A novel chloroplast gene reported for flagellate plants

Premise of the Study Gene space in plant plastid genomes is well characterized and annotated, yet we discovered an unrecognized open reading frame ( ORF ) in the fern lineage that is conserved across flagellate plants. Methods We initially detected a putative uncharacterized ORF by the existence of a highly conserved region between rps16 and matK in a series of matK alignments of leptosporangiate ferns. We mined available plastid genomes for this ORF , which we now refer to as ycf94 , to infer evolutionary selection pressures and assist in functional prediction. To further examine the transcription of ycf94 , we assembled the plastid genome and sequenced the transcriptome of the leptosporangiate fern Adiantum shastense Huiet & A.R. Sm. Key Results The ycf94 predicted protein has a distinct transmembrane domain but with no sequence homology to other proteins with known function. The nonsynonymous/synonymous substitution rate ratio of ycf94 is on par with other fern plastid protein‐encoding genes, and additional homologs can be found in a few lycophyte, moss, hornwort, and liverwort plastid genomes. Homologs of ycf94 were not found in seed plants. In addition, we report a high level of RNA editing for ycf94 transcripts—a hallmark of protein‐coding genes in fern plastomes. Conclusions The degree of sequence conservation, together with the presence of a distinct transmembrane domain and RNA ‐editing sites, suggests that ycf94 is a protein‐coding gene of functional significance in ferns and, potentially, bryophytes and lycophytes. However, the origin and exact function of this gene require further investigation.