About: 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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About: Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses
Creator	Yuen, Kwok-Yung Huang, Yi Lau, Susanna Wong, Beatrice Woo, Patrick
Source	Elsevier; Medline; PMC
abstract	Abstract Using 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.
has issue date	2007-12-20(xsd:dateTime)
bibo:doi	10.1016/j.virol.2007.08.010
bibo:pmid	17881030
has license	els-covid
sha1sum (hex)	520b2eaf8d2e9a3473534f56a1241c0d425b7547
schema:url	https://doi.org/10.1016/j.virol.2007.08.010
resource representing a document's title	Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses
has PubMed Central identifier	PMC7103290
has PubMed identifier	17881030
schema:publication	Virology
resource representing a document's body	covid:520b2eaf8d2e9a3473534f56a1241c0d425b7547#body_text
is schema:about of	named entity 'SHAPE' named entity 'BIOLOGICAL' named entity 'abundance' named entity 'NNC' named entity 'deamination' named entity 'deamination' named entity 'codon usage bias' named entity 'codon' named entity 'warrants' named entity 'FORCES' named entity 'EXTREME' named entity 'GENOMES' named entity 'CODON USAGE BIAS' covid:arg/520b2eaf8d2e9a3473534f56a1241c0d425b7547 named entity 'AMINO ACIDS' named entity 'RATIO' named entity 'CONTENT' named entity 'UNDERLYING' named entity 'CORRELATION' named entity 'GENOME' named entity 'HIGH' named entity 'DEAMINATION' named entity 'SELECTION' named entity 'INDEPENDENT' named entity 'CYTOSINE' named entity '509' named entity 'CORONAVIRUS' named entity 'CPG' named entity 'CORONAVIRUSES' named entity 'MAJOR' named entity 'CLONES' named entity 'STUDIES' named entity 'FORCES' named entity 'DINUCLEOTIDE' named entity 'CPG' named entity 'RELATIVE ABUNDANCE' named entity 'SUPPRESSED' named entity 'MAJOR' named entity 'ABUNDANCE' named entity 'SHAPE' named entity 'ANALYZED' named entity 'EXTREMELY' named entity 'CODON' named entity 'CODONS' named entity 'SEQUENCES' named entity 'EITHER' named entity 'CORONAVIRUSES' named entity 'USING' named entity 'BIOCHEMICAL' named entity 'OBSERVED' named entity 'CYTOSINE' named entity 'SELECTION' named entity 'COMPLETE' named entity 'MARKEDLY' named entity '262' named entity 'IMMUNE SYSTEM' named entity 'MECHANISM' named entity 'BIOLOGICAL' named entity 'DEAMINATION' named entity 'CONTAIN' named entity 'MEAN' named entity 'SELECTIVE' named entity 'CODON USAGE BIAS' named entity 'CLONES' named entity 'INDEPENDENT' named entity 'SUPPRESSED' named entity 'COV-HKU1' named entity 'codon' named entity 'codons' named entity 'NNC' named entity 'biological' named entity 'coronavirus' named entity 'Cytosine' named entity 'codon' named entity 'NNU' named entity 'sequences' named entity 'CpG'

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