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A novel chloroplast gene reported for flagellate plants
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| Zeitschriftentitel: | American Journal of Botany |
|---|---|
| Personen und Körperschaften: | , , , , , |
| In: | American Journal of Botany, 105, 2018, 1, S. 117-121 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Wiley
|
| Schlagwörter: |
| author_facet |
Song, Michael Kuo, Li‐Yaung Huiet, Layne Pryer, Kathleen M. Rothfels, Carl J. Li, Fay‐Wei Song, Michael Kuo, Li‐Yaung Huiet, Layne Pryer, Kathleen M. Rothfels, Carl J. Li, Fay‐Wei |
|---|---|
| author |
Song, Michael Kuo, Li‐Yaung Huiet, Layne Pryer, Kathleen M. Rothfels, Carl J. Li, Fay‐Wei |
| spellingShingle |
Song, Michael Kuo, Li‐Yaung Huiet, Layne Pryer, Kathleen M. Rothfels, Carl J. Li, Fay‐Wei American Journal of Botany A novel chloroplast gene reported for flagellate plants Plant Science Genetics Ecology, Evolution, Behavior and Systematics |
| author_sort |
song, michael |
| spelling |
Song, Michael Kuo, Li‐Yaung Huiet, Layne Pryer, Kathleen M. Rothfels, Carl J. Li, Fay‐Wei 0002-9122 1537-2197 Wiley Plant Science Genetics Ecology, Evolution, Behavior and Systematics http://dx.doi.org/10.1002/ajb2.1010 <jats:sec><jats:title>Premise of the Study</jats:title><jats:p>Gene space in plant plastid genomes is well characterized and annotated, yet we discovered an unrecognized open reading frame (<jats:styled-content style="fixed-case">ORF</jats:styled-content>) in the fern lineage that is conserved across flagellate plants.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>We initially detected a putative uncharacterized <jats:styled-content style="fixed-case">ORF</jats:styled-content> by the existence of a highly conserved region between <jats:italic>rps16</jats:italic> and <jats:italic>matK</jats:italic> in a series of <jats:italic>matK</jats:italic> alignments of leptosporangiate ferns. We mined available plastid genomes for this <jats:styled-content style="fixed-case">ORF</jats:styled-content>, which we now refer to as <jats:italic>ycf94</jats:italic>, to infer evolutionary selection pressures and assist in functional prediction. To further examine the transcription of <jats:italic>ycf94</jats:italic>, we assembled the plastid genome and sequenced the transcriptome of the leptosporangiate fern <jats:italic>Adiantum shastense</jats:italic> Huiet & A.R. Sm.</jats:p></jats:sec><jats:sec><jats:title>Key Results</jats:title><jats:p>The <jats:italic>ycf94</jats:italic> 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 <jats:italic>ycf94</jats:italic> 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 <jats:italic>ycf94</jats:italic> were not found in seed plants. In addition, we report a high level of <jats:styled-content style="fixed-case">RNA</jats:styled-content> editing for <jats:italic>ycf94</jats:italic> transcripts—a hallmark of protein‐coding genes in fern plastomes.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>The degree of sequence conservation, together with the presence of a distinct transmembrane domain and <jats:styled-content style="fixed-case">RNA</jats:styled-content>‐editing sites, suggests that <jats:italic>ycf94</jats:italic> 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.</jats:p></jats:sec> A novel chloroplast gene reported for flagellate plants American Journal of Botany |
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10.1002/ajb2.1010 |
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Biologie Geographie |
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Wiley, 2018 |
| imprint_str_mv |
Wiley, 2018 |
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0002-9122 1537-2197 |
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0002-9122 1537-2197 |
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2018 |
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Wiley |
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American Journal of Botany |
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| title |
A novel chloroplast gene reported for flagellate plants |
| title_unstemmed |
A novel chloroplast gene reported for flagellate plants |
| title_full |
A novel chloroplast gene reported for flagellate plants |
| title_fullStr |
A novel chloroplast gene reported for flagellate plants |
| title_full_unstemmed |
A novel chloroplast gene reported for flagellate plants |
| title_short |
A novel chloroplast gene reported for flagellate plants |
| title_sort |
a novel chloroplast gene reported for flagellate plants |
| topic |
Plant Science Genetics Ecology, Evolution, Behavior and Systematics |
| url |
http://dx.doi.org/10.1002/ajb2.1010 |
| publishDate |
2018 |
| physical |
117-121 |
| description |
<jats:sec><jats:title>Premise of the Study</jats:title><jats:p>Gene space in plant plastid genomes is well characterized and annotated, yet we discovered an unrecognized open reading frame (<jats:styled-content style="fixed-case">ORF</jats:styled-content>) in the fern lineage that is conserved across flagellate plants.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>We initially detected a putative uncharacterized <jats:styled-content style="fixed-case">ORF</jats:styled-content> by the existence of a highly conserved region between <jats:italic>rps16</jats:italic> and <jats:italic>matK</jats:italic> in a series of <jats:italic>matK</jats:italic> alignments of leptosporangiate ferns. We mined available plastid genomes for this <jats:styled-content style="fixed-case">ORF</jats:styled-content>, which we now refer to as <jats:italic>ycf94</jats:italic>, to infer evolutionary selection pressures and assist in functional prediction. To further examine the transcription of <jats:italic>ycf94</jats:italic>, we assembled the plastid genome and sequenced the transcriptome of the leptosporangiate fern <jats:italic>Adiantum shastense</jats:italic> Huiet & A.R. Sm.</jats:p></jats:sec><jats:sec><jats:title>Key Results</jats:title><jats:p>The <jats:italic>ycf94</jats:italic> 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 <jats:italic>ycf94</jats:italic> 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 <jats:italic>ycf94</jats:italic> were not found in seed plants. In addition, we report a high level of <jats:styled-content style="fixed-case">RNA</jats:styled-content> editing for <jats:italic>ycf94</jats:italic> transcripts—a hallmark of protein‐coding genes in fern plastomes.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>The degree of sequence conservation, together with the presence of a distinct transmembrane domain and <jats:styled-content style="fixed-case">RNA</jats:styled-content>‐editing sites, suggests that <jats:italic>ycf94</jats:italic> 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.</jats:p></jats:sec> |
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| author | Song, Michael, Kuo, Li‐Yaung, Huiet, Layne, Pryer, Kathleen M., Rothfels, Carl J., Li, Fay‐Wei |
| author_facet | Song, Michael, Kuo, Li‐Yaung, Huiet, Layne, Pryer, Kathleen M., Rothfels, Carl J., Li, Fay‐Wei, Song, Michael, Kuo, Li‐Yaung, Huiet, Layne, Pryer, Kathleen M., Rothfels, Carl J., Li, Fay‐Wei |
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| description | <jats:sec><jats:title>Premise of the Study</jats:title><jats:p>Gene space in plant plastid genomes is well characterized and annotated, yet we discovered an unrecognized open reading frame (<jats:styled-content style="fixed-case">ORF</jats:styled-content>) in the fern lineage that is conserved across flagellate plants.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>We initially detected a putative uncharacterized <jats:styled-content style="fixed-case">ORF</jats:styled-content> by the existence of a highly conserved region between <jats:italic>rps16</jats:italic> and <jats:italic>matK</jats:italic> in a series of <jats:italic>matK</jats:italic> alignments of leptosporangiate ferns. We mined available plastid genomes for this <jats:styled-content style="fixed-case">ORF</jats:styled-content>, which we now refer to as <jats:italic>ycf94</jats:italic>, to infer evolutionary selection pressures and assist in functional prediction. To further examine the transcription of <jats:italic>ycf94</jats:italic>, we assembled the plastid genome and sequenced the transcriptome of the leptosporangiate fern <jats:italic>Adiantum shastense</jats:italic> Huiet & A.R. Sm.</jats:p></jats:sec><jats:sec><jats:title>Key Results</jats:title><jats:p>The <jats:italic>ycf94</jats:italic> 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 <jats:italic>ycf94</jats:italic> 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 <jats:italic>ycf94</jats:italic> were not found in seed plants. In addition, we report a high level of <jats:styled-content style="fixed-case">RNA</jats:styled-content> editing for <jats:italic>ycf94</jats:italic> transcripts—a hallmark of protein‐coding genes in fern plastomes.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>The degree of sequence conservation, together with the presence of a distinct transmembrane domain and <jats:styled-content style="fixed-case">RNA</jats:styled-content>‐editing sites, suggests that <jats:italic>ycf94</jats:italic> 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.</jats:p></jats:sec> |
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| institution | DE-D275, DE-Bn3, DE-Brt1, DE-Zwi2, DE-D161, DE-Gla1, DE-Zi4, DE-15, DE-Pl11, DE-Rs1, DE-105, DE-14, DE-Ch1, DE-L229 |
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| spelling | Song, Michael Kuo, Li‐Yaung Huiet, Layne Pryer, Kathleen M. Rothfels, Carl J. Li, Fay‐Wei 0002-9122 1537-2197 Wiley Plant Science Genetics Ecology, Evolution, Behavior and Systematics http://dx.doi.org/10.1002/ajb2.1010 <jats:sec><jats:title>Premise of the Study</jats:title><jats:p>Gene space in plant plastid genomes is well characterized and annotated, yet we discovered an unrecognized open reading frame (<jats:styled-content style="fixed-case">ORF</jats:styled-content>) in the fern lineage that is conserved across flagellate plants.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>We initially detected a putative uncharacterized <jats:styled-content style="fixed-case">ORF</jats:styled-content> by the existence of a highly conserved region between <jats:italic>rps16</jats:italic> and <jats:italic>matK</jats:italic> in a series of <jats:italic>matK</jats:italic> alignments of leptosporangiate ferns. We mined available plastid genomes for this <jats:styled-content style="fixed-case">ORF</jats:styled-content>, which we now refer to as <jats:italic>ycf94</jats:italic>, to infer evolutionary selection pressures and assist in functional prediction. To further examine the transcription of <jats:italic>ycf94</jats:italic>, we assembled the plastid genome and sequenced the transcriptome of the leptosporangiate fern <jats:italic>Adiantum shastense</jats:italic> Huiet & A.R. Sm.</jats:p></jats:sec><jats:sec><jats:title>Key Results</jats:title><jats:p>The <jats:italic>ycf94</jats:italic> 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 <jats:italic>ycf94</jats:italic> 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 <jats:italic>ycf94</jats:italic> were not found in seed plants. In addition, we report a high level of <jats:styled-content style="fixed-case">RNA</jats:styled-content> editing for <jats:italic>ycf94</jats:italic> transcripts—a hallmark of protein‐coding genes in fern plastomes.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>The degree of sequence conservation, together with the presence of a distinct transmembrane domain and <jats:styled-content style="fixed-case">RNA</jats:styled-content>‐editing sites, suggests that <jats:italic>ycf94</jats:italic> 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.</jats:p></jats:sec> A novel chloroplast gene reported for flagellate plants American Journal of Botany |
| spellingShingle | Song, Michael, Kuo, Li‐Yaung, Huiet, Layne, Pryer, Kathleen M., Rothfels, Carl J., Li, Fay‐Wei, American Journal of Botany, A novel chloroplast gene reported for flagellate plants, Plant Science, Genetics, Ecology, Evolution, Behavior and Systematics |
| title | A novel chloroplast gene reported for flagellate plants |
| title_full | A novel chloroplast gene reported for flagellate plants |
| title_fullStr | A novel chloroplast gene reported for flagellate plants |
| title_full_unstemmed | A novel chloroplast gene reported for flagellate plants |
| title_short | A novel chloroplast gene reported for flagellate plants |
| title_sort | a novel chloroplast gene reported for flagellate plants |
| title_unstemmed | A novel chloroplast gene reported for flagellate plants |
| topic | Plant Science, Genetics, Ecology, Evolution, Behavior and Systematics |
| url | http://dx.doi.org/10.1002/ajb2.1010 |