Coronavirus phylogeny based on a geometric approach.
Identifieur interne : 002774 ( PubMed/Checkpoint ); précédent : 002773; suivant : 002775Coronavirus phylogeny based on a geometric approach.
Auteurs : Wen-Xin Zheng [République populaire de Chine] ; Ling-Ling Chen ; Hong-Yu Ou ; Feng Gao ; Chun-Ting ZhangSource :
- Molecular phylogenetics and evolution [ 1055-7903 ] ; 2005.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Coronavirus, Virus du SRAS.
- Algorithmes, Animaux, Coronavirus, Génome viral, Humains, Phylogénie, Évolution moléculaire.
English descriptors
- KwdEn :
- MESH :
- classification : Coronavirus.
- genetics : Coronavirus, SARS Virus.
- Algorithms, Animals, Evolution, Molecular, Genome, Viral, Humans, Phylogeny.
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 Z-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 Z-curves. The Z-curve is approximately described by its geometric center and the associated three eigenvectors, which indicate the center position and the trend of the Z-curve, respectively. Although some information is lost due to the approximate description of the Z-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.
DOI: 10.1016/j.ympev.2005.03.030
PubMed: 15890535
Affiliations:
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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 Z-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 Z-curves. The Z-curve is approximately described by its geometric center and the associated three eigenvectors, which indicate the center position and the trend of the Z-curve, respectively. Although some information is lost due to the approximate description of the Z-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.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">15890535</PMID><DateCompleted><Year>2005</Year><Month>11</Month><Day>21</Day></DateCompleted><DateRevised><Year>2020</Year><Month>04</Month><Day>07</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">1055-7903</ISSN><JournalIssue CitedMedium="Print"><Volume>36</Volume><Issue>2</Issue><PubDate><Year>2005</Year><Month>Aug</Month></PubDate></JournalIssue><Title>Molecular phylogenetics and evolution</Title><ISOAbbreviation>Mol. Phylogenet. Evol.</ISOAbbreviation></Journal><ArticleTitle>Coronavirus phylogeny based on a geometric approach.</ArticleTitle><Pagination><MedlinePgn>224-32</MedlinePgn></Pagination><Abstract><AbstractText>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 Z-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 Z-curves. The Z-curve is approximately described by its geometric center and the associated three eigenvectors, which indicate the center position and the trend of the Z-curve, respectively. Although some information is lost due to the approximate description of the Z-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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zheng</LastName><ForeName>Wen-Xin</ForeName><Initials>WX</Initials><AffiliationInfo><Affiliation>Department of Physics, Tianjin University, Tianjin 300072, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Ling-Ling</ForeName><Initials>LL</Initials></Author><Author ValidYN="Y"><LastName>Ou</LastName><ForeName>Hong-Yu</ForeName><Initials>HY</Initials></Author><Author ValidYN="Y"><LastName>Gao</LastName><ForeName>Feng</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Chun-Ting</ForeName><Initials>CT</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal 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