Coronavirus phylogeny based on a geometric approach
Identifieur interne : 001299 ( Pmc/Curation ); précédent : 001298; suivant : 001300Coronavirus phylogeny based on a geometric approach
Auteurs : Wen-Xin Zheng [République populaire de Chine] ; Ling-Ling Chen [République populaire de Chine] ; Hong-Yu Ou [République populaire de Chine] ; Feng Gao [République populaire de Chine] ; Chun-Ting Zhang [République populaire de Chine]Source :
- Molecular Phylogenetics and Evolution [ 1055-7903 ] ; 2005.
Abstract
A novel coronavirus has been identified as the cause of the outbreak of severe acute respiratory syndrome (SARS). Previous phylogenetic analyses based on sequence alignments show that SARS-CoVs form a new group distantly related to the other three groups of previously characterized coronaviruses. In this paper, a geometric approach based on the
Url:
DOI: 10.1016/j.ympev.2005.03.030
PubMed: 15890535
PubMed Central: 7111192
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Coronavirus phylogeny based on a geometric approach</title><author><name sortKey="Zheng, Wen Xin" sort="Zheng, Wen Xin" uniqKey="Zheng W" first="Wen-Xin" last="Zheng">Wen-Xin Zheng</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Physics, Tianjin University, Tianjin 300072, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Physics, Tianjin University, Tianjin 300072</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">Department of Physics, Tianjin University, Tianjin 300072, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Physics, Tianjin University, Tianjin 300072</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2">Laboratory for Computational Biology, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Shandong University of Technology, Zibo 255049, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Laboratory for Computational Biology, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Shandong University of Technology, Zibo 255049</wicri:regionArea></affiliation></author><author><name sortKey="Ou, Hong Yu" sort="Ou, Hong Yu" uniqKey="Ou H" first="Hong-Yu" last="Ou">Hong-Yu Ou</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Physics, Tianjin University, Tianjin 300072, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Physics, Tianjin University, Tianjin 300072</wicri:regionArea></affiliation></author><author><name sortKey="Gao, Feng" sort="Gao, Feng" uniqKey="Gao F" first="Feng" last="Gao">Feng Gao</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Physics, Tianjin University, Tianjin 300072, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Physics, Tianjin University, Tianjin 300072</wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Chun Ting" sort="Zhang, Chun Ting" uniqKey="Zhang C" first="Chun-Ting" last="Zhang">Chun-Ting Zhang</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Physics, Tianjin University, Tianjin 300072, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Physics, Tianjin University, Tianjin 300072</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">15890535</idno><idno type="pmc">7111192</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7111192</idno><idno type="RBID">PMC:7111192</idno><idno type="doi">10.1016/j.ympev.2005.03.030</idno><date when="2005">2005</date><idno type="wicri:Area/Pmc/Corpus">001299</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001299</idno><idno type="wicri:Area/Pmc/Curation">001299</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001299</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Coronavirus phylogeny based on a geometric approach</title><author><name sortKey="Zheng, Wen Xin" sort="Zheng, Wen Xin" uniqKey="Zheng W" first="Wen-Xin" last="Zheng">Wen-Xin Zheng</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Physics, Tianjin University, Tianjin 300072, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Physics, Tianjin University, Tianjin 300072</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">Department of Physics, Tianjin University, Tianjin 300072, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Physics, Tianjin University, Tianjin 300072</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2">Laboratory for Computational Biology, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Shandong University of Technology, Zibo 255049, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Laboratory for Computational Biology, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Shandong University of Technology, Zibo 255049</wicri:regionArea></affiliation></author><author><name sortKey="Ou, Hong Yu" sort="Ou, Hong Yu" uniqKey="Ou H" first="Hong-Yu" last="Ou">Hong-Yu Ou</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Physics, Tianjin University, Tianjin 300072, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Physics, Tianjin University, Tianjin 300072</wicri:regionArea></affiliation></author><author><name sortKey="Gao, Feng" sort="Gao, Feng" uniqKey="Gao F" first="Feng" last="Gao">Feng Gao</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Physics, Tianjin University, Tianjin 300072, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Physics, Tianjin University, Tianjin 300072</wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Chun Ting" sort="Zhang, Chun Ting" uniqKey="Zhang C" first="Chun-Ting" last="Zhang">Chun-Ting Zhang</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Physics, Tianjin University, Tianjin 300072, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Physics, Tianjin University, Tianjin 300072</wicri:regionArea></affiliation></author></analytic><series><title level="j">Molecular Phylogenetics and Evolution</title><idno type="ISSN">1055-7903</idno><idno type="eISSN">1095-9513</idno><imprint><date when="2005">2005</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>A novel coronavirus has been identified as the cause of the outbreak of severe acute respiratory syndrome (SARS). Previous phylogenetic analyses based on sequence alignments show that SARS-CoVs form a new group distantly related to the other three groups of previously characterized coronaviruses. In this paper, a geometric approach based on the <italic>Z</italic>-curve representation of the whole genome sequence is proposed to analyze the phylogenetic relationships of coronaviruses. The evolutionary distances are obtained through measuring the differences among the three-dimensional <italic>Z</italic>-curves. The <italic>Z</italic>-curve is approximately described by its geometric center and the associated three eigenvectors, which indicate the center position and the trend of the <italic>Z</italic>-curve, respectively. Although some information is lost due to the approximate description of the <italic>Z</italic>-curve, the phylogenetic tree constructed based on these parameters is consistent with those of previous analyses. The present method has the merits of simplicity and intuitiveness, but it is still in its premature stage. Because the phylogenetic relationships are inferred from the whole genome, instead of some individual genes, the present method represents a new direction of phylogeny study in the post-genome era.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Chen, L L" uniqKey="Chen L">L.L. Chen</name></author><author><name sortKey="Ou, H Y" uniqKey="Ou H">H.Y. Ou</name></author><author><name sortKey="Zhang, R" uniqKey="Zhang R">R. Zhang</name></author><author><name sortKey="Zhang, C T" uniqKey="Zhang C">C.-T. Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cork, D J" uniqKey="Cork D">D.J. Cork</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Cornish Bowden, A" uniqKey="Cornish Bowden A">A. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Mol Phylogenet Evol</journal-id><journal-id journal-id-type="iso-abbrev">Mol. Phylogenet. Evol</journal-id><journal-title-group><journal-title>Molecular Phylogenetics and Evolution</journal-title></journal-title-group><issn pub-type="ppub">1055-7903</issn><issn pub-type="epub">1095-9513</issn><publisher><publisher-name>Elsevier Inc.</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">15890535</article-id><article-id pub-id-type="pmc">7111192</article-id><article-id pub-id-type="publisher-id">S1055-7903(05)00107-7</article-id><article-id pub-id-type="doi">10.1016/j.ympev.2005.03.030</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Coronavirus phylogeny based on a geometric approach</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Zheng</surname><given-names>Wen-Xin</given-names></name><xref rid="aff1" ref-type="aff">a</xref></contrib><contrib contrib-type="author"><name><surname>Chen</surname><given-names>Ling-Ling</given-names></name><xref rid="aff1" ref-type="aff">a</xref><xref rid="aff2" ref-type="aff">b</xref></contrib><contrib contrib-type="author"><name><surname>Ou</surname><given-names>Hong-Yu</given-names></name><xref rid="aff1" ref-type="aff">a</xref></contrib><contrib contrib-type="author"><name><surname>Gao</surname><given-names>Feng</given-names></name><xref rid="aff1" ref-type="aff">a</xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Chun-Ting</given-names></name><email>ctzhang@tju.edu.cn</email><xref rid="aff1" ref-type="aff">a</xref><xref rid="cor1" ref-type="corresp">⁎</xref></contrib></contrib-group><aff id="aff1"><label>a</label>Department of Physics, Tianjin University, Tianjin 300072, China</aff><aff id="aff2"><label>b</label>Laboratory for Computational Biology, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Shandong University of Technology, Zibo 255049, China</aff><author-notes><corresp id="cor1"><label>⁎</label>Corresponding author. Fax: +86 22 2740 2697 <email>ctzhang@tju.edu.cn</email></corresp></author-notes><pub-date pub-type="pmc-release"><day>10</day><month>5</month><year>2005</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on .</pmc-comment>
<pub-date pub-type="ppub"><month>8</month><year>2005</year></pub-date><pub-date pub-type="epub"><day>10</day><month>5</month><year>2005</year></pub-date><volume>36</volume><issue>2</issue><fpage>224</fpage><lpage>232</lpage><history><date date-type="received"><day>24</day><month>5</month><year>2004</year></date><date date-type="rev-recd"><day>12</day><month>1</month><year>2005</year></date></history><permissions><copyright-statement>Copyright © 2005 Elsevier Inc. All rights reserved.</copyright-statement><copyright-year>2005</copyright-year><copyright-holder>Elsevier Inc.</copyright-holder><license><license-p>Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.</license-p></license></permissions><abstract><p>A novel coronavirus has been identified as the cause of the outbreak of severe acute respiratory syndrome (SARS). Previous phylogenetic analyses based on sequence alignments show that SARS-CoVs form a new group distantly related to the other three groups of previously characterized coronaviruses. In this paper, a geometric approach based on the <italic>Z</italic>-curve representation of the whole genome sequence is proposed to analyze the phylogenetic relationships of coronaviruses. The evolutionary distances are obtained through measuring the differences among the three-dimensional <italic>Z</italic>-curves. The <italic>Z</italic>-curve is approximately described by its geometric center and the associated three eigenvectors, which indicate the center position and the trend of the <italic>Z</italic>-curve, respectively. Although some information is lost due to the approximate description of the <italic>Z</italic>-curve, the phylogenetic tree constructed based on these parameters is consistent with those of previous analyses. The present method has the merits of simplicity and intuitiveness, but it is still in its premature stage. Because the phylogenetic relationships are inferred from the whole genome, instead of some individual genes, the present method represents a new direction of phylogeny study in the post-genome era.</p></abstract><kwd-group><title>Keywords</title><kwd>Phylogenetic tree</kwd><kwd>Coronavirus</kwd><kwd>Severe acute respiratory syndrome</kwd><kwd>SARS-CoV</kwd><kwd><italic>Z</italic>-curve</kwd></kwd-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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