Citrus sinensis Annotation Project (CAP): A Comprehensive Database for Sweet Orange Genome
Identifieur interne : 001185 ( Pmc/Curation ); précédent : 001184; suivant : 001186Citrus sinensis Annotation Project (CAP): A Comprehensive Database for Sweet Orange Genome
Auteurs : Jia Wang [République populaire de Chine] ; Dijun Chen [République populaire de Chine] ; Yang Lei [République populaire de Chine] ; Ji-Wei Chang [République populaire de Chine] ; Bao-Hai Hao [République populaire de Chine] ; Feng Xing [République populaire de Chine] ; Sen Li [République populaire de Chine] ; Qiang Xu [République populaire de Chine] ; Xiu-Xin Deng [République populaire de Chine] ; Ling-Ling Chen [République populaire de Chine]Source :
- PLoS ONE [ 1932-6203 ] ; 2014.
Abstract
Url:
DOI: 10.1371/journal.pone.0087723
PubMed: 24489955
PubMed Central: 3905029
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China</addr-line></nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan</wicri:regionArea></affiliation></author><author><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, P.R. 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China</addr-line></nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan</wicri:regionArea></affiliation></author><author><name sortKey="Chen, Ling Ling" sort="Chen, Ling Ling" uniqKey="Chen L" first="Ling-Ling" last="Chen">Ling-Ling Chen</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, P.R. 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China</addr-line></nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan</wicri:regionArea></affiliation></author><author><name sortKey="Lei, Yang" sort="Lei, Yang" uniqKey="Lei Y" first="Yang" last="Lei">Yang Lei</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China</addr-line></nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan</wicri:regionArea></affiliation></author><author><name sortKey="Chang, Ji Wei" sort="Chang, Ji Wei" uniqKey="Chang J" first="Ji-Wei" last="Chang">Ji-Wei Chang</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China</addr-line></nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan</wicri:regionArea></affiliation></author><author><name sortKey="Hao, Bao Hai" sort="Hao, Bao Hai" uniqKey="Hao B" first="Bao-Hai" last="Hao">Bao-Hai Hao</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China</addr-line></nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan</wicri:regionArea></affiliation></author><author><name sortKey="Xing, Feng" sort="Xing, Feng" uniqKey="Xing F" first="Feng" last="Xing">Feng Xing</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China</addr-line></nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan</wicri:regionArea></affiliation></author><author><name sortKey="Li, Sen" sort="Li, Sen" uniqKey="Li S" first="Sen" last="Li">Sen Li</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China</addr-line></nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan</wicri:regionArea></affiliation></author><author><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, P.R. China</addr-line></nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan</wicri:regionArea></affiliation></author><author><name sortKey="Deng, Xiu Xin" sort="Deng, Xiu Xin" uniqKey="Deng X" first="Xiu-Xin" last="Deng">Xiu-Xin Deng</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, P.R. China</addr-line></nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan</wicri:regionArea></affiliation></author><author><name sortKey="Chen, Ling Ling" sort="Chen, Ling Ling" uniqKey="Chen L" first="Ling-Ling" last="Chen">Ling-Ling Chen</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China</addr-line></nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan</wicri:regionArea></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><italic>Citrus</italic> is one of the most important and widely grown fruit crop with global production ranking firstly among all the fruit crops in the world. Sweet orange accounts for more than half of the <italic>Citrus</italic> production both in fresh fruit and processed juice. We have sequenced the draft genome of a double-haploid sweet orange (<italic>C. sinensis</italic> cv. Valencia), and constructed the <italic>Citrus sinensis</italic> annotation project (CAP) to store and visualize the sequenced genomic and transcriptome data. CAP provides GBrowse-based organization of sweet orange genomic data, which integrates <italic>ab initio</italic> gene prediction, EST, RNA-seq and RNA-paired end tag (RNA-PET) evidence-based gene annotation. Furthermore, we provide a user-friendly web interface to show the predicted protein-protein interactions (PPIs) and metabolic pathways in sweet orange. CAP provides comprehensive information beneficial to the researchers of sweet orange and other woody plants, which is freely available at <ext-link ext-link-type="uri" xlink:href="http://citrus.hzau.edu.cn/">http://citrus.hzau.edu.cn/</ext-link>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Arumuganathan, K" uniqKey="Arumuganathan K">K Arumuganathan</name></author><author><name sortKey="Earle, Ed" uniqKey="Earle E">ED Earle</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Xu, Q" uniqKey="Xu Q">Q Xu</name></author><author><name sortKey="Chen, Ll" uniqKey="Chen L">LL Chen</name></author><author><name sortKey="Ruan, X" uniqKey="Ruan X">X Ruan</name></author><author><name sortKey="Chen, D" uniqKey="Chen D">D Chen</name></author><author><name sortKey="Zhu, A" uniqKey="Zhu A">A Zhu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kanehisa, 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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">24489955</article-id><article-id pub-id-type="pmc">3905029</article-id><article-id pub-id-type="publisher-id">PONE-D-13-48672</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0087723</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>Crops</subject><subj-group><subject>Fruits</subject></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Biology</subject><subj-group><subject>Computational Biology</subject><subj-group><subject>Genomics</subject><subj-group><subject>Genome Analysis Tools</subject><subj-group><subject>Transcriptomes</subject></subj-group></subj-group><subj-group><subject>Genome Databases</subject></subj-group></subj-group></subj-group><subj-group><subject>Genomics</subject><subj-group><subject>Genome Analysis Tools</subject><subj-group><subject>Transcriptomes</subject></subj-group></subj-group><subj-group><subject>Genome Databases</subject></subj-group></subj-group><subj-group><subject>Plant Science</subject><subj-group><subject>Plants</subject><subj-group><subject>Fruits</subject></subj-group></subj-group><subj-group><subject>Plant Genomics</subject></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Computer Science</subject><subj-group><subject>Information Technology</subject><subj-group><subject>Databases</subject></subj-group></subj-group></subj-group></article-categories><title-group><article-title><italic>Citrus sinensis</italic> Annotation Project (CAP): A Comprehensive Database for Sweet Orange Genome</article-title><alt-title alt-title-type="running-head">A Database for Sweet Orange Genome</alt-title></title-group><contrib-group><contrib contrib-type="author" equal-contrib="yes"><name><surname>Wang</surname><given-names>Jia</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author" equal-contrib="yes"><name><surname>Chen</surname><given-names>Dijun</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author" equal-contrib="yes"><name><surname>Lei</surname><given-names>Yang</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Chang</surname><given-names>Ji-Wei</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Hao</surname><given-names>Bao-Hai</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Xing</surname><given-names>Feng</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Sen</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Xu</surname><given-names>Qiang</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Deng</surname><given-names>Xiu-Xin</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Chen</surname><given-names>Ling-Ling</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib></contrib-group><aff id="aff1"><label>1</label><addr-line>Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China</addr-line></aff><aff id="aff2"><label>2</label><addr-line>School of Science, Huazhong Agricultural University, Wuhan, P.R. China</addr-line></aff><aff id="aff3"><label>3</label><addr-line>Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, P.R. China</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Sun</surname><given-names>Meng-xiang</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>Wuhan University, China</addr-line></aff><author-notes><corresp id="cor1">* E-mail: <email>llchen@mail.hzau.edu.cn</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: LLC DC. Performed the experiments: JW YL DC. Analyzed the data: JWC BHH FX SL. Contributed reagents/materials/analysis tools: QX XXD. Wrote the paper: LLC DC.</p></fn></author-notes><pub-date pub-type="collection"><year>2014</year></pub-date><pub-date pub-type="epub"><day>28</day><month>1</month><year>2014</year></pub-date><volume>9</volume><issue>1</issue><elocation-id>e87723</elocation-id><history><date date-type="received"><day>19</day><month>11</month><year>2013</year></date><date date-type="accepted"><day>29</day><month>12</month><year>2013</year></date></history><permissions><copyright-year>2014</copyright-year><copyright-holder>Wang et al</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 <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><italic>Citrus</italic> is one of the most important and widely grown fruit crop with global production ranking firstly among all the fruit crops in the world. Sweet orange accounts for more than half of the <italic>Citrus</italic> production both in fresh fruit and processed juice. We have sequenced the draft genome of a double-haploid sweet orange (<italic>C. sinensis</italic> cv. Valencia), and constructed the <italic>Citrus sinensis</italic> annotation project (CAP) to store and visualize the sequenced genomic and transcriptome data. CAP provides GBrowse-based organization of sweet orange genomic data, which integrates <italic>ab initio</italic> gene prediction, EST, RNA-seq and RNA-paired end tag (RNA-PET) evidence-based gene annotation. Furthermore, we provide a user-friendly web interface to show the predicted protein-protein interactions (PPIs) and metabolic pathways in sweet orange. CAP provides comprehensive information beneficial to the researchers of sweet orange and other woody plants, which is freely available at <ext-link ext-link-type="uri" xlink:href="http://citrus.hzau.edu.cn/">http://citrus.hzau.edu.cn/</ext-link>.</p></abstract><funding-group><funding-statement>The present study was supported by the National Basic Research Program of China (2012AA10A304) and the National Natural Science Foundation of China (31271406 and 31222047). 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="7"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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