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Article: Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses
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TitleCytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses
 
AuthorsWoo, PCY1
Wong, BHL1
Huang, Y1
Lau, SKP1
Yuen, KY1
 
Issue Date2007
 
PublisherAcademic Press. The Journal's web site is located at http://www.elsevier.com/locate/yviro
 
CitationVirology, 2007, v. 369 n. 2, p. 431-442 [How to Cite?]
DOI: http://dx.doi.org/10.1016/j.virol.2007.08.010
 
AbstractUsing the complete genome sequences of 19 coronavirus genomes, we analyzed the codon usage bias, dinucleotide relative abundance and cytosine deamination in coronavirus genomes. Of the eight codons that contain CpG, six were markedly suppressed. The mean NNU/NNC ratio of the six amino acids using either NNC or NNU as codon is 3.262, suggesting cytosine deamination. Among the 16 dinucleotides, CpG was most markedly suppressed (mean relative abundance 0.509). No correlation was observed between CpG abundance and mean NNU/NNC ratio. Among the 19 coronaviruses, CoV-HKU1 showed the most extreme codon usage bias and extremely high NNU/NNC ratio of 8.835. Cytosine deamination and selection of CpG suppressed clones by the immune system are the two major independent biochemical and biological selective forces that shape codon usage bias in coronavirus genomes. The underlying mechanism for the extreme codon usage bias, cytosine deamination and G + C content in CoV-HKU1 warrants further studies. © 2007 Elsevier Inc. All rights reserved.
 
ISSN0042-6822
2012 Impact Factor: 3.367
2012 SCImago Journal Rankings: 1.428
 
DOIhttp://dx.doi.org/10.1016/j.virol.2007.08.010
 
ISI Accession Number IDWOS:000251263200019
 
ReferencesReferences in Scopus
 
DC FieldValue
dc.contributor.authorWoo, PCY
 
dc.contributor.authorWong, BHL
 
dc.contributor.authorHuang, Y
 
dc.contributor.authorLau, SKP
 
dc.contributor.authorYuen, KY
 
dc.date.accessioned2010-09-06T07:48:20Z
 
dc.date.available2010-09-06T07:48:20Z
 
dc.date.issued2007
 
dc.description.abstractUsing the complete genome sequences of 19 coronavirus genomes, we analyzed the codon usage bias, dinucleotide relative abundance and cytosine deamination in coronavirus genomes. Of the eight codons that contain CpG, six were markedly suppressed. The mean NNU/NNC ratio of the six amino acids using either NNC or NNU as codon is 3.262, suggesting cytosine deamination. Among the 16 dinucleotides, CpG was most markedly suppressed (mean relative abundance 0.509). No correlation was observed between CpG abundance and mean NNU/NNC ratio. Among the 19 coronaviruses, CoV-HKU1 showed the most extreme codon usage bias and extremely high NNU/NNC ratio of 8.835. Cytosine deamination and selection of CpG suppressed clones by the immune system are the two major independent biochemical and biological selective forces that shape codon usage bias in coronavirus genomes. The underlying mechanism for the extreme codon usage bias, cytosine deamination and G + C content in CoV-HKU1 warrants further studies. © 2007 Elsevier Inc. All rights reserved.
 
dc.description.natureLink_to_subscribed_fulltext
 
dc.identifier.citationVirology, 2007, v. 369 n. 2, p. 431-442 [How to Cite?]
DOI: http://dx.doi.org/10.1016/j.virol.2007.08.010
 
dc.identifier.citeulike3058319
 
dc.identifier.doihttp://dx.doi.org/10.1016/j.virol.2007.08.010
 
dc.identifier.epage442
 
dc.identifier.hkuros149552
 
dc.identifier.isiWOS:000251263200019
 
dc.identifier.issn0042-6822
2012 Impact Factor: 3.367
2012 SCImago Journal Rankings: 1.428
 
dc.identifier.issue2
 
dc.identifier.openurl
 
dc.identifier.pmid17881030
 
dc.identifier.scopuseid_2-s2.0-36049005257
 
dc.identifier.spage431
 
dc.identifier.urihttp://hdl.handle.net/10722/78915
 
dc.identifier.volume369
 
dc.languageeng
 
dc.publisherAcademic Press. The Journal's web site is located at http://www.elsevier.com/locate/yviro
 
dc.publisher.placeUnited States
 
dc.relation.ispartofVirology
 
dc.relation.referencesReferences in Scopus
 
dc.subject.meshAnimals
 
dc.subject.meshBase Sequence
 
dc.subject.meshCodon - genetics
 
dc.subject.meshCoronaviridae - classification - genetics
 
dc.subject.meshCpG Islands
 
dc.subject.meshCytosine - chemistry
 
dc.subject.meshGenome, Viral
 
dc.subject.meshHumans
 
dc.subject.meshRNA, Viral - chemistry - genetics
 
dc.subject.meshSpecies Specificity
 
dc.titleCytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses
 
dc.typeArticle
 
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Author Affiliations
  1. The University of Hong Kong