Complete Chloroplast Genome of Nicotiana otophora and its Comparison with Related Species
Identifieur interne : 002097 ( Ncbi/Merge ); précédent : 002096; suivant : 002098Complete Chloroplast Genome of Nicotiana otophora and its Comparison with Related Species
Auteurs : Sajjad Asaf [Corée du Sud] ; Abdul L. Khan [Oman] ; Abdur R. Khan [Corée du Sud] ; Muhammad Waqas [Corée du Sud, Pakistan] ; Sang-Mo Kang [Corée du Sud] ; Muhammad A. Khan [Corée du Sud] ; Seok-Min Lee [Corée du Sud] ; In-Jung Lee [Corée du Sud]Source :
- Frontiers in Plant Science [ 1664-462X ] ; 2016.
Abstract
Url:
DOI: 10.3389/fpls.2016.00843
PubMed: 27379132
PubMed Central: 4906380
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Complete Chloroplast Genome of <italic>Nicotiana otophora</italic> and its Comparison with Related Species</title><author><name sortKey="Asaf, Sajjad" sort="Asaf, Sajjad" uniqKey="Asaf S" first="Sajjad" last="Asaf">Sajjad Asaf</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>School of Applied Biosciences, Kyungpook National University</institution><country>Daegu, South Korea</country></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Khan, Abdul L" sort="Khan, Abdul L" uniqKey="Khan A" first="Abdul L." last="Khan">Abdul L. Khan</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Chair of Oman's Medicinal Plants and Marine Natural Products, University of Nizwa</institution><country>Nizwa, Oman</country></nlm:aff><country xml:lang="fr">Oman</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Khan, Abdur R" sort="Khan, Abdur R" uniqKey="Khan A" first="Abdur R." last="Khan">Abdur R. Khan</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>School of Applied Biosciences, Kyungpook National University</institution><country>Daegu, South Korea</country></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Waqas, Muhammad" sort="Waqas, Muhammad" uniqKey="Waqas M" first="Muhammad" last="Waqas">Muhammad Waqas</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>School of Applied Biosciences, Kyungpook National University</institution><country>Daegu, South Korea</country></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Department of Agriculture, Abdul Wali Khan University Mardan</institution><country>Mardan, Pakistan</country></nlm:aff><country xml:lang="fr">Pakistan</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Kang, Sang Mo" sort="Kang, Sang Mo" uniqKey="Kang S" first="Sang-Mo" last="Kang">Sang-Mo Kang</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>School of Applied Biosciences, Kyungpook National University</institution><country>Daegu, South Korea</country></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Khan, Muhammad A" sort="Khan, Muhammad A" uniqKey="Khan M" first="Muhammad A." last="Khan">Muhammad A. Khan</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>School of Applied Biosciences, Kyungpook National University</institution><country>Daegu, South Korea</country></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Lee, Seok Min" sort="Lee, Seok Min" uniqKey="Lee S" first="Seok-Min" last="Lee">Seok-Min Lee</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>School of Applied Biosciences, Kyungpook National University</institution><country>Daegu, South Korea</country></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Lee, In Jung" sort="Lee, In Jung" uniqKey="Lee I" first="In-Jung" last="Lee">In-Jung Lee</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>School of Applied Biosciences, Kyungpook National University</institution><country>Daegu, South Korea</country></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea></wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27379132</idno><idno type="pmc">4906380</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4906380</idno><idno type="RBID">PMC:4906380</idno><idno type="doi">10.3389/fpls.2016.00843</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000326</idno><idno type="wicri:Area/Pmc/Curation">000325</idno><idno type="wicri:Area/Pmc/Checkpoint">000222</idno><idno type="wicri:Area/Ncbi/Merge">002097</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Complete Chloroplast Genome of <italic>Nicotiana otophora</italic> and its Comparison with Related Species</title><author><name sortKey="Asaf, Sajjad" sort="Asaf, Sajjad" uniqKey="Asaf S" first="Sajjad" last="Asaf">Sajjad Asaf</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>School of Applied Biosciences, Kyungpook National University</institution><country>Daegu, South Korea</country></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Khan, Abdul L" sort="Khan, Abdul L" uniqKey="Khan A" first="Abdul L." last="Khan">Abdul L. Khan</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Chair of Oman's Medicinal Plants and Marine Natural Products, University of Nizwa</institution><country>Nizwa, Oman</country></nlm:aff><country xml:lang="fr">Oman</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Khan, Abdur R" sort="Khan, Abdur R" uniqKey="Khan A" first="Abdur R." last="Khan">Abdur R. Khan</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>School of Applied Biosciences, Kyungpook National University</institution><country>Daegu, South Korea</country></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Waqas, Muhammad" sort="Waqas, Muhammad" uniqKey="Waqas M" first="Muhammad" last="Waqas">Muhammad Waqas</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>School of Applied Biosciences, Kyungpook National University</institution><country>Daegu, South Korea</country></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Department of Agriculture, Abdul Wali Khan University Mardan</institution><country>Mardan, Pakistan</country></nlm:aff><country xml:lang="fr">Pakistan</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Kang, Sang Mo" sort="Kang, Sang Mo" uniqKey="Kang S" first="Sang-Mo" last="Kang">Sang-Mo Kang</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>School of Applied Biosciences, Kyungpook National University</institution><country>Daegu, South Korea</country></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Khan, Muhammad A" sort="Khan, Muhammad A" uniqKey="Khan M" first="Muhammad A." last="Khan">Muhammad A. Khan</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>School of Applied Biosciences, Kyungpook National University</institution><country>Daegu, South Korea</country></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Lee, Seok Min" sort="Lee, Seok Min" uniqKey="Lee S" first="Seok-Min" last="Lee">Seok-Min Lee</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>School of Applied Biosciences, Kyungpook National University</institution><country>Daegu, South Korea</country></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Lee, In Jung" sort="Lee, In Jung" uniqKey="Lee I" first="In-Jung" last="Lee">In-Jung Lee</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>School of Applied Biosciences, Kyungpook National University</institution><country>Daegu, South Korea</country></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea></wicri:regionArea></affiliation></author></analytic><series><title level="j">Frontiers in Plant Science</title><idno type="eISSN">1664-462X</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><italic>Nicotiana otophora</italic> is a wild parental species of <italic>Nicotiana tabacum</italic>, an interspecific hybrid of <italic>Nicotiana tomentosiformis</italic> and <italic>Nicotiana sylvestris</italic>. However, <italic>N. otophora</italic> is least understood as an alternative paternal donor. Here, we compared the fully assembled chloroplast (cp) genome of <italic>N. otophora</italic> and with those of closely related species. The analysis showed a cp genome size of 156,073 bp and exhibited a typical quadripartite structure, which contains a pair of inverted repeats separated by small and large single copies, containing 163 representative genes, with 165 microsatellites distributed unevenly throughout the genome. Comparative analysis of a gene with known function across <italic>Nicotiana</italic> species revealed 76 protein-coding sequences, 20 tRNA sequences, and 3 rRNA sequence shared between the cp genomes. The analysis revealed that <italic>N</italic>. <italic>otophora</italic> is a sister species to <italic>N</italic>. <italic>tomentosiformis</italic> within the <italic>Nicotiana</italic> genus, and <italic>Atropha belladonna</italic> and <italic>Datura stramonium</italic> are their closest relatives. These findings provide a valuable analysis of the complete <italic>N</italic>. <italic>otophora</italic> cp genome, which can identify species, elucidate taxonomy, and reconstruct the phylogeny of genus <italic>Nicotiana</italic>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Asano, T" uniqKey="Asano T">T. Asano</name></author><author><name sortKey="Tsudzuki, T" uniqKey="Tsudzuki T">T. Tsudzuki</name></author><author><name sortKey="Takahashi, S" uniqKey="Takahashi S">S. Takahashi</name></author><author><name sortKey="Shimada, H" uniqKey="Shimada H">H. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Front Plant Sci</journal-id><journal-id journal-id-type="iso-abbrev">Front Plant Sci</journal-id><journal-id journal-id-type="publisher-id">Front. Plant Sci.</journal-id><journal-title-group><journal-title>Frontiers in Plant Science</journal-title></journal-title-group><issn pub-type="epub">1664-462X</issn><publisher><publisher-name>Frontiers Media S.A.</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">27379132</article-id><article-id pub-id-type="pmc">4906380</article-id><article-id pub-id-type="doi">10.3389/fpls.2016.00843</article-id><article-categories><subj-group subj-group-type="heading"><subject>Genetics</subject><subj-group><subject>Original Research</subject></subj-group></subj-group></article-categories><title-group><article-title>Complete Chloroplast Genome of <italic>Nicotiana otophora</italic> and its Comparison with Related Species</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Asaf</surname><given-names>Sajjad</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/281787/overview"></uri></contrib><contrib contrib-type="author"><name><surname>Khan</surname><given-names>Abdul L.</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/268421/overview"></uri></contrib><contrib contrib-type="author"><name><surname>Khan</surname><given-names>Abdur R.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/201745/overview"></uri></contrib><contrib contrib-type="author"><name><surname>Waqas</surname><given-names>Muhammad</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff3"><sup>3</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/199620/overview"></uri></contrib><contrib contrib-type="author"><name><surname>Kang</surname><given-names>Sang-Mo</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Khan</surname><given-names>Muhammad A.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/303942/overview"></uri></contrib><contrib contrib-type="author"><name><surname>Lee</surname><given-names>Seok-Min</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Lee</surname><given-names>In-Jung</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="author-notes" rid="fn001"><sup>*</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/272655/overview"></uri></contrib></contrib-group><aff id="aff1"><sup>1</sup><institution>School of Applied Biosciences, Kyungpook National University</institution><country>Daegu, South Korea</country></aff><aff id="aff2"><sup>2</sup><institution>Chair of Oman's Medicinal Plants and Marine Natural Products, University of Nizwa</institution><country>Nizwa, Oman</country></aff><aff id="aff3"><sup>3</sup><institution>Department of Agriculture, Abdul Wali Khan University Mardan</institution><country>Mardan, Pakistan</country></aff><author-notes><fn fn-type="edited-by"><p>Edited by: Miguel Arenas, Institute of Molecular Pathology and Immunology of the University of Porto, Portugal</p></fn><fn fn-type="edited-by"><p>Reviewed by: Milind Ratnaparkhe, ICAR-Indian Institute of Soybean Research, India; Yang Liu, Sun Yat-sen University, China; Longjiang Fan, Zhejiang University, China</p></fn><corresp id="fn001">*Correspondence: In-Jung Lee <email xlink:type="simple">ijlee@knu.ac.kr</email></corresp><fn fn-type="other" id="fn002"><p>This article was submitted to Evolutionary and Population Genetics, a section of the journal Frontiers in Plant Science</p></fn></author-notes><pub-date pub-type="epub"><day>14</day><month>6</month><year>2016</year></pub-date><pub-date pub-type="collection"><year>2016</year></pub-date><volume>7</volume><elocation-id>843</elocation-id><history><date date-type="received"><day>12</day><month>2</month><year>2016</year></date><date date-type="accepted"><day>30</day><month>5</month><year>2016</year></date></history><permissions><copyright-statement>Copyright © 2016 Asaf, Khan, Khan, Waqas, Kang, Khan, Lee and Lee.</copyright-statement><copyright-year>2016</copyright-year><copyright-holder>Asaf, Khan, Khan, Waqas, Kang, Khan, Lee and Lee</copyright-holder><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</license-p></license></permissions><abstract><p><italic>Nicotiana otophora</italic> is a wild parental species of <italic>Nicotiana tabacum</italic>, an interspecific hybrid of <italic>Nicotiana tomentosiformis</italic> and <italic>Nicotiana sylvestris</italic>. However, <italic>N. otophora</italic> is least understood as an alternative paternal donor. Here, we compared the fully assembled chloroplast (cp) genome of <italic>N. otophora</italic> and with those of closely related species. The analysis showed a cp genome size of 156,073 bp and exhibited a typical quadripartite structure, which contains a pair of inverted repeats separated by small and large single copies, containing 163 representative genes, with 165 microsatellites distributed unevenly throughout the genome. Comparative analysis of a gene with known function across <italic>Nicotiana</italic> species revealed 76 protein-coding sequences, 20 tRNA sequences, and 3 rRNA sequence shared between the cp genomes. The analysis revealed that <italic>N</italic>. <italic>otophora</italic> is a sister species to <italic>N</italic>. <italic>tomentosiformis</italic> within the <italic>Nicotiana</italic> genus, and <italic>Atropha belladonna</italic> and <italic>Datura stramonium</italic> are their closest relatives. These findings provide a valuable analysis of the complete <italic>N</italic>. <italic>otophora</italic> cp genome, which can identify species, elucidate taxonomy, and reconstruct the phylogeny of genus <italic>Nicotiana</italic>.</p></abstract><kwd-group><kwd><italic>Nicotiana</italic></kwd><kwd>cp genome</kwd><kwd>repeat analysis</kwd><kwd>phylogeny</kwd><kwd>sequence divergence</kwd><kwd>SSRs</kwd></kwd-group><funding-group><award-group><funding-source id="cn001">Ministry for Food, Agriculture, Forestry and Fisheries<named-content content-type="fundref-id">10.13039/501100003952</named-content></funding-source><award-id rid="cn001">311058-05-3-CG000</award-id></award-group></funding-group><counts><fig-count count="8"></fig-count><table-count count="3"></table-count><equation-count count="0"></equation-count><ref-count count="65"></ref-count><page-count count="12"></page-count><word-count count="6795"></word-count></counts></article-meta></front></pmc><affiliations><list><country><li>Corée du Sud</li><li>Oman</li><li>Pakistan</li></country></list><tree><country name="Corée du Sud"><noRegion><name sortKey="Asaf, Sajjad" sort="Asaf, Sajjad" uniqKey="Asaf S" first="Sajjad" last="Asaf">Sajjad Asaf</name></noRegion><name sortKey="Kang, Sang Mo" sort="Kang, Sang Mo" uniqKey="Kang S" first="Sang-Mo" last="Kang">Sang-Mo Kang</name><name sortKey="Khan, Abdur R" sort="Khan, Abdur R" uniqKey="Khan A" first="Abdur R." last="Khan">Abdur R. Khan</name><name sortKey="Khan, Muhammad A" sort="Khan, Muhammad A" uniqKey="Khan M" first="Muhammad A." last="Khan">Muhammad A. Khan</name><name sortKey="Lee, In Jung" sort="Lee, In Jung" uniqKey="Lee I" first="In-Jung" last="Lee">In-Jung Lee</name><name sortKey="Lee, Seok Min" sort="Lee, Seok Min" uniqKey="Lee S" first="Seok-Min" last="Lee">Seok-Min Lee</name><name sortKey="Waqas, Muhammad" sort="Waqas, Muhammad" uniqKey="Waqas M" first="Muhammad" last="Waqas">Muhammad Waqas</name></country><country name="Oman"><noRegion><name sortKey="Khan, Abdul L" sort="Khan, Abdul L" uniqKey="Khan A" first="Abdul L." last="Khan">Abdul L. Khan</name></noRegion></country><country name="Pakistan"><noRegion><name sortKey="Waqas, Muhammad" sort="Waqas, Muhammad" uniqKey="Waqas M" first="Muhammad" last="Waqas">Muhammad Waqas</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Merge/RBID.i -Sk "pubmed:27379132" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Merge/biblio.hfd \
| NlmPubMed2Wicri -a OrangerV1
| This area was generated with Dilib version V0.6.25. |  |