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Selective pressure dominates the synonymous codon usage in parvoviridae

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Abstract

Parvoviridae is a family of small non-enveloped viruses and divided into two subfamilies. The family members infect a wide range of organisms from insects to humans and some of the members (e.g., nonpathogenic adeno-associated viruses) are effective gene therapy delivery vectors. We detailed the synonymous codon usage pattern of Parvoviridae family from the available 58 sequenced genomes through multivariate statistical methods. Our results revealed that nine viruses showed some degree of strong codon bias, and the others possessed a general weak trend of codon bias. ENc-plot and neutrality plot results showed that selective pressure dominated over mutation in shapes coding sequence’s composition. The overall GC content and GC content at the third synonymous codon position were the principal determinants behind the variations within the codon usage patterns, as they both significantly correlated with the first axis of correspondence analysis. In addition, gene length had no direct influence on the codon usage pattern. Densovirinae subfamily and Parvovirinae subfamily possessed nine identical preferred codons, though most of the two subfamilies codon usage frequencies were significantly different. The result of cluster analysis based on synonymous codon usage was discordant with that of taxonomic classification. Adeno-associated viruses formed a separated clade far from other Parvoviridae members in the dendrogram. Thus, we concluded that natural selection rather than mutation pressure accounts for the main factor that affects the codon bias in Parvoviridae family.

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Acknowledgments

We would like to thank the anonymous reviewers for their kind and constructive comments. This research was supported in part by the National Modern Agricultural Industrial Technology System of China (No. CARS-22), and the Postdoctoral Daily Fund of Shenyang Agricultural University.

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Authors and Affiliations

  1. Postdoctoral Station of Plant Protection, Shenyang Agricultural University, No.120 Dongling Road, Shenyang, 110866, P.R.China

    Sheng-Lin Shi & Li Qin

  2. Insect Resource Engineering Research Center of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, China

    Sheng-Lin Shi, Yi-Ren Jiang, Yan-Qun Liu, Run-Xi Xia & Li Qin

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  1. Sheng-Lin Shi
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Correspondence to Li Qin.

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Shi, SL., Jiang, YR., Liu, YQ. et al. Selective pressure dominates the synonymous codon usage in parvoviridae . Virus Genes 46, 10–19 (2013). https://doi.org/10.1007/s11262-012-0818-6

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