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A comparative analysis on the synonymous codon usage pattern in viral functional genes and their translational initiation region of ASFV

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Abstract

The synonymous codon usage pattern of African swine fever virus (ASFV), the similarity degree of the synonymous codon usage between this virus and some organisms and the synonymous codon usage bias for the translation initiation region of viral functional genes in the whole genome of ASFV have been investigated by some simply statistical analyses. Although both GC12% (the GC content at the first and second codon positions) and GC3% (the GC content at the third codon position) of viral functional genes have a large fluctuation, the significant correlations between GC12 and GC3% and between GC3% and the first principal axis of principle component analysis on the relative synonymous codon usage of the viral functional genes imply that mutation pressure of ASFV plays an important role in the synonymous codon usage pattern. Turning to the synonymous codon usage of this virus, the codons with U/A end predominate in the synonymous codon family for the same amino acid and a weak codon usage bias in both leading and lagging strands suggests that strand compositional asymmetry does not take part in the formation of codon usage in ASFV. The interaction between the absolute codon usage bias and GC3% suggests that other selections take part in the formation of codon usage, except for the mutation pressure. It is noted that the similarity degree of codon usage between ASFV and soft tick is higher than that between the virus and the pig, suggesting that the soft tick plays a more important role than the pig in the codon usage pattern of ASFV. The translational initiation region of the viral functional genes generally have a strong tendency to select some synonymous codons with low GC content, suggesting that the synonymous codon usage bias caused by translation selection from the host takes part in modulating the translation initiation efficiency of ASFV functional genes.

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Acknowledgments

This study was supported in parts by grants International Science & Technology Cooperation Program of China (No. 2010DFA32640 and No. 2012DFG31890) and Gansu Provincial Funds for Distinguished Young Scientists. This study was also supported by the National Natural Science foundation of China (No. 31172335 and No. 31072143).

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Authors and Affiliations

  1. State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, People’s Republic of China

    Jian-hua Zhou, Zong-liang Gao, Dong-jie Sun, Yao-zhong Ding, Jie Zhang & Yong-sheng Liu

  2. RT-Europe Center, Budapest, Hungary

    Laszlo Stipkovits & Susan Szathmary

  3. Department of Swine Diseases, National Veterinary Research Institute, 57 Partyzantow, 24-100, Puławy, Poland

    Zygmunt Pejsak

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  1. Jian-hua Zhou
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Correspondence to Zygmunt Pejsak or Yong-sheng Liu.

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Supplementary material 1 (DOC 84 kb)

Fig. S1

The usage bias of synonymous codons for Ala in different length (the first 5 codons, the first 10 codons, the first 15 codons, the first 20 codons, the first 25 codons, and the first 30 codons) of the translation initiation region (the first 30 codons) in the functional genes of ASFV genome (TIFF 32 kb)

Fig. S2

The preference of synonymous codons for Asp, Glu, and Cys in different length (the first 5 codons, the first 10 codons, the first 15 codons, the first 20 codons, the first 25 codons, and the first 30 codons) of the translation initiation region (the first 30 codons) in the functional genes of ASFV genome (TIFF 33 kb)

Fig. S3

The preference of synonymous codons for Phe, Tyr, and His in different length (the first 5 codons, the first 10 codons, the first 15 codons, the first 20 codons, the first 25 codons, and the first 30 codons) of the translation initiation region (the first 30 codons) in the functional genes of ASFV genome (TIFF 33 kb)

Fig. S4

The preference of synonymous codons for Gly in different length (the first 5 codons, the first 10 codons, the first 15 codons, the first 20 codons, the first 25 codons, and the first 30 codons) of the translation initiation region (the first 30 codons) in the functional genes of ASFV genome (TIFF 31 kb)

Fig. S5

The preference of synonymous codons for Leu in different length (the first 5 codons, the first 10 codons, the first 15 codons, the first 20 codons, the first 25 codons, and the first 30 codons) of the translation initiation region (the first 30 codons) in the functional genes of ASFV genome (TIFF 33 kb)

Fig. S6

The preference of synonymous codons for Pro in different length (the first 5 codons, the first 10 codons, the first 15 codons, the first 20 codons, the first 25 codons, and the first 30 codons) of the translation initiation region (the first 30 codons) in the functional genes of ASFV genome (TIFF 31 kb)

Fig. S7

The preference of synonymous codons for Gln, Asn, and Lys in different length (the first 5 codons, the first 10 codons, the first 15 codons, the first 20 codons, the first 25 codons, and the first 30 codons) of the translation initiation region (the first 30 codons) in the functional genes of ASFV genome (TIFF 32 kb)

Fig. S8

The preference of synonymous codons for Arg in different length (the first 5 codons, the first 10 codons, the first 15 codons, the first 20 codons, the first 25 codons, and the first 30 codons) of the translation initiation region (the first 30 codons) in the functional genes of ASFV genome (TIFF 32 kb)

Fig. S9

The preference of synonymous codons for Ser in different length (the first 5 codons, the first 10 codons, the first 15 codons, the first 20 codons, the first 25 codons, and the first 30 codons) of the translation initiation region (the first 30 codons) in the functional genes of ASFV genome (TIFF 33 kb)

Fig. S10

The preference of synonymous codons for Thr in different length (the first 5 codons, the first 10 codons, the first 15 codons, the first 20 codons, the first 25 codons, and the first 30 codons) of the translation initiation region (the first 30 codons) in the functional genes of ASFV genome (TIFF 30 kb)

Fig. S11

The preference of synonymous codons for Val in different length (the first 5 codons, the first 10 codons, the first 15 codons, the first 20 codons, the first 25 codons, and the first 30 codons) of the translation initiation region (the first 30 codons) in the functional genes of ASFV genome (TIFF 31 kb)

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Zhou, Jh., Gao, Zl., Sun, Dj. et al. A comparative analysis on the synonymous codon usage pattern in viral functional genes and their translational initiation region of ASFV. Virus Genes 46, 271–279 (2013). https://doi.org/10.1007/s11262-012-0847-1

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