Complete Chloroplast Genome Sequence of Omani Lime (Citrus aurantiifolia) and Comparative Analysis within the Rosids
Identifieur interne : 001900 ( Ncbi/Merge ); précédent : 001899; suivant : 001901Complete Chloroplast Genome Sequence of Omani Lime (Citrus aurantiifolia) and Comparative Analysis within the Rosids
Auteurs : Huei-Jiun Su [Taïwan] ; Saskia A. Hogenhout [Royaume-Uni] ; Abdullah M. Al-Sadi [Oman] ; Chih-Horng Kuo [Taïwan]Source :
- PLoS ONE [ 1932-6203 ] ; 2014.
Abstract
The genus
Url:
DOI: 10.1371/journal.pone.0113049
PubMed: 25398081
PubMed Central: 4232571
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Complete Chloroplast Genome Sequence of Omani Lime (<italic>Citrus aurantiifolia</italic>) and Comparative Analysis within the Rosids</title><author><name sortKey="Su, Huei Jiun" sort="Su, Huei Jiun" uniqKey="Su H" first="Huei-Jiun" last="Su">Huei-Jiun Su</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author><author><name sortKey="Hogenhout, Saskia A" sort="Hogenhout, Saskia A" uniqKey="Hogenhout S" first="Saskia A." last="Hogenhout">Saskia A. Hogenhout</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Cell and Developmental Biology, John Innes Centre, Norwich</wicri:regionArea><wicri:noRegion>Norwich</wicri:noRegion></affiliation></author><author><name sortKey="Al Sadi, Abdullah M" sort="Al Sadi, Abdullah M" uniqKey="Al Sadi A" first="Abdullah M." last="Al-Sadi">Abdullah M. Al-Sadi</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Department of Crop Sciences, Sultan Qaboos University, Al Khoud, Oman</addr-line></nlm:aff><country xml:lang="fr">Oman</country><wicri:regionArea>Department of Crop Sciences, Sultan Qaboos University, Al Khoud</wicri:regionArea><wicri:noRegion>Al Khoud</wicri:noRegion></affiliation></author><author><name sortKey="Kuo, Chih Horng" sort="Kuo, Chih Horng" uniqKey="Kuo C" first="Chih-Horng" last="Kuo">Chih-Horng Kuo</name><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Institute of Plant and Microbial Biology, Academia Sinica, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff5"><addr-line>Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff6"><addr-line>Biotechnology Center, National Chung Hsing University, Taichung, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Biotechnology Center, National Chung Hsing University, Taichung</wicri:regionArea><wicri:noRegion>Taichung</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25398081</idno><idno type="pmc">4232571</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4232571</idno><idno type="RBID">PMC:4232571</idno><idno type="doi">10.1371/journal.pone.0113049</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000219</idno><idno type="wicri:Area/Pmc/Curation">000219</idno><idno type="wicri:Area/Pmc/Checkpoint">000871</idno><idno type="wicri:Area/Ncbi/Merge">001900</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Complete Chloroplast Genome Sequence of Omani Lime (<italic>Citrus aurantiifolia</italic>) and Comparative Analysis within the Rosids</title><author><name sortKey="Su, Huei Jiun" sort="Su, Huei Jiun" uniqKey="Su H" first="Huei-Jiun" last="Su">Huei-Jiun Su</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author><author><name sortKey="Hogenhout, Saskia A" sort="Hogenhout, Saskia A" uniqKey="Hogenhout S" first="Saskia A." last="Hogenhout">Saskia A. Hogenhout</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Cell and Developmental Biology, John Innes Centre, Norwich</wicri:regionArea><wicri:noRegion>Norwich</wicri:noRegion></affiliation></author><author><name sortKey="Al Sadi, Abdullah M" sort="Al Sadi, Abdullah M" uniqKey="Al Sadi A" first="Abdullah M." last="Al-Sadi">Abdullah M. Al-Sadi</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Department of Crop Sciences, Sultan Qaboos University, Al Khoud, Oman</addr-line></nlm:aff><country xml:lang="fr">Oman</country><wicri:regionArea>Department of Crop Sciences, Sultan Qaboos University, Al Khoud</wicri:regionArea><wicri:noRegion>Al Khoud</wicri:noRegion></affiliation></author><author><name sortKey="Kuo, Chih Horng" sort="Kuo, Chih Horng" uniqKey="Kuo C" first="Chih-Horng" last="Kuo">Chih-Horng Kuo</name><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Institute of Plant and Microbial Biology, Academia Sinica, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff5"><addr-line>Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff6"><addr-line>Biotechnology Center, National Chung Hsing University, Taichung, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Biotechnology Center, National Chung Hsing University, Taichung</wicri:regionArea><wicri:noRegion>Taichung</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"><p>The genus <italic>Citrus</italic> contains many economically important fruits that are grown worldwide for their high nutritional and medicinal value. Due to frequent hybridizations among species and cultivars, the exact number of natural species and the taxonomic relationships within this genus are unclear. To compare the differences between the <italic>Citrus</italic> chloroplast genomes and to develop useful genetic markers, we used a reference-assisted approach to assemble the complete chloroplast genome of Omani lime (<italic>C</italic>. <italic>aurantiifolia</italic>). The complete <italic>C</italic>. <italic>aurantiifolia</italic> chloroplast genome is 159,893 bp in length; the organization and gene content are similar to most of the rosids lineages characterized to date. Through comparison with the sweet orange (<italic>C. sinensis</italic>) chloroplast genome, we identified three intergenic regions and 94 simple sequence repeats (SSRs) that are potentially informative markers with resolution for interspecific relationships. These markers can be utilized to better understand the origin of cultivated <italic>Citrus</italic>. 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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">25398081</article-id><article-id pub-id-type="pmc">4232571</article-id><article-id pub-id-type="publisher-id">PONE-D-14-24554</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0113049</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>Biotechnology</subject><subj-group><subject>Plant Biotechnology</subject><subj-group><subject>Plant Genomics</subject><subj-group><subject>Plant Genomes</subject></subj-group></subj-group></subj-group></subj-group><subj-group><subject>Cell Biology</subject><subj-group><subject>Cellular Structures and Organelles</subject><subj-group><subject>Chloroplasts</subject></subj-group></subj-group><subj-group><subject>Cellular Types</subject><subj-group><subject>Plant Cells</subject></subj-group></subj-group><subj-group><subject>Plant Cell Biology</subject></subj-group></subj-group><subj-group><subject>Computational Biology</subject><subj-group><subject>Genome Analysis</subject><subject>Genome Evolution</subject></subj-group></subj-group><subj-group><subject>Evolutionary Biology</subject><subj-group><subject>Evolutionary Systematics</subject><subj-group><subject>Phylogenetics</subject><subj-group><subject>Plant Phylogenetics</subject></subj-group></subj-group></subj-group><subj-group><subject>Organismal Evolution</subject><subj-group><subject>Plant Evolution</subject></subj-group></subj-group><subj-group><subject>Molecular Evolution</subject></subj-group></subj-group><subj-group><subject>Genetics</subject><subj-group><subject>Genomics</subject><subject>Plant Genetics</subject></subj-group></subj-group><subj-group><subject>Plant Science</subject></subj-group><subj-group><subject>Taxonomy</subject></subj-group></subj-group></article-categories><title-group><article-title>Complete Chloroplast Genome Sequence of Omani Lime (<italic>Citrus aurantiifolia</italic>) and Comparative Analysis within the Rosids</article-title><alt-title alt-title-type="running-head">Chloroplast Genome Sequence of Omani Lime (<italic>Citrus aurantiifolia</italic>)</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Su</surname><given-names>Huei-Jiun</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Hogenhout</surname><given-names>Saskia A.</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Al-Sadi</surname><given-names>Abdullah M.</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Kuo</surname><given-names>Chih-Horng</given-names></name><xref ref-type="aff" rid="aff4"><sup>4</sup></xref><xref ref-type="aff" rid="aff5"><sup>5</sup></xref><xref ref-type="aff" rid="aff6"><sup>6</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib></contrib-group><aff id="aff1"><label>1</label><addr-line>Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan</addr-line></aff><aff id="aff2"><label>2</label><addr-line>Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom</addr-line></aff><aff id="aff3"><label>3</label><addr-line>Department of Crop Sciences, Sultan Qaboos University, Al Khoud, Oman</addr-line></aff><aff id="aff4"><label>4</label><addr-line>Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan</addr-line></aff><aff id="aff5"><label>5</label><addr-line>Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan</addr-line></aff><aff id="aff6"><label>6</label><addr-line>Biotechnology Center, National Chung Hsing University, Taichung, Taiwan</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Yin</surname><given-names>Tongming</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>Nanjing Forestry University, China</addr-line></aff><author-notes><corresp id="cor1">* E-mail: <email>chk@gate.sinica.edu.tw</email></corresp><fn fn-type="conflict"><p><bold>Competing Interests: </bold>The authors confirm the following: Corresponding author Chih-Horng Kuo is an Academic Editor for PLOS ONE (since Jul. 2014). This does not alter the authors’ adherence to PLOS ONE Editorial policies and criteria.</p></fn><fn fn-type="con"><p>Conceived and designed the experiments: HJS CHK. Performed the experiments: SAH AMA. Analyzed the data: HJS CHK. Contributed reagents/materials/analysis tools: HJS AMA CHK. Contributed to the writing of the manuscript: HJS SAH AMA CHK.</p></fn></author-notes><pub-date pub-type="collection"><year>2014</year></pub-date><pub-date pub-type="epub"><day>14</day><month>11</month><year>2014</year></pub-date><volume>9</volume><issue>11</issue><elocation-id>e113049</elocation-id><history><date date-type="received"><day>5</day><month>6</month><year>2014</year></date><date date-type="accepted"><day>18</day><month>10</month><year>2014</year></date></history><permissions><copyright-year>2014</copyright-year><copyright-holder>Su 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><p>The genus <italic>Citrus</italic> contains many economically important fruits that are grown worldwide for their high nutritional and medicinal value. Due to frequent hybridizations among species and cultivars, the exact number of natural species and the taxonomic relationships within this genus are unclear. To compare the differences between the <italic>Citrus</italic> chloroplast genomes and to develop useful genetic markers, we used a reference-assisted approach to assemble the complete chloroplast genome of Omani lime (<italic>C</italic>. <italic>aurantiifolia</italic>). The complete <italic>C</italic>. <italic>aurantiifolia</italic> chloroplast genome is 159,893 bp in length; the organization and gene content are similar to most of the rosids lineages characterized to date. Through comparison with the sweet orange (<italic>C. sinensis</italic>) chloroplast genome, we identified three intergenic regions and 94 simple sequence repeats (SSRs) that are potentially informative markers with resolution for interspecific relationships. These markers can be utilized to better understand the origin of cultivated <italic>Citrus</italic>. A comparison among 72 species belonging to 10 families of representative rosids lineages also provides new insights into their chloroplast genome evolution.</p></abstract><funding-group><funding-statement>Funding for this work was provided by research grants from Biotechnology and Biological Sciences Research Council (BB/J004553/1) and the Gatsby Charitable Foundation to SAH, Sultan Qaboos University (SR/AGR/CROP/13/01) to AMA, and the Institute of Plant and Microbial Biology at Academia Sinica to CHK. 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="11"></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. The raw Illumina reads are publicly available from the NCBI SRA under the accession number SRR1611615 (<ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/sra/SRR1611615">http://www.ncbi.nlm.nih.gov/sra/SRR1611615</ext-link>). The complete genome sequence is available from the NCBI GenBank under the accession number KJ865401.1 (<ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/nuccore/KJ865401.1">http://www.ncbi.nlm.nih.gov/nuccore/KJ865401.1</ext-link>).</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. The raw Illumina reads are publicly available from the NCBI SRA under the accession number SRR1611615 (<ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/sra/SRR1611615">http://www.ncbi.nlm.nih.gov/sra/SRR1611615</ext-link>). The complete genome sequence is available from the NCBI GenBank under the accession number KJ865401.1 (<ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/nuccore/KJ865401.1">http://www.ncbi.nlm.nih.gov/nuccore/KJ865401.1</ext-link>).</p></notes></front></pmc><affiliations><list><country><li>Oman</li><li>Royaume-Uni</li><li>Taïwan</li></country></list><tree><country name="Taïwan"><noRegion><name sortKey="Su, Huei Jiun" sort="Su, Huei Jiun" uniqKey="Su H" first="Huei-Jiun" last="Su">Huei-Jiun Su</name></noRegion><name sortKey="Kuo, Chih Horng" sort="Kuo, Chih Horng" uniqKey="Kuo C" first="Chih-Horng" last="Kuo">Chih-Horng Kuo</name><name sortKey="Kuo, Chih Horng" sort="Kuo, Chih Horng" uniqKey="Kuo C" first="Chih-Horng" last="Kuo">Chih-Horng Kuo</name><name sortKey="Kuo, Chih Horng" sort="Kuo, Chih Horng" uniqKey="Kuo C" first="Chih-Horng" last="Kuo">Chih-Horng Kuo</name></country><country name="Royaume-Uni"><noRegion><name sortKey="Hogenhout, Saskia A" sort="Hogenhout, Saskia A" uniqKey="Hogenhout S" first="Saskia A." last="Hogenhout">Saskia A. Hogenhout</name></noRegion></country><country name="Oman"><noRegion><name sortKey="Al Sadi, Abdullah M" sort="Al Sadi, Abdullah M" uniqKey="Al Sadi A" first="Abdullah M." last="Al-Sadi">Abdullah M. Al-Sadi</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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