Complete Chloroplast Genome Sequence of an Orchid Model Plant Candidate: Erycina pusilla Apply in Tropical Oncidium Breeding
Identifieur interne : 001108 ( Pmc/Curation ); précédent : 001107; suivant : 001109Complete Chloroplast Genome Sequence of an Orchid Model Plant Candidate: Erycina pusilla Apply in Tropical Oncidium Breeding
Auteurs : I-Chun Pan [Taïwan] ; Der-Chih Liao [Taïwan] ; Fu-Huei Wu [Taïwan] ; Henry Daniell [États-Unis] ; Nameirakpam Dolendro Singh [États-Unis] ; Chen Chang [Taïwan] ; Ming-Che Shih [Taïwan] ; Ming-Tsair Chan [Taïwan] ; Choun-Sea Lin [Taïwan]Source :
- PLoS ONE [ 1932-6203 ] ; 2012.
Abstract
Url:
DOI: 10.1371/journal.pone.0034738
PubMed: 22496851
PubMed Central: 3319614
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Apply in Tropical <italic>Oncidium</italic>
Breeding</title>
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<author><name sortKey="Lin, Choun Sea" sort="Lin, Choun Sea" uniqKey="Lin C" first="Choun-Sea" last="Lin">Choun-Sea Lin</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Complete Chloroplast Genome Sequence of an Orchid Model Plant Candidate: <italic>Erycina pusilla</italic>
Apply in Tropical <italic>Oncidium</italic>
Breeding</title>
<author><name sortKey="Pan, I Chun" sort="Pan, I Chun" uniqKey="Pan I" first="I-Chun" last="Pan">I-Chun Pan</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan</addr-line>
</nlm:aff>
<country xml:lang="fr">Taïwan</country>
<wicri:regionArea>Institute of Biotechnology, National Cheng Kung University, Tainan</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan</addr-line>
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<country xml:lang="fr">Taïwan</country>
<wicri:regionArea>Agricultural Biotechnology Research Center, Academia Sinica, Taipei</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Academia Sinica Biotechnology Center in Southern Taiwan, Tainan, Taiwan</addr-line>
</nlm:aff>
<country xml:lang="fr">Taïwan</country>
<wicri:regionArea>Academia Sinica Biotechnology Center in Southern Taiwan, Tainan</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Liao, Der Chih" sort="Liao, Der Chih" uniqKey="Liao D" first="Der-Chih" last="Liao">Der-Chih Liao</name>
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<country xml:lang="fr">Taïwan</country>
<wicri:regionArea>Agricultural Biotechnology Research Center, Academia Sinica, Taipei</wicri:regionArea>
</affiliation>
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<author><name sortKey="Wu, Fu Huei" sort="Wu, Fu Huei" uniqKey="Wu F" first="Fu-Huei" last="Wu">Fu-Huei Wu</name>
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</nlm:aff>
<country xml:lang="fr">Taïwan</country>
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</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Molecular Biology and Microbiology, University of Central Florida, Orlando, Florida</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Singh, Nameirakpam Dolendro" sort="Singh, Nameirakpam Dolendro" uniqKey="Singh N" first="Nameirakpam Dolendro" last="Singh">Nameirakpam Dolendro Singh</name>
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<wicri:regionArea>Department of Molecular Biology and Microbiology, University of Central Florida, Orlando, Florida</wicri:regionArea>
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<author><name sortKey="Chang, Chen" sort="Chang, Chen" uniqKey="Chang C" first="Chen" last="Chang">Chen Chang</name>
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</nlm:aff>
<country xml:lang="fr">Taïwan</country>
<wicri:regionArea>Department of Horticulture, National Chung Hsing University, Taichung</wicri:regionArea>
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<author><name sortKey="Shih, Ming Che" sort="Shih, Ming Che" uniqKey="Shih M" first="Ming-Che" last="Shih">Ming-Che Shih</name>
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<country xml:lang="fr">Taïwan</country>
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<author><name sortKey="Chan, Ming Tsair" sort="Chan, Ming Tsair" uniqKey="Chan M" first="Ming-Tsair" last="Chan">Ming-Tsair Chan</name>
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<country xml:lang="fr">Taïwan</country>
<wicri:regionArea>Institute of Biotechnology, National Cheng Kung University, Tainan</wicri:regionArea>
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</nlm:aff>
<country xml:lang="fr">Taïwan</country>
<wicri:regionArea>Academia Sinica Biotechnology Center in Southern Taiwan, Tainan</wicri:regionArea>
</affiliation>
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<author><name sortKey="Lin, Choun Sea" sort="Lin, Choun Sea" uniqKey="Lin C" first="Choun-Sea" last="Lin">Choun-Sea Lin</name>
<affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan</addr-line>
</nlm:aff>
<country xml:lang="fr">Taïwan</country>
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<series><title level="j">PLoS ONE</title>
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<imprint><date when="2012">2012</date>
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<front><div type="abstract" xml:lang="en"><p><italic>Oncidium</italic>
is an important ornamental plant but the study of its functional genomics is difficult. <italic>Erycina pusilla</italic>
is a fast-growing Oncidiinae species. Several characteristics including low chromosome number, small genome size, short growth period, and its ability to complete its life cycle <italic>in vitro</italic>
make <italic>E. pusilla</italic>
a good model candidate and parent for hybridization for orchids. Although genetic information remains limited, systematic molecular analysis of its chloroplast genome might provide useful genetic information. By combining bacterial artificial chromosome (BAC) clones and next-generation sequencing (NGS), the chloroplast (cp) genome of <italic>E. pusilla</italic>
was sequenced accurately, efficiently and economically. The cp genome of <italic>E. pusilla</italic>
shares 89 and 84% similarity with <italic>Oncidium</italic>
Gower Ramsey and <italic>Phalanopsis aphrodite</italic>
, respectively. Comparing these 3 cp genomes, 5 regions have been identified as showing diversity. Using PCR analysis of 19 species belonging to the Epidendroideae subfamily, a conserved deletion was found in the <italic>rps15-trnN</italic>
region of the Cymbidieae tribe. Because commercial <italic>Oncidium</italic>
varieties in Taiwan are limited, identification of potential parents using molecular breeding method has become very important. To demonstrate the relationship between taxonomic position and hybrid compatibility of <italic>E. pusilla</italic>
, 4 DNA regions of 36 tropically adapted Oncidiinae varieties have been analyzed. The results indicated that <italic>trnF</italic>
-<italic>ndhJ</italic>
and <italic>trnH</italic>
-<italic>psbA</italic>
were suitable for phylogenetic analysis. <italic>E. pusilla</italic>
proved to be phylogenetically closer to <italic>Rodriguezia</italic>
and <italic>Tolumnia</italic>
than <italic>Oncidium</italic>
, despite its similar floral appearance to <italic>Oncidium</italic>
. These results indicate the hybrid compatibility of <italic>E. pusilla</italic>
, its cp genome providing important information for <italic>Oncidium</italic>
breeding.</p>
</div>
</front>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<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">22496851</article-id>
<article-id pub-id-type="pmc">3319614</article-id>
<article-id pub-id-type="publisher-id">PONE-D-12-01599</article-id>
<article-id pub-id-type="doi">10.1371/journal.pone.0034738</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
<subj-group subj-group-type="Discipline-v2"><subject>Agriculture</subject>
<subj-group><subject>Agricultural Biotechnology</subject>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v2"><subject>Biology</subject>
<subj-group><subject>Genetics</subject>
<subj-group><subject>Plant Genetics</subject>
</subj-group>
</subj-group>
<subj-group><subject>Plant Science</subject>
<subj-group><subject>Agronomy</subject>
<subj-group><subject>Plant Breeding</subject>
</subj-group>
</subj-group>
<subj-group><subject>Plants</subject>
<subj-group><subject>Flowering Plants</subject>
</subj-group>
</subj-group>
<subj-group><subject>Plant Genomics</subject>
<subject>Plant Phylogenetics</subject>
</subj-group>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title>Complete Chloroplast Genome Sequence of an Orchid Model Plant Candidate: <italic>Erycina pusilla</italic>
Apply in Tropical <italic>Oncidium</italic>
Breeding</article-title>
<alt-title alt-title-type="running-head">The Application of Orchid Model Plant, <italic>E. pusilla</italic>
</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Pan</surname>
<given-names>I-Chun</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
<xref ref-type="aff" rid="aff3"><sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Liao</surname>
<given-names>Der-Chih</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Wu</surname>
<given-names>Fu-Huei</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Daniell</surname>
<given-names>Henry</given-names>
</name>
<xref ref-type="aff" rid="aff4"><sup>4</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Singh</surname>
<given-names>Nameirakpam Dolendro</given-names>
</name>
<xref ref-type="aff" rid="aff4"><sup>4</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Chang</surname>
<given-names>Chen</given-names>
</name>
<xref ref-type="aff" rid="aff5"><sup>5</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Shih</surname>
<given-names>Ming-Che</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Chan</surname>
<given-names>Ming-Tsair</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
<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>Lin</surname>
<given-names>Choun-Sea</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
<xref ref-type="corresp" rid="cor1"><sup>*</sup>
</xref>
</contrib>
</contrib-group>
<aff id="aff1"><label>1</label>
<addr-line>Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan</addr-line>
</aff>
<aff id="aff2"><label>2</label>
<addr-line>Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan</addr-line>
</aff>
<aff id="aff3"><label>3</label>
<addr-line>Academia Sinica Biotechnology Center in Southern Taiwan, Tainan, Taiwan</addr-line>
</aff>
<aff id="aff4"><label>4</label>
<addr-line>Department of Molecular Biology and Microbiology, University of Central Florida, Orlando, Florida, United States of America</addr-line>
</aff>
<aff id="aff5"><label>5</label>
<addr-line>Department of Horticulture, National Chung Hsing University, Taichung, Taiwan</addr-line>
</aff>
<contrib-group><contrib contrib-type="editor"><name><surname>Wu</surname>
<given-names>Keqiang</given-names>
</name>
<role>Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1">National Taiwan University, Taiwan</aff>
<author-notes><corresp id="cor1">* E-mail: <email>mbmtchan@gate.sinica.edu.tw</email>
(M-TC); <email>cslin99@gate.sinica.edu.tw</email>
(C-SL)</corresp>
<fn fn-type="con"><p>Conceived and designed the experiments: MTC CSL. Performed the experiments: ICP DCL FHW. Analyzed the data: HD NDS. Contributed reagents/materials/analysis tools: CC MCS MTC CSL. Wrote the paper: ICP CSL.</p>
</fn>
</author-notes>
<pub-date pub-type="collection"><year>2012</year>
</pub-date>
<pub-date pub-type="epub"><day>4</day>
<month>4</month>
<year>2012</year>
</pub-date>
<volume>7</volume>
<issue>4</issue>
<elocation-id>e34738</elocation-id>
<history><date date-type="received"><day>12</day>
<month>1</month>
<year>2012</year>
</date>
<date date-type="accepted"><day>9</day>
<month>3</month>
<year>2012</year>
</date>
</history>
<permissions><copyright-statement>Pan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</copyright-statement>
<copyright-year>2012</copyright-year>
</permissions>
<abstract><p><italic>Oncidium</italic>
is an important ornamental plant but the study of its functional genomics is difficult. <italic>Erycina pusilla</italic>
is a fast-growing Oncidiinae species. Several characteristics including low chromosome number, small genome size, short growth period, and its ability to complete its life cycle <italic>in vitro</italic>
make <italic>E. pusilla</italic>
a good model candidate and parent for hybridization for orchids. Although genetic information remains limited, systematic molecular analysis of its chloroplast genome might provide useful genetic information. By combining bacterial artificial chromosome (BAC) clones and next-generation sequencing (NGS), the chloroplast (cp) genome of <italic>E. pusilla</italic>
was sequenced accurately, efficiently and economically. The cp genome of <italic>E. pusilla</italic>
shares 89 and 84% similarity with <italic>Oncidium</italic>
Gower Ramsey and <italic>Phalanopsis aphrodite</italic>
, respectively. Comparing these 3 cp genomes, 5 regions have been identified as showing diversity. Using PCR analysis of 19 species belonging to the Epidendroideae subfamily, a conserved deletion was found in the <italic>rps15-trnN</italic>
region of the Cymbidieae tribe. Because commercial <italic>Oncidium</italic>
varieties in Taiwan are limited, identification of potential parents using molecular breeding method has become very important. To demonstrate the relationship between taxonomic position and hybrid compatibility of <italic>E. pusilla</italic>
, 4 DNA regions of 36 tropically adapted Oncidiinae varieties have been analyzed. The results indicated that <italic>trnF</italic>
-<italic>ndhJ</italic>
and <italic>trnH</italic>
-<italic>psbA</italic>
were suitable for phylogenetic analysis. <italic>E. pusilla</italic>
proved to be phylogenetically closer to <italic>Rodriguezia</italic>
and <italic>Tolumnia</italic>
than <italic>Oncidium</italic>
, despite its similar floral appearance to <italic>Oncidium</italic>
. These results indicate the hybrid compatibility of <italic>E. pusilla</italic>
, its cp genome providing important information for <italic>Oncidium</italic>
breeding.</p>
</abstract>
<counts><page-count count="12"></page-count>
</counts>
</article-meta>
</front>
</pmc>
</record>
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