About: Compare the differences of synonymous codon usage between the two species within cardiovirus

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About: Compare the differences of synonymous codon usage between the two species within cardiovirus 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	Compare the differences of synonymous codon usage between the two species within cardiovirus
Creator	Liu, Yongsheng Zhang, Jie Zhou, Jian-Hua Chen, Hao-Tai Ding, Yao-Zhong Liu, Wen-Qian Ma, Li-Na Zhang, Yi-Qiang
Source	Medline; PMC
abstract	BACKGROUND: Cardioviruses are positive-strand RNA viruses in the Picornaviridae family that can cause enteric infection in rodents and also been detected at lower frequencies in other mammals such as pigs and human beings. The Cardiovirus genus consists two distinct species: Encephalomyocarditis virus (EMCV) and Theilovirus (ThV). There are a lot differences between the two species. In this study, the differences of codon usage in EMCV and ThV were compared. RESULTS: The mean ENC values of EMCV and ThV are 54.86 and 51.08 respectively, higher than 40.And there are correlations between (C+G)(12)% and (C+G)(3)% for both EMCV and ThV (r = -0.736;r = 0.986, P < 0.01, repectively). For ThV the (C+G)(12)%, (C+G)(3)%, axis f'(1 )and axis f'(2 )had a significant correlations respectively but not for EMCV. According to the RSCU values, the EMCV species seemed to prefer U, G and C ending codon, while the ThV spice seemed to like using U and A ending codon. However, in both genus AGA for Arg, AUU for Ile, UCU for Ser, and GGA for Gly were chosen preferentially. Correspondence analysis detected one major trend in the first axis (f'(1)) which accounted for 22.89% of the total variation, and another major trend in the second axis (f'(2)) which accounted for 17.64% of the total variation. And the plots of the same serotype seemed at the same region at the coordinate. CONCLUSION: The overall extents of codon usage bias in both EMCV and ThV are low. The mutational pressure is the main factor that determines the codon usage bias, but the (C+G) content plays a more important role in codon usage bias for ThV than for EMCV. The synonymous codon usage pattern in both EMCV and ThV genes is gene function and geography specific, but not host specific. Maybe the serotype is one factor effected the codon bias for ThV, and location has no significant effect on the variations of synonymous codon usage in these virus genes.
has issue date	2011-06-27(xsd:dateTime)
bibo:doi	10.1186/1743-422x-8-325
bibo:pmid	21708006
has license	cc-by
sha1sum (hex)	a730b4d5a5a0353503a1cd46d458635f93618805
schema:url	https://doi.org/10.1186/1743-422x-8-325
resource representing a document's title	Compare the differences of synonymous codon usage between the two species within cardiovirus
has PubMed Central identifier	PMC3148564
has PubMed identifier	21708006
schema:publication	Virol J
resource representing a document's body	covid:a730b4d5a5a0353503a1cd46d458635f93618805#body_text
is schema:about of	named entity 'EMCV' named entity 'frequencies' named entity 'SYNONYMOUS CODON' named entity 'BACKGROUND' named entity 'CORRELATIONS' named entity 'ACCORDING' named entity 'RODENTS' named entity 'ENTERIC INFECTION' named entity 'POSITIVE' named entity 'TREND' named entity 'CODON' named entity 'CAUSE' named entity 'SPECIES' named entity 'ENCEPHALOMYOCARDITIS VIRUS' named entity 'USING' named entity 'RESULTS' named entity 'DISTINCT' named entity 'ILE' named entity 'CODON USAGE' named entity 'SPICE' named entity 'CORRESPONDENCE' named entity '0.01' named entity 'TOTAL' named entity 'BUT' named entity 'SEROTYPE' named entity 'UCU' named entity 'GGA' named entity 'RNA VIRUSES' named entity 'CHOSEN' named entity 'PICORNAVIRIDAE' named entity 'SER' named entity 'STUDY' named entity 'MAJOR' named entity 'ENDING' named entity 'CARDIOVIRUS' named entity 'DETECTED' named entity 'FAMILY' named entity 'MAMMALS' named entity 'LOWER' named entity 'CARDIOVIRUS' named entity 'HIGHER' named entity '736' named entity 'AUU' named entity 'ARG' named entity 'GENUS' named entity 'GLY' named entity 'COORDINATE' named entity 'VALUES' named entity 'VARIATION' named entity 'PIGS' named entity 'AGA' named entity 'ENC' named entity 'COMPARED' named entity 'HUMAN' named entity 'FREQUENCIES' named entity 'MEAN' named entity 'STRAND' named entity 'SECOND' named entity 'LIKE' named entity 'A LOT' named entity 'CODON USAGE' named entity 'SPECIES' named entity 'COMPARE' named entity 'SIGNIFICANT' named entity 'REGION' named entity 'CARDIOVIRUSES' named entity 'AXIS' named entity 'ANALYSIS' named entity 'THEILOVIRUS' covid:arg/a730b4d5a5a0353503a1cd46d458635f93618805 named entity 'Ile' named entity 'EMCV' named entity 'However' named entity 'RNA'

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