A novel chloroplast gene reported for flagellate plants.
Abstract
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.
Type
Journal articleSubject
AdiantumDNA, Plant
Sequence Analysis, DNA
Genes, Plant
Genome, Plant
Open Reading Frames
Genome, Plastid
Genes, Chloroplast
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https://hdl.handle.net/10161/21748Published Version (Please cite this version)
10.1002/ajb2.1010Publication Info
Song, M; Kuo, L; Huiet, L; Pryer, KM; Rothfels, CJ; & Li, F (2018). A novel chloroplast gene reported for flagellate plants. American journal of botany, 105(1). pp. 117-121. 10.1002/ajb2.1010. Retrieved from https://hdl.handle.net/10161/21748.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
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Kathleen M. Pryer
Professor of Biology

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