About: Genome-Wide Analysis of Codon Usage and Influencing Factors in Chikungunya Viruses

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About: Genome-Wide Analysis of Codon Usage and Influencing Factors in Chikungunya Viruses 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	Genome-Wide Analysis of Codon Usage and Influencing Factors in Chikungunya Viruses
Creator	Tong, Y Butt, A Nasrullah, I
Source	PMC
abstract	Chikungunya virus (CHIKV) is an arthropod-borne virus of the family Togaviridae that is transmitted to humans by Aedes spp. mosquitoes. Its genome comprises a 12 kb single-strand positive-sense RNA. In the present study, we report the patterns of synonymous codon usage in 141 CHIKV genomes by calculating several codon usage indices and applying multivariate statistical methods. Relative synonymous codon usage (RSCU) analysis showed that the preferred synonymous codons were G/C and A-ended. A comparative analysis of RSCU between CHIKV and its hosts showed that codon usage patterns of CHIKV are a mixture of coincidence and antagonism. Similarity index analysis showed that the overall codon usage patterns of CHIKV have been strongly influenced by Pan troglodytes and Aedes albopictus during evolution. The overall codon usage bias was low in CHIKV genomes, as inferred from the analysis of effective number of codons (ENC) and codon adaptation index (CAI). Our data suggested that although mutation pressure dominates codon usage in CHIKV, patterns of codon usage in CHIKV are also under the influence of natural selection from its hosts and geography. To the best of our knowledge, this is first report describing codon usage analysis in CHIKV genomes. The findings from this study are expected to increase our understanding of factors involved in viral evolution, and fitness towards hosts and the environment.
has issue date	2014-03-04(xsd:dateTime)
bibo:doi	10.1371/journal.pone.0090905
bibo:pmid	24595095
has license	cc-by
sha1sum (hex)	6b40e3b543867aa91f5d01345cf3ed074300159c
schema:url	https://doi.org/10.1371/journal.pone.0090905
resource representing a document's title	Genome-Wide Analysis of Codon Usage and Influencing Factors in Chikungunya Viruses
has PubMed Central identifier	PMC3942501
has PubMed identifier	24595095
schema:publication	PLoS One
resource representing a document's body	covid:6b40e3b543867aa91f5d01345cf3ed074300159c#body_text
is schema:about of	named entity 'TO INCREASE' named entity 'CODONS' named entity 'COMPARATIVE ANALYSIS' named entity 'PRESSURE' named entity 'GENOME' named entity 'GENOMES' named entity 'PRESENT' named entity 'CODON ADAPTATION INDEX' named entity 'BEST' named entity 'A 12' named entity 'RNA' named entity 'STUDY' named entity 'INFLUENCE' named entity 'NUMBER OF' named entity '141' named entity 'NATURAL SELECTION' named entity 'FAMILY' named entity 'HUMANS' named entity 'MUTATION' named entity 'SYNONYMOUS CODON' named entity 'SYNONYMOUS' named entity 'ANTAGONISM' named entity 'EVOLUTION' named entity 'ENDED' named entity 'PREFERRED' named entity 'CODON USAGE' named entity 'FITNESS' named entity 'MIXTURE' named entity 'INVOLVED' named entity 'SENSE' named entity 'AEDES ALBOPICTUS' named entity 'ENVIRONMENT' named entity 'FINDINGS' named entity 'PATTERNS' named entity 'DATA' named entity 'ARTHROPOD-BORNE VIRUS' named entity 'ITS' named entity 'SINGLE' named entity 'CODON USAGE ANALYSIS' named entity 'INDICES' named entity 'HAVE' named entity 'TRANSMITTED' named entity 'CHIKUNGUNYA VIRUS' covid:arg/6b40e3b543867aa91f5d01345cf3ed074300159c named entity 'TOGAVIRIDAE' named entity 'EFFECTIVE' named entity 'STATISTICAL METHODS' named entity 'POSITIVE' named entity 'GENOME-WIDE ANALYSIS' named entity 'AEDES' named entity 'VIRUSES' named entity 'CHIKUNGUNYA' named entity 'LOW' named entity 'MOSQUITOES' named entity 'UNDERSTANDING' named entity 'STRAND' named entity 'OVERALL' named entity 'OUR' named entity 'CODON USAGE BIAS' named entity 'PAN TROGLODYTES' named entity 'ANALYSIS' named entity 'DESCRIBING' named entity 'APPLYING' named entity 'SPP' named entity 'SIMILARITY INDEX' named entity 'GEOGRAPHY' named entity 'REPORT' named entity 'VIRAL EVOLUTION' named entity 'HOSTS' named entity 'CALCULATING' named entity 'CODON USAGE' named entity 'RELATIVE' named entity 'KNOWLEDGE' named entity 'EXPECTED' named entity 'INFERRED' named entity 'CHIKV' named entity 'effective number of codons' named entity 'CHIKV' named entity 'arthropod-borne virus'

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