Evidence of Purifying Selection and Co-Evolution at the Fold-Back Arm of the Novel Precursor MicroRNA159 Gene in Phalaenopsis Species (Orchidaceae)
Identifieur interne : 001931 ( Ncbi/Merge ); précédent : 001930; suivant : 001932Evidence of Purifying Selection and Co-Evolution at the Fold-Back Arm of the Novel Precursor MicroRNA159 Gene in Phalaenopsis Species (Orchidaceae)
Auteurs : Chi-Chu Tsai [Taïwan] ; Yu-Chung Chiang [Taïwan] ; I-Szu Weng [Taïwan] ; Yu-Shium Lin [Taïwan] ; Chang-Hung Chou [Taïwan]Source :
- PLoS ONE [ 1932-6203 ] ; 2014.
Abstract
MicroRNAs (miRNAs) are small, endogenously transcribed, non-protein-coding RNAs that play important roles in regulation of gene expression in animals and plants. Here, selective constraints on the novel precursor microRNA159 (pre-miR159) gene were investigated in 42
A novel precursor microRNA159 gene was isolated from 42
Functional selective pressure might arise from the constraint of forming a hairpin structure and demonstrate co-evolution of sequences between the 5′ and 3′ fold-back regions of the novel pre-miR159 gene in
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DOI: 10.1371/journal.pone.0114493
PubMed: 25470008
PubMed Central: 4254996
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Evidence of Purifying Selection and Co-Evolution at the Fold-Back Arm of the Novel Precursor MicroRNA159 Gene in <italic>Phalaenopsis</italic> Species (Orchidaceae)</title><author><name sortKey="Tsai, Chi Chu" sort="Tsai, Chi Chu" uniqKey="Tsai C" first="Chi-Chu" last="Tsai">Chi-Chu Tsai</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Kaohsiung District Agricultural Research and Extension Station, Pingtung, 908, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Kaohsiung District Agricultural Research and Extension Station, Pingtung, 908</wicri:regionArea><wicri:noRegion>908</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, 912, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, 912</wicri:regionArea><wicri:noRegion>912</wicri:noRegion></affiliation></author><author><name sortKey="Chiang, Yu Chung" sort="Chiang, Yu Chung" uniqKey="Chiang Y" first="Yu-Chung" last="Chiang">Yu-Chung Chiang</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 804, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 804</wicri:regionArea><wicri:noRegion>804</wicri:noRegion></affiliation></author><author><name sortKey="Weng, I Szu" sort="Weng, I Szu" uniqKey="Weng I" first="I-Szu" last="Weng">I-Szu Weng</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Kaohsiung District Agricultural Research and Extension Station, Pingtung, 908, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Kaohsiung District Agricultural Research and Extension Station, Pingtung, 908</wicri:regionArea><wicri:noRegion>908</wicri:noRegion></affiliation></author><author><name sortKey="Lin, Yu Shium" sort="Lin, Yu Shium" uniqKey="Lin Y" first="Yu-Shium" last="Lin">Yu-Shium Lin</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Kaohsiung District Agricultural Research and Extension Station, Pingtung, 908, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Kaohsiung District Agricultural Research and Extension Station, Pingtung, 908</wicri:regionArea><wicri:noRegion>908</wicri:noRegion></affiliation></author><author><name sortKey="Chou, Chang Hung" sort="Chou, Chang Hung" uniqKey="Chou C" first="Chang-Hung" last="Chou">Chang-Hung Chou</name><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>Research Center for Biodiversity, China Medical University, Taichung, 404, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Research Center for Biodiversity, China Medical University, Taichung, 404</wicri:regionArea><wicri:noRegion>404</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25470008</idno><idno type="pmc">4254996</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4254996</idno><idno type="RBID">PMC:4254996</idno><idno type="doi">10.1371/journal.pone.0114493</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000224</idno><idno type="wicri:Area/Pmc/Curation">000224</idno><idno type="wicri:Area/Pmc/Checkpoint">000826</idno><idno type="wicri:Area/Ncbi/Merge">001931</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Evidence of Purifying Selection and Co-Evolution at the Fold-Back Arm of the Novel Precursor MicroRNA159 Gene in <italic>Phalaenopsis</italic> Species (Orchidaceae)</title><author><name sortKey="Tsai, Chi Chu" sort="Tsai, Chi Chu" uniqKey="Tsai C" first="Chi-Chu" last="Tsai">Chi-Chu Tsai</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Kaohsiung District Agricultural Research and Extension Station, Pingtung, 908, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Kaohsiung District Agricultural Research and Extension Station, Pingtung, 908</wicri:regionArea><wicri:noRegion>908</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, 912, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, 912</wicri:regionArea><wicri:noRegion>912</wicri:noRegion></affiliation></author><author><name sortKey="Chiang, Yu Chung" sort="Chiang, Yu Chung" uniqKey="Chiang Y" first="Yu-Chung" last="Chiang">Yu-Chung Chiang</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 804, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 804</wicri:regionArea><wicri:noRegion>804</wicri:noRegion></affiliation></author><author><name sortKey="Weng, I Szu" sort="Weng, I Szu" uniqKey="Weng I" first="I-Szu" last="Weng">I-Szu Weng</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Kaohsiung District Agricultural Research and Extension Station, Pingtung, 908, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Kaohsiung District Agricultural Research and Extension Station, Pingtung, 908</wicri:regionArea><wicri:noRegion>908</wicri:noRegion></affiliation></author><author><name sortKey="Lin, Yu Shium" sort="Lin, Yu Shium" uniqKey="Lin Y" first="Yu-Shium" last="Lin">Yu-Shium Lin</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Kaohsiung District Agricultural Research and Extension Station, Pingtung, 908, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Kaohsiung District Agricultural Research and Extension Station, Pingtung, 908</wicri:regionArea><wicri:noRegion>908</wicri:noRegion></affiliation></author><author><name sortKey="Chou, Chang Hung" sort="Chou, Chang Hung" uniqKey="Chou C" first="Chang-Hung" last="Chou">Chang-Hung Chou</name><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>Research Center for Biodiversity, China Medical University, Taichung, 404, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Research Center for Biodiversity, China Medical University, Taichung, 404</wicri:regionArea><wicri:noRegion>404</wicri:noRegion></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>MicroRNAs (miRNAs) are small, endogenously transcribed, non-protein-coding RNAs that play important roles in regulation of gene expression in animals and plants. Here, selective constraints on the novel precursor microRNA159 (pre-miR159) gene were investigated in 42 <italic>Phalaenopsis</italic> species (Orchidaceae).</p></sec><sec><title>Methods/Results</title><p>A novel precursor microRNA159 gene was isolated from 42 <italic>Phalaenopsis</italic> species using a new microRNA-PCR (miR-PCR) approach. Sequencing of pre-miR159 genes revealed differences from the canonical pre-miR159 gene in <italic>Phalaenopsis</italic> species and other plants. Results demonstrated that the 5′ and 3′ fold-back arms and the terminal loop of the novel pre-miR159 gene have undergone purifying selection and selective constraint for stabilizing the secondary hairpin structure. Two conserved motifs within the 5′ fold-back arm had the highest purifying selective pressure within the novel pre-miR159 gene. Evidence of sequence co-evolution between the 5′ and 3′ fold-back regions was observed.</p></sec><sec><title>Conclusions</title><p>Functional selective pressure might arise from the constraint of forming a hairpin structure and demonstrate co-evolution of sequences between the 5′ and 3′ fold-back regions of the novel pre-miR159 gene in <italic>Phalaenopsis</italic> species.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Bartel, Dp" uniqKey="Bartel D">DP Bartel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kurihara, Y" uniqKey="Kurihara Y">Y Kurihara</name></author><author><name sortKey="Watanabe, Y" uniqKey="Watanabe Y">Y Watanabe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Parizotto, Ea" uniqKey="Parizotto E">EA Parizotto</name></author><author><name sortKey="Dunoyer, P" uniqKey="Dunoyer P">P Dunoyer</name></author><author><name sortKey="Rahm, N" 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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25470008</article-id><article-id pub-id-type="pmc">4254996</article-id><article-id pub-id-type="publisher-id">PONE-D-14-32738</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0114493</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Biology and Life Sciences</subject><subj-group><subject>Evolutionary Biology</subject><subj-group><subject>Evolutionary Processes</subject><subj-group><subject>Natural Selection</subject><subj-group><subject>Signatures of Natural Selection</subject></subj-group></subj-group><subj-group><subject>Microevolution</subject></subj-group></subj-group><subj-group><subject>Evolutionary Genetics</subject></subj-group></subj-group></subj-group></article-categories><title-group><article-title>Evidence of Purifying Selection and Co-Evolution at the Fold-Back Arm of the Novel Precursor MicroRNA159 Gene in <italic>Phalaenopsis</italic> Species (Orchidaceae)</article-title><alt-title alt-title-type="running-head">Purifying Selection and Co-Evolution at <italic>Phalaenopsis</italic> MicroRNA159 Gene</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Tsai</surname><given-names>Chi-Chu</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Chiang</surname><given-names>Yu-Chung</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Weng</surname><given-names>I-Szu</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Lin</surname><given-names>Yu-Shium</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Chou</surname><given-names>Chang-Hung</given-names></name><xref ref-type="aff" rid="aff4"><sup>4</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib></contrib-group><aff id="aff1"><label>1</label><addr-line>Kaohsiung District Agricultural Research and Extension Station, Pingtung, 908, Taiwan</addr-line></aff><aff id="aff2"><label>2</label><addr-line>Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, 912, Taiwan</addr-line></aff><aff id="aff3"><label>3</label><addr-line>Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 804, Taiwan</addr-line></aff><aff id="aff4"><label>4</label><addr-line>Research Center for Biodiversity, China Medical University, Taichung, 404, Taiwan</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Chiang</surname><given-names>Tzen-Yuh</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>National Cheng-Kung University, Taiwan</addr-line></aff><author-notes><corresp id="cor1">* E-mail: <email>yuchung@mail.nsysu.edu.tw</email> (YCC); <email>choumasa@mail.cmu.edu.tw</email> (CHC)</corresp><fn fn-type="conflict"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con"><p>Conceived and designed the experiments: CCT YCC CHC. Performed the experiments: CCT YCC CHC. Analyzed the data: CCT YCC CHC. Contributed reagents/materials/analysis tools: ISW YSL. Wrote the paper: CCT YCC CHC.</p></fn></author-notes><pub-date pub-type="collection"><year>2014</year></pub-date><pub-date pub-type="epub"><day>3</day><month>12</month><year>2014</year></pub-date><volume>9</volume><issue>12</issue><elocation-id>e114493</elocation-id><history><date date-type="received"><day>23</day><month>7</month><year>2014</year></date><date date-type="accepted"><day>7</day><month>11</month><year>2014</year></date></history><permissions><copyright-year>2014</copyright-year><copyright-holder>Tsai et al</copyright-holder><license><license-p>This is an open-access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p></license></permissions><abstract><sec><title>Background</title><p>MicroRNAs (miRNAs) are small, endogenously transcribed, non-protein-coding RNAs that play important roles in regulation of gene expression in animals and plants. Here, selective constraints on the novel precursor microRNA159 (pre-miR159) gene were investigated in 42 <italic>Phalaenopsis</italic> species (Orchidaceae).</p></sec><sec><title>Methods/Results</title><p>A novel precursor microRNA159 gene was isolated from 42 <italic>Phalaenopsis</italic> species using a new microRNA-PCR (miR-PCR) approach. Sequencing of pre-miR159 genes revealed differences from the canonical pre-miR159 gene in <italic>Phalaenopsis</italic> species and other plants. Results demonstrated that the 5′ and 3′ fold-back arms and the terminal loop of the novel pre-miR159 gene have undergone purifying selection and selective constraint for stabilizing the secondary hairpin structure. Two conserved motifs within the 5′ fold-back arm had the highest purifying selective pressure within the novel pre-miR159 gene. Evidence of sequence co-evolution between the 5′ and 3′ fold-back regions was observed.</p></sec><sec><title>Conclusions</title><p>Functional selective pressure might arise from the constraint of forming a hairpin structure and demonstrate co-evolution of sequences between the 5′ and 3′ fold-back regions of the novel pre-miR159 gene in <italic>Phalaenopsis</italic> species.</p></sec></abstract><funding-group><funding-statement>This research was supported by funding from the Ministry of Science and Technology, Taiwan. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement></funding-group><counts><page-count count="21"></page-count></counts><custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name><meta-value>The authors confirm that all data underlying the findings are fully available without restriction. All of the validated pre-miR159 sequences for the Phalaenopsis species in the study have been deposited into GenBank with the accession numbers GU166689-GU166733.</meta-value></custom-meta></custom-meta-group></article-meta><notes><title>Data Availability</title><p>The authors confirm that all data underlying the findings are fully available without restriction. All of the validated pre-miR159 sequences for the Phalaenopsis species in the study have been deposited into GenBank with the accession numbers GU166689-GU166733.</p></notes></front></pmc><affiliations><list><country><li>Taïwan</li></country></list><tree><country name="Taïwan"><noRegion><name sortKey="Tsai, Chi Chu" sort="Tsai, Chi Chu" uniqKey="Tsai C" first="Chi-Chu" last="Tsai">Chi-Chu Tsai</name></noRegion><name sortKey="Chiang, Yu Chung" sort="Chiang, Yu Chung" uniqKey="Chiang Y" first="Yu-Chung" last="Chiang">Yu-Chung Chiang</name><name sortKey="Chou, Chang Hung" sort="Chou, Chang Hung" uniqKey="Chou C" first="Chang-Hung" last="Chou">Chang-Hung Chou</name><name sortKey="Lin, Yu Shium" sort="Lin, Yu Shium" uniqKey="Lin Y" first="Yu-Shium" last="Lin">Yu-Shium Lin</name><name sortKey="Tsai, Chi Chu" sort="Tsai, Chi Chu" uniqKey="Tsai C" first="Chi-Chu" last="Tsai">Chi-Chu Tsai</name><name sortKey="Weng, I Szu" sort="Weng, I Szu" uniqKey="Weng I" first="I-Szu" last="Weng">I-Szu Weng</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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