Comparative analysis of complete chloroplast genome sequences of two tropical trees Machilus yunnanensis and Machilus balansae in the family Lauraceae
Identifieur interne : 000080 ( Pmc/Curation ); précédent : 000079; suivant : 000081Comparative analysis of complete chloroplast genome sequences of two tropical trees Machilus yunnanensis and Machilus balansae in the family Lauraceae
Auteurs : Yu Song [République populaire de Chine] ; Wenpan Dong [République populaire de Chine] ; Bing Liu [République populaire de Chine] ; Chao Xu [République populaire de Chine] ; Xin Yao [République populaire de Chine] ; Jie Gao [République populaire de Chine] ; Richard T. Corlett [République populaire de Chine]Source :
- Frontiers in Plant Science [ 1664-462X ] ; 2015.
Abstract
Url:
DOI: 10.3389/fpls.2015.00662
PubMed: 26379689
PubMed Central: 4548089
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Comparative analysis of complete chloroplast genome sequences of two tropical trees <italic>Machilus yunnanensis</italic> and <italic>Machilus balansae</italic> in the family Lauraceae</title><author><name sortKey="Song, Yu" sort="Song, Yu" uniqKey="Song Y" first="Yu" last="Song">Yu Song</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences</institution><country>Mengla, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Graduate School of the Chinese Academy of Sciences</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Dong, Wenpan" sort="Dong, Wenpan" uniqKey="Dong W" first="Wenpan" last="Dong">Wenpan Dong</name><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff4"><institution>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Liu, Bing" sort="Liu, Bing" uniqKey="Liu B" first="Bing" last="Liu">Bing Liu</name><affiliation wicri:level="1"><nlm:aff id="aff4"><institution>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Xu, Chao" sort="Xu, Chao" uniqKey="Xu C" first="Chao" last="Xu">Chao Xu</name><affiliation wicri:level="1"><nlm:aff id="aff4"><institution>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Yao, Xin" sort="Yao, Xin" uniqKey="Yao X" first="Xin" last="Yao">Xin Yao</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences</institution><country>Mengla, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Graduate School of the Chinese Academy of Sciences</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Gao, Jie" sort="Gao, Jie" uniqKey="Gao J" first="Jie" last="Gao">Jie Gao</name><affiliation wicri:level="1"><nlm:aff id="aff5"><institution>Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences</institution><country>Mengla, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Corlett, Richard T" sort="Corlett, Richard T" uniqKey="Corlett R" first="Richard T." last="Corlett">Richard T. Corlett</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences</institution><country>Mengla, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26379689</idno><idno type="pmc">4548089</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4548089</idno><idno type="RBID">PMC:4548089</idno><idno type="doi">10.3389/fpls.2015.00662</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000080</idno><idno type="wicri:Area/Pmc/Curation">000080</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Comparative analysis of complete chloroplast genome sequences of two tropical trees <italic>Machilus yunnanensis</italic> and <italic>Machilus balansae</italic> in the family Lauraceae</title><author><name sortKey="Song, Yu" sort="Song, Yu" uniqKey="Song Y" first="Yu" last="Song">Yu Song</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences</institution><country>Mengla, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Graduate School of the Chinese Academy of Sciences</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Dong, Wenpan" sort="Dong, Wenpan" uniqKey="Dong W" first="Wenpan" last="Dong">Wenpan Dong</name><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff4"><institution>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Liu, Bing" sort="Liu, Bing" uniqKey="Liu B" first="Bing" last="Liu">Bing Liu</name><affiliation wicri:level="1"><nlm:aff id="aff4"><institution>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Xu, Chao" sort="Xu, Chao" uniqKey="Xu C" first="Chao" last="Xu">Chao Xu</name><affiliation wicri:level="1"><nlm:aff id="aff4"><institution>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Yao, Xin" sort="Yao, Xin" uniqKey="Yao X" first="Xin" last="Yao">Xin Yao</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences</institution><country>Mengla, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Graduate School of the Chinese Academy of Sciences</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Gao, Jie" sort="Gao, Jie" uniqKey="Gao J" first="Jie" last="Gao">Jie Gao</name><affiliation wicri:level="1"><nlm:aff id="aff5"><institution>Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences</institution><country>Mengla, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Corlett, Richard T" sort="Corlett, Richard T" uniqKey="Corlett R" first="Richard T." last="Corlett">Richard T. Corlett</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences</institution><country>Mengla, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</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="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><italic>Machilus</italic> is a large (c. 100 sp.) genus of trees in the family Lauraceae, distributed in tropical and subtropical East Asia. Both molecular species identification and phylogenetic studies of this morphologically uniform genus have been constrained by insufficient variable sites among frequently used biomarkers. To better understand the mutation patterns in the chloroplast genome of <italic>Machilus</italic>, the complete plastomes of two species were sequenced. The plastomes of <italic>Machilus yunnanensis</italic> and <italic>M. balansae</italic> were 152, 622 and 152, 721 bp, respectively. Seven highly variable regions between the two <italic>Machilus</italic> species were identified and 297 mutation events, including one micro-inversion in the <italic>ccsA-ndhD</italic> region, 65 indels, and 231 substitutions, were accurately located. Thirty-six microsatellite sites were found for use in species identification and 95 single-nucleotide changes were identified in gene coding regions.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Aiyar, A" uniqKey="Aiyar A">A. Aiyar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chang, C C" uniqKey="Chang C">C. C. 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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">26379689</article-id><article-id pub-id-type="pmc">4548089</article-id><article-id pub-id-type="doi">10.3389/fpls.2015.00662</article-id><article-categories><subj-group subj-group-type="heading"><subject>Plant Science</subject><subj-group><subject>Original Research</subject></subj-group></subj-group></article-categories><title-group><article-title>Comparative analysis of complete chloroplast genome sequences of two tropical trees <italic>Machilus yunnanensis</italic> and <italic>Machilus balansae</italic> in the family Lauraceae</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Song</surname><given-names>Yu</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="author-notes" rid="fn002"><sup>†</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/248722"></uri></contrib><contrib contrib-type="author"><name><surname>Dong</surname><given-names>Wenpan</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref><xref ref-type="aff" rid="aff4"><sup>4</sup></xref><xref ref-type="author-notes" rid="fn002"><sup>†</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/265793"></uri></contrib><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Bing</given-names></name><xref ref-type="aff" rid="aff4"><sup>4</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/265788"></uri></contrib><contrib contrib-type="author"><name><surname>Xu</surname><given-names>Chao</given-names></name><xref ref-type="aff" rid="aff4"><sup>4</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/266002"></uri></contrib><contrib contrib-type="author"><name><surname>Yao</surname><given-names>Xin</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/266224"></uri></contrib><contrib contrib-type="author"><name><surname>Gao</surname><given-names>Jie</given-names></name><xref ref-type="aff" rid="aff5"><sup>5</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/258035"></uri></contrib><contrib contrib-type="author"><name><surname>Corlett</surname><given-names>Richard T.</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/266840"></uri></contrib></contrib-group><aff id="aff1"><sup>1</sup><institution>Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences</institution><country>Mengla, China</country></aff><aff id="aff2"><sup>2</sup><institution>Graduate School of the Chinese Academy of Sciences</institution><country>Beijing, China</country></aff><aff id="aff3"><sup>3</sup><institution>Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University</institution><country>Beijing, China</country></aff><aff id="aff4"><sup>4</sup><institution>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences</institution><country>Beijing, China</country></aff><aff id="aff5"><sup>5</sup><institution>Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences</institution><country>Mengla, China</country></aff><author-notes><fn fn-type="edited-by"><p>Edited by: <italic>Maureen Hanson, Cornell University, USA</italic></p></fn><fn fn-type="edited-by"><p>Reviewed by: <italic>Tao Sun, Stanford University, USA; Kenneth Wolfe, University College Dublin, Ireland</italic></p></fn><corresp id="fn001">*Correspondence: <italic>Richard T. Corlett, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China, <email xlink:type="simple">corlett@xtbg.org.cn</email></italic></corresp><fn fn-type="other" id="fn002"><p><sup>†</sup><italic>These authors have contributed equally to this work.</italic></p></fn><fn fn-type="other" id="fn003"><p>This article was submitted to Plant Genetics and Genomics, a section of the journal Frontiers in Plant Science</p></fn></author-notes><pub-date pub-type="epub"><day>25</day><month>8</month><year>2015</year></pub-date><pub-date pub-type="collection"><year>2015</year></pub-date><volume>6</volume><elocation-id>662</elocation-id><history><date date-type="received"><day>24</day><month>6</month><year>2015</year></date><date date-type="accepted"><day>11</day><month>8</month><year>2015</year></date></history><permissions><copyright-statement>Copyright © 2015 Song, Dong, Liu, Xu, Yao, Gao and Corlett.</copyright-statement><copyright-year>2015</copyright-year><copyright-holder>Song, Dong, Liu, Xu, Yao, Gao and Corlett</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>Machilus</italic> is a large (c. 100 sp.) genus of trees in the family Lauraceae, distributed in tropical and subtropical East Asia. Both molecular species identification and phylogenetic studies of this morphologically uniform genus have been constrained by insufficient variable sites among frequently used biomarkers. To better understand the mutation patterns in the chloroplast genome of <italic>Machilus</italic>, the complete plastomes of two species were sequenced. The plastomes of <italic>Machilus yunnanensis</italic> and <italic>M. balansae</italic> were 152, 622 and 152, 721 bp, respectively. Seven highly variable regions between the two <italic>Machilus</italic> species were identified and 297 mutation events, including one micro-inversion in the <italic>ccsA-ndhD</italic> region, 65 indels, and 231 substitutions, were accurately located. Thirty-six microsatellite sites were found for use in species identification and 95 single-nucleotide changes were identified in gene coding regions.</p></abstract><kwd-group><kwd>mutation</kwd><kwd>genome</kwd><kwd>chloroplast</kwd><kwd><italic>Machilus</italic></kwd><kwd>Lauraceae</kwd></kwd-group><counts><fig-count count="3"></fig-count><table-count count="4"></table-count><equation-count count="0"></equation-count><ref-count count="43"></ref-count><page-count count="8"></page-count><word-count count="0"></word-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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