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Variation in frequency of plastid RNA editing within Adiantum (Pteridaceae) implies rapid evolution in fern plastomes

Citation

Fauskee, Blake; Sigel, Erin; Pryer, Kathleen; Grusz, Amanda (2021), Variation in frequency of plastid RNA editing within Adiantum (Pteridaceae) implies rapid evolution in fern plastomes, Dryad, Dataset, https://doi.org/10.5061/dryad.g1jwstqp3

Abstract

Premise

Recent advances in studies of plant RNA editing have demonstrated that the number of editing sites can vary widely among large taxonomic groups (orders, families). Yet, very little is known about intrageneric variation in frequency of plant RNA editing, and no study has been conducted in ferns.

Methods

We determined plastid RNA editing counts for two species of Adiantum (Pteridaceae), A. shastense and A. aleuticum, by implementing a pipeline that integrated read mapping and SNP calling software to identify RNA editing sites. We then compared the edits found in A. aleuticum and A. shastense with previously published edits from A. capillus-veneris by generating alignments for each plastid gene.

Results

We found direct evidence for 505 and 509 plastid RNA editing sites in A. aleuticum and A. shastense, respectively, compared with 350 sites in A. capillus-veneris. We observed striking variation in the number and location of the RNA editing sites among the three species, with reverse (U-to-C) editing sites showing a higher degree of conservation than forward (C-to-U) sites. Additionally, sites involving start and stop codons were highly conserved.

Conclusions

Variation in RNA editing frequency observed within Adiantum implies that RNA editing sites can be rapidly gained or lost throughout evolution. However, varying degrees of conservation between both C-to-U and U-to-C sites and sites in start or stop codons, versus other codons, hints at the likely independent origin of both types of edits and a potential selective advantage conferred by RNA editing.

Methods

Adiantum shastense and Adiautum aleuticum editing sites were identified as described in Fauskee et al., 2020. For methods involving the identification of RNA editing sites in Adiantum capillus-verneris see Wolf et al., 2003.