About: Analysis of synonymous codon usage in porcine reproductive and respiratory syndrome virus

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About: Analysis of synonymous codon usage in porcine reproductive and respiratory syndrome virus 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	Analysis of synonymous codon usage in porcine reproductive and respiratory syndrome virus
Creator	Zhang, Jie Wang, Meng Zhou, Jian-Hua Chen, Hao-Tai Ding, Yao-Zhong Liu, Yong-Sheng Ma, Li-Na
Source	Elsevier; Medline; PMC
abstract	In this study, we calculated the relative synonymous codon usage (RSCU) values and codon usage bias (CUB) values to implement a comparative analysis of codon usage pattern of open reading frames (ORFs) which belong to the two main genotypes of porcine reproductive and respiratory syndrome virus (PRRSV). By analysis of synonymous codon usage values in each ORF of PRRSV, the optimal codons for most amino acids were all C or G-ended codons except GAU for Asp, CAU for His, UUU for Phe and CCU for Pro. The synonymous codon usage patterns in different ORFs of PRRSV were different and genetically conserved. Among them, ORF1a, ORF4, ORF5 and ORF7 could cluster these strains into the two main serotypes (EU and US). Due to mutational pressure, compositional constraint played an important role in shaping the synonymous codon usage pattern in different ORFs, and the synonymous codon usage diversity in ORFs was correlated with gene function. The degree of CUB for some particular amino acids under strong selection pressure probably served as a potential genetic marker for each ORF in PRRSV. However, gene length and translational selection in nature had no effect on the synonymous codon usage pattern in PRRSV. These conclusions could not only offer an insight into the synonymous codon usage pattern and differentiation of gene function, but also assist in understanding the discrepancy of evolution among ORFs in PRRSV.
has issue date	2010-05-01(xsd:dateTime)
bibo:doi	10.1016/j.meegid.2010.04.010
bibo:pmid	20438864
has license	no-cc
sha1sum (hex)	26029ce6e9b908af320d79f5386380f45578fb82
schema:url	https://doi.org/10.1016/j.meegid.2010.04.010
resource representing a document's title	Analysis of synonymous codon usage in porcine reproductive and respiratory syndrome virus
has PubMed Central identifier	PMC7106271
has PubMed identifier	20438864
schema:publication	Infect Genet Evol
resource representing a document's body	covid:26029ce6e9b908af320d79f5386380f45578fb82#body_text
is schema:about of	named entity 'PORCINE REPRODUCTIVE AND RESPIRATORY SYNDROME VIRUS' named entity 'CODON USAGE' named entity 'SYNONYMOUS CODON' named entity 'ANALYSIS' named entity 'codon usage' named entity 'PRRSV' named entity 'codon' named entity 'ORFs' named entity 'PRRSV' named entity 'ORF' named entity 'conserved pattern' named entity 'ORF1' named entity 'mutational pressure' named entity 'amino acid' named entity 'CUB' named entity 'immunogenic' named entity 'amino acid' named entity 'host cells' named entity 'viruses' named entity 'codon usage' named entity 'CUB' named entity 'codons' named entity 'mutational pressure' named entity 'codons' named entity 'PRRSV' named entity 'codon usage' named entity 'non-synonymous' named entity 'PRRSV' named entity 'non-synonymous' named entity 'serotypes' named entity 'codons' named entity 'codon usage' named entity 'Sequence analysis' named entity 'Thr' named entity 'viruses' named entity 'codons' named entity 'Gln' named entity 'CUB' named entity 'codon usage bias' named entity 'glycoprotein' named entity 'vector' named entity '0.01' named entity 'amino acids' named entity 'rank correlation' named entity 'serotypes' named entity 'evolution' named entity 'codons' named entity 'codon usage' named entity 'PRRSV' named entity 'genetic diversity' named entity 'PRRSV' named entity 'standard amino acids' named entity 'cysteine protease' named entity 'codon usage' named entity 'ORFs' named entity 'papain' named entity 'National Center for Biotechnology Information' named entity 'codon usage' named entity 'codons' named entity 'Phe' named entity 'G 3' named entity 'codon usage' named entity 'PRRSV' named entity 'codons' named entity 'nucleotide' named entity 'viral nonstructural proteins' named entity 'mutational pressure' named entity 'PRRSV' named entity 'codons' named entity 'codons' named entity 'PRRSV' named entity 'PRRSV' named entity 'amino acid' named entity 'serotypes' named entity 'codon usage'

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