Complete Sequence and Comparative Analysis of the Chloroplast Genome of Coconut Palm (Cocos nucifera)
Identifieur interne : 001158 ( Pmc/Curation ); précédent : 001157; suivant : 001159Complete Sequence and Comparative Analysis of the Chloroplast Genome of Coconut Palm (Cocos nucifera)
Auteurs : Ya-Yi Huang ; Antonius J. M. Matzke ; Marjori MatzkeSource :
- PLoS ONE [ 1932-6203 ] ; 2013.
Abstract
Coconut, a member of the palm family (Arecaceae), is one of the most economically important trees used by mankind. Despite its diverse morphology, coconut is recognized taxonomically as only a single species (
Url:
DOI: 10.1371/journal.pone.0074736
PubMed: 24023703
PubMed Central: 3758300
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Complete Sequence and Comparative Analysis of the Chloroplast Genome of Coconut Palm (<italic>Cocos nucifera</italic>)</title><author><name sortKey="Huang, Ya Yi" sort="Huang, Ya Yi" uniqKey="Huang Y" first="Ya-Yi" last="Huang">Ya-Yi Huang</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Matzke, Antonius J M" sort="Matzke, Antonius J M" uniqKey="Matzke A" first="Antonius J. M." last="Matzke">Antonius J. M. Matzke</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Matzke, Marjori" sort="Matzke, Marjori" uniqKey="Matzke M" first="Marjori" last="Matzke">Marjori Matzke</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24023703</idno><idno type="pmc">3758300</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3758300</idno><idno type="RBID">PMC:3758300</idno><idno type="doi">10.1371/journal.pone.0074736</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">001159</idno><idno type="wicri:Area/Pmc/Curation">001158</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Complete Sequence and Comparative Analysis of the Chloroplast Genome of Coconut Palm (<italic>Cocos nucifera</italic>)</title><author><name sortKey="Huang, Ya Yi" sort="Huang, Ya Yi" uniqKey="Huang Y" first="Ya-Yi" last="Huang">Ya-Yi Huang</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Matzke, Antonius J M" sort="Matzke, Antonius J M" uniqKey="Matzke A" first="Antonius J. M." last="Matzke">Antonius J. M. Matzke</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Matzke, Marjori" sort="Matzke, Marjori" uniqKey="Matzke M" first="Marjori" last="Matzke">Marjori Matzke</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Coconut, a member of the palm family (Arecaceae), is one of the most economically important trees used by mankind. Despite its diverse morphology, coconut is recognized taxonomically as only a single species (<italic>Cocos nucifera</italic> L.). There are two major coconut varieties, tall and dwarf, the latter of which displays traits resulting from selection by humans. We report here the complete chloroplast (cp) genome of a dwarf coconut plant, and describe the gene content and organization, inverted repeat fluctuations, repeated sequence structure, and occurrence of RNA editing. Phylogenetic relationships of monocots were inferred based on 47 chloroplast protein-coding genes. Potential nodes for events of gene duplication and pseudogenization related to inverted repeat fluctuation were mapped onto the tree using parsimony criteria. We compare our findings with those from other palm species for which complete cp genome sequences are available.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Palmer, J" uniqKey="Palmer J">J Palmer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, M" uniqKey="Yang M">M Yang</name></author><author><name sortKey="Zhang, X" uniqKey="Zhang X">X Zhang</name></author><author><name sortKey="Liu, G" uniqKey="Liu G">G Liu</name></author><author><name sortKey="Yin, Y" uniqKey="Yin Y">Y Yin</name></author><author><name sortKey="Chen, K" uniqKey="Chen K">K Chen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Uthaipaisanwong, P" uniqKey="Uthaipaisanwong P">P Uthaipaisanwong</name></author><author><name sortKey="Chanprasert, J" uniqKey="Chanprasert J">J Chanprasert</name></author><author><name sortKey="Shearman, Jr" uniqKey="Shearman J">JR 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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">24023703</article-id><article-id pub-id-type="pmc">3758300</article-id><article-id pub-id-type="publisher-id">PONE-D-13-26152</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0074736</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>Complete Sequence and Comparative Analysis of the Chloroplast Genome of Coconut Palm (<italic>Cocos nucifera</italic>)</article-title><alt-title alt-title-type="running-head">Coconut Chloroplast Genome Sequence</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Huang</surname><given-names>Ya-Yi</given-names></name><xref ref-type="aff" rid="aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Matzke</surname><given-names>Antonius J. M.</given-names></name><xref ref-type="aff" rid="aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Matzke</surname><given-names>Marjori</given-names></name><xref ref-type="aff" rid="aff1"></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib></contrib-group><aff id="aff1"><addr-line>Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Candela</surname><given-names>Hector</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>Universidad Miguel Hernández de Elche, Spain</addr-line></aff><author-notes><corresp id="cor1">* E-mail: <email>marjorimatzke@gate.sinica.edu.tw</email></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: YYH AJMM MM. Analyzed the data: YYH. Contributed reagents/materials/analysis tools: YYH. Wrote the paper: YYH MM.</p></fn></author-notes><pub-date pub-type="collection"><year>2013</year></pub-date><pub-date pub-type="epub"><day>30</day><month>8</month><year>2013</year></pub-date><volume>8</volume><issue>8</issue><elocation-id>e74736</elocation-id><history><date date-type="received"><day>25</day><month>6</month><year>2013</year></date><date date-type="accepted"><day>6</day><month>8</month><year>2013</year></date></history><permissions><copyright-year>2013</copyright-year><copyright-holder>Huang et al</copyright-holder><license><license-p>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.</license-p></license></permissions><abstract><p>Coconut, a member of the palm family (Arecaceae), is one of the most economically important trees used by mankind. Despite its diverse morphology, coconut is recognized taxonomically as only a single species (<italic>Cocos nucifera</italic> L.). There are two major coconut varieties, tall and dwarf, the latter of which displays traits resulting from selection by humans. We report here the complete chloroplast (cp) genome of a dwarf coconut plant, and describe the gene content and organization, inverted repeat fluctuations, repeated sequence structure, and occurrence of RNA editing. Phylogenetic relationships of monocots were inferred based on 47 chloroplast protein-coding genes. Potential nodes for events of gene duplication and pseudogenization related to inverted repeat fluctuation were mapped onto the tree using parsimony criteria. We compare our findings with those from other palm species for which complete cp genome sequences are available.</p></abstract><funding-group><funding-statement>This work was funded by Academia Sinica (<ext-link ext-link-type="uri" xlink:href="http://www.sinica.edu.tw/main_e.shtml">http://www.sinica.edu.tw/main_e.shtml</ext-link>). The funders 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="12"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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