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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

TitleCytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses
Authors
Issue Date2007
PublisherAcademic Press. The Journal's web site is located at http://www.elsevier.com/locate/yviro
Citation
Virology, 2007, v. 369 n. 2, p. 431-442 How to Cite?
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.
Persistent Identifierhttp://hdl.handle.net/10722/78915
ISSN
2015 Impact Factor: 3.2
2015 SCImago Journal Rankings: 1.805
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorWoo, PCYen_HK
dc.contributor.authorWong, BHLen_HK
dc.contributor.authorHuang, Yen_HK
dc.contributor.authorLau, SKPen_HK
dc.contributor.authorYuen, KYen_HK
dc.date.accessioned2010-09-06T07:48:20Z-
dc.date.available2010-09-06T07:48:20Z-
dc.date.issued2007en_HK
dc.identifier.citationVirology, 2007, v. 369 n. 2, p. 431-442en_HK
dc.identifier.issn0042-6822en_HK
dc.identifier.urihttp://hdl.handle.net/10722/78915-
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.en_HK
dc.languageengen_HK
dc.publisherAcademic Press. The Journal's web site is located at http://www.elsevier.com/locate/yviroen_HK
dc.relation.ispartofVirologyen_HK
dc.subject.meshAnimalsen_HK
dc.subject.meshBase Sequenceen_HK
dc.subject.meshCodon - geneticsen_HK
dc.subject.meshCoronaviridae - classification - geneticsen_HK
dc.subject.meshCpG Islandsen_HK
dc.subject.meshCytosine - chemistryen_HK
dc.subject.meshGenome, Viralen_HK
dc.subject.meshHumansen_HK
dc.subject.meshRNA, Viral - chemistry - geneticsen_HK
dc.subject.meshSpecies Specificityen_HK
dc.titleCytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronavirusesen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0042-6822&volume=369&spage=431&epage=442&date=2007&atitle=Cytosine+deamination+and+selection+of+CpG+suppressed+clones+are+the+two+major+independent+biological+forces+that+shape+codon+usage+bias+in+coronavirusesen_HK
dc.identifier.emailWoo, PCY:pcywoo@hkucc.hku.hken_HK
dc.identifier.emailLau, SKP:skplau@hkucc.hku.hken_HK
dc.identifier.emailYuen, KY:kyyuen@hkucc.hku.hken_HK
dc.identifier.authorityWoo, PCY=rp00430en_HK
dc.identifier.authorityLau, SKP=rp00486en_HK
dc.identifier.authorityYuen, KY=rp00366en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1016/j.virol.2007.08.010en_HK
dc.identifier.pmid17881030-
dc.identifier.scopuseid_2-s2.0-36049005257en_HK
dc.identifier.hkuros149552en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-36049005257&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume369en_HK
dc.identifier.issue2en_HK
dc.identifier.spage431en_HK
dc.identifier.epage442en_HK
dc.identifier.isiWOS:000251263200019-
dc.publisher.placeUnited Statesen_HK
dc.identifier.scopusauthoridWoo, PCY=7201801340en_HK
dc.identifier.scopusauthoridWong, BHL=7402023413en_HK
dc.identifier.scopusauthoridHuang, Y=35597414700en_HK
dc.identifier.scopusauthoridLau, SKP=7401596211en_HK
dc.identifier.scopusauthoridYuen, KY=36078079100en_HK
dc.identifier.citeulike3058319-

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