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A novel chloroplast gene reported for flagellate plants.

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Date
2018-01
Authors
Song, M
Kuo, L
Huiet, L
Pryer, KM
Rothfels, CJ
Li, F
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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 article
Subject
Adiantum
DNA, Plant
Sequence Analysis, DNA
Genes, Plant
Genome, Plant
Open Reading Frames
Genome, Plastid
Genes, Chloroplast
Permalink
https://hdl.handle.net/10161/21748
Published Version (Please cite this version)
10.1002/ajb2.1010
Publication 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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Pryer

Kathleen M. Pryer

Professor of Biology
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