About: Comprehensive analysis of synonymous codon usage patterns in orf3 gene of porcine epidemic diarrhea virus in China

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About: Comprehensive analysis of synonymous codon usage patterns in orf3 gene of porcine epidemic diarrhea virus in China 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	Comprehensive analysis of synonymous codon usage patterns in orf3 gene of porcine epidemic diarrhea virus in China
Creator	Xu, Xin Cao, Hongwei Wu, Zhijun Li, Yuchang Li, Pengfei Zhang, Hua Li, Liyang Liu, Xinyang Ma, Jinzhu Shen, Yujiang Song, Baifen Wang, Xianhe Wu, Xuening Xu, Jiaxin Yao, Lili Zhang, Yating Guo, Dexuan Xu, Shuyan
Source	Elsevier; Medline; PMC
abstract	Abstract The ORF3 protein of porcine epidemic diarrhea virus (PEDV) is found to function as an ion channel which influences virus virulence and production. Taking consideration of the importance of PEDV orf3 gene, we have performed comprehensive analysis to investigate its synonymous codon usage patterns. In this study, the results of base composition analysis showed A/T rich and G/C poor in PEDV orf3 genes, and the most abundant base was nucleotide T. The relative synonymous codon usage value in each codon revealed that codon usage bias existed. The mean ENC value of each gene was 48.75, indicating a low codon usage bias, as well as a relatively instable change in PEDV orf3 genes. The general correlation analysis between base composition and codon usage bias indicated that mutational bias has an impact on the PEDV codon usage bias. Neutral analysis suggested that natural selection pressure takes a more important influence than mutational bias in shaping codon usage bias. Moreover, other factors including hydrophobicity and aromaticity have been also found to influence the codon usage variation among the PEDV orf3 genes. This study not only represents the most systematic analysis of codon usage patterns in PEDV orf3 genes, but also provides a basic shaping mechanism of the codon usage bias.
has issue date	2019-12-31(xsd:dateTime)
bibo:doi	10.1016/j.rvsc.2019.09.012
bibo:pmid	31677415
has license	els-covid
sha1sum (hex)	4b63f28146f06de4615b9e698cc5f7c6c7c86816
schema:url	https://doi.org/10.1016/j.rvsc.2019.09.012
resource representing a document's title	Comprehensive analysis of synonymous codon usage patterns in orf3 gene of porcine epidemic diarrhea virus in China
has PubMed Central identifier	PMC7172109
has PubMed identifier	31677415
schema:publication	Research in Veterinary Science
resource representing a document's body	covid:4b63f28146f06de4615b9e698cc5f7c6c7c86816#body_text
is schema:about of	named entity 'Comprehensive' named entity 'aromaticity' named entity 'G3s' named entity 'dehydration' named entity 'codon usage bias' named entity 'correlation coefficient' named entity 'neonatal' named entity 'codon usage bias' named entity 'PEDV' named entity 'total variation' named entity 'natural selection' named entity 'codon usage bias' named entity 'vomiting' named entity 'classical swine fever virus' named entity 'ion channel' named entity 'codon usage' named entity 'codons' named entity 'gene' named entity 'natural selection' named entity 'molecular evolution' named entity 'ORF2' named entity 'correspondence analysis' named entity 'viruses' named entity 'bat' named entity 'amino acids' named entity 'PEDV' named entity 'critical role' named entity 'codon usage bias' named entity 'gene' named entity 'PEDV' named entity 'protein' named entity 'China' named entity 'genome' named entity 'PEDV' named entity 'fungi' named entity 'PEDV' named entity 'Axis2' named entity 'vaccine design' named entity 'codon usage' named entity 'PEDV' named entity 'mutational pressure' named entity 'codon bias' named entity 'codon usage' named entity 'codon usage' named entity 'codon' named entity 'rank correlation' named entity 'amino acids' named entity 'PEDV' named entity 'principal axis' named entity 'codon usage bias' named entity 'gene' named entity 'highly contagious' named entity 'China' named entity 'virulent' named entity 'PEDV' named entity 'codons' named entity 'PEDV' named entity 'CSFV' named entity 'correlation' named entity '1.2' named entity '5'-UTR' named entity 'RNA virus' named entity 'gene' named entity 'gene'

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