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. 2017 Jun 17;14(1):115.
doi: 10.1186/s12985-017-0780-y.

Genome-wide analysis of codon usage bias in Bovine Coronavirus

Matías Castells  1 , Matías Victoria  1 , Rodney Colina  1 , Héctor Musto  2 , Juan Cristina  3
Affiliations

Genome-wide analysis of codon usage bias in Bovine Coronavirus

Matías Castells et al. Virol J. .

Abstract

Background: Bovine coronavirus (BCoV) belong to the genus Betacoronavirus of the family Coronaviridae. BCoV are widespread around the world and cause enteric or respiratory infections among cattle, leading to important economic losses to the beef and dairy industry worldwide. To study the relation of codon usage among viruses and their hosts is essential to understand host-pathogen interaction, evasion from host's immune system and evolution.

Methods: We performed a comprehensive analysis of codon usage and composition of BCoV.

Results: The global codon usage among BCoV strains is similar. Significant differences of codon preferences in BCoV genes in relation to codon usage of Bos taurus host genes were found. Most of the highly frequent codons are U-ending. G + C compositional constraint and dinucleotide composition also plays a role in the overall pattern of BCoV codon usage.

Conclusions: The results of these studies revealed that mutational bias is a leading force shaping codon usage in this virus. Additionally, relative dinucleotide frequencies, geographical distribution, and evolutionary processes also influenced the codon usage pattern.

Keywords: Bovine; Codon usage; Coronavirus; Evolution.

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Figures

Fig. 1
Fig. 1
Effective number of codons (ENC) used in BCoV ORFs plotted against the GC3S The orange curve plots the relationship between GC3S and ENC in absence of selection. Blue dots show the results obtained for BCoV strains. Note that the values obtained for ENC and GC3S of all 15 BCoVs enrolled in these studies are very similar (SD of ±0.07 and ±0.0009, respectively) and for that reason they resemble a single dot in the figure
See this image and copyright information in PMC

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