopeptide repeat (PPR) proteins, each typically recognizing a specific RNA target. While many editing sites are functionally neutral, edits at cryptic start and internal stop codons have been implicated in modulating organellar gene expression. Ferns--and some lycophytes--are unique among vascular plants in exhibiting both C-to-U and U-to-C editing, making them valuable for studying the evolution of both forms. Here, we examine chloroplast RNA editing in four Schizaeales species (Schizaea dichotoma, Actinostachys digitata, Anemia phyllitidis, Lygodium microphyllum), two of which possess non-photosynthetic gametophytes, providing a natural contrast with fully photosynthetic relatives. Despite extensive plastome reduction, including loss of the ndh suite and, in Actinostachys, all chl genes, Schizaea and Actinostachys exhibit dramatically elevated numbers of C-to-U edits. Genes evolving under relaxed selection accumulate more editing sites, and editing abundance per gene correlates with the magnitude of relaxed constraint, suggesting relaxed selection promotes edit proliferation. S. dichotoma and A. digitata also show expansion of the chloroplast inverted repeat (IR), and genes translocated into the IR exhibit reduced substitution rates and higher editing densities, indicating that IR expansion slows the loss of edits. Finally, annotation of PPR proteins revealed few full-length editing factors, consistent with catalytic domains assembling in trans and highlighting the modular nature of the fern editosome.