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Analysis of codon usage in bovine viral diarrhea virus

Bovine viral diarrhea virus (BVDV) is a widespread virus in beef and dairy herds. BVDV has been grouped into two genotypes, genotype 1 and genotype 2. In this study, the relative synonymous codon usage (RSCU) values, effective number of codon (ENC) values and nucleotide content were investigated, an...

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Autores principales: Wang, Meng, Zhang, Jie, Zhou, Jian-hua, Chen, Hao-tai, Ma, Li-na, Ding, Yao-zhong, Liu, Wen-qian, Liu, Yong-sheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Vienna 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087306/
https://www.ncbi.nlm.nih.gov/pubmed/21069395
http://dx.doi.org/10.1007/s00705-010-0848-0
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author Wang, Meng
Zhang, Jie
Zhou, Jian-hua
Chen, Hao-tai
Ma, Li-na
Ding, Yao-zhong
Liu, Wen-qian
Liu, Yong-sheng
author_facet Wang, Meng
Zhang, Jie
Zhou, Jian-hua
Chen, Hao-tai
Ma, Li-na
Ding, Yao-zhong
Liu, Wen-qian
Liu, Yong-sheng
author_sort Wang, Meng
collection PubMed
description Bovine viral diarrhea virus (BVDV) is a widespread virus in beef and dairy herds. BVDV has been grouped into two genotypes, genotype 1 and genotype 2. In this study, the relative synonymous codon usage (RSCU) values, effective number of codon (ENC) values and nucleotide content were investigated, and a comparative analysis of codon usage patterns for open reading frames (ORFs) of 22 BVDV genomes, including 14 of genotype 1 and 8 of genotype 2, was carried out. A high A+U content and low codon bias were found in BVDV genomes. Depending on the RSCU data, it was found that there was a significant variation in bias of codon usage between the two genotypes, and a geographic factor exists only in genotype-1 of BVDV. The RSCU data have a negative correlation with general average hydrophobicity (GRAVY), aromaticity and nucleotide content. Furthermore, the overall abundance of C and U has no effect on the synonymous codon usage patterns. In contrast, the A and G content showed a significant correlation with the nucleotide content at the third position. In addition, the codon usage patterns of BVDV are similar to those of 22 conserved genes of Bos taurus. Taken together, the genetic characteristics of BVDV possibly result from interactions between natural seclection and mutation pressure. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00705-010-0848-0) contains supplementary material, which is available to authorized users.
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spelling pubmed-70873062020-03-23 Analysis of codon usage in bovine viral diarrhea virus Wang, Meng Zhang, Jie Zhou, Jian-hua Chen, Hao-tai Ma, Li-na Ding, Yao-zhong Liu, Wen-qian Liu, Yong-sheng Arch Virol Rapid Communication Bovine viral diarrhea virus (BVDV) is a widespread virus in beef and dairy herds. BVDV has been grouped into two genotypes, genotype 1 and genotype 2. In this study, the relative synonymous codon usage (RSCU) values, effective number of codon (ENC) values and nucleotide content were investigated, and a comparative analysis of codon usage patterns for open reading frames (ORFs) of 22 BVDV genomes, including 14 of genotype 1 and 8 of genotype 2, was carried out. A high A+U content and low codon bias were found in BVDV genomes. Depending on the RSCU data, it was found that there was a significant variation in bias of codon usage between the two genotypes, and a geographic factor exists only in genotype-1 of BVDV. The RSCU data have a negative correlation with general average hydrophobicity (GRAVY), aromaticity and nucleotide content. Furthermore, the overall abundance of C and U has no effect on the synonymous codon usage patterns. In contrast, the A and G content showed a significant correlation with the nucleotide content at the third position. In addition, the codon usage patterns of BVDV are similar to those of 22 conserved genes of Bos taurus. Taken together, the genetic characteristics of BVDV possibly result from interactions between natural seclection and mutation pressure. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00705-010-0848-0) contains supplementary material, which is available to authorized users. Springer Vienna 2010-11-11 2011 /pmc/articles/PMC7087306/ /pubmed/21069395 http://dx.doi.org/10.1007/s00705-010-0848-0 Text en © Springer-Verlag 2010 This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.
spellingShingle Rapid Communication
Wang, Meng
Zhang, Jie
Zhou, Jian-hua
Chen, Hao-tai
Ma, Li-na
Ding, Yao-zhong
Liu, Wen-qian
Liu, Yong-sheng
Analysis of codon usage in bovine viral diarrhea virus
title Analysis of codon usage in bovine viral diarrhea virus
title_full Analysis of codon usage in bovine viral diarrhea virus
title_fullStr Analysis of codon usage in bovine viral diarrhea virus
title_full_unstemmed Analysis of codon usage in bovine viral diarrhea virus
title_short Analysis of codon usage in bovine viral diarrhea virus
title_sort analysis of codon usage in bovine viral diarrhea virus
topic Rapid Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087306/
https://www.ncbi.nlm.nih.gov/pubmed/21069395
http://dx.doi.org/10.1007/s00705-010-0848-0
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