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

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.