Analysis of codon usage in bovine viral diarrhea virus - PubMed (original) (raw)

Analysis of codon usage in bovine viral diarrhea virus

Meng Wang et al. Arch Virol. 2011 Jan.

Abstract

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 selection and mutation pressure.

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Figures

Fig. 1

The relationship between the effective number of codons (ENC) and the GC content of the third codon position (GC3)

Fig. 2

A plot of average proportions of codons of BVDV within its synonymous family (excluding strain no. 14, which was isolated from swine) and Bos taurus (excluding the codons for Trp, Met and the three termination codons)

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Analysis of codon usage in bovine viral diarrhea virus - PubMed (original) (raw)