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
2011 Impact Factor: 3.351
2011 SCImago Journal Rankings: 0.355
DOIhttp://dx.doi.org/10.1016/j.virol.2007.08.010
ISI Accession Number IDWOS:000251263200019
ReferencesReferences in Scopus
DC Field
Value
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
2011 Impact Factor: 3.351
2011 SCImago Journal Rankings: 0.355
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
Author Affiliations
  1. The University of Hong Kong