Virus Genes

, Volume 46, Issue 2, pp 271–279

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

  • Jian-hua Zhou
  • Zong-liang Gao
  • Dong-jie Sun
  • Yao-zhong Ding
  • Jie Zhang
  • Laszlo Stipkovits
  • Susan Szathmary
  • Zygmunt Pejsak
  • Yong-sheng Liu
Article

DOI: 10.1007/s11262-012-0847-1

Cite this article as:
Zhou, J., Gao, Z., Sun, D. et al. Virus Genes (2013) 46: 271. doi:10.1007/s11262-012-0847-1

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.

Keywords

African swine fever virusSynonymous codon usageMutation pressureTranslation selectionTranslational initiation region

Supplementary material

11262_2012_847_MOESM1_ESM.doc (84 kb)
Supplementary material 1 (DOC 84 kb)
11262_2012_847_MOESM2_ESM.tif (33 kb)
Fig. S1The 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)
11262_2012_847_MOESM3_ESM.tif (33 kb)
Fig. S2The 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)
11262_2012_847_MOESM4_ESM.tif (34 kb)
Fig. S3The 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)
11262_2012_847_MOESM5_ESM.tif (32 kb)
Fig. S4The 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)
11262_2012_847_MOESM6_ESM.tif (33 kb)
Fig. S5The 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)
11262_2012_847_MOESM7_ESM.tif (31 kb)
Fig. S6The 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)
11262_2012_847_MOESM8_ESM.tif (33 kb)
Fig. S7The 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)
11262_2012_847_MOESM9_ESM.tif (32 kb)
Fig. S8The 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)
11262_2012_847_MOESM10_ESM.tif (33 kb)
Fig. S9The 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)
11262_2012_847_MOESM11_ESM.tif (31 kb)
Fig. S10The 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)
11262_2012_847_MOESM12_ESM.tif (31 kb)
Fig. S11The 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)

Copyright information

© Springer Science+Business Media New York 2012

Authors and Affiliations

  • Jian-hua Zhou
    • 1
  • Zong-liang Gao
    • 1
  • Dong-jie Sun
    • 1
  • Yao-zhong Ding
    • 1
  • Jie Zhang
    • 1
  • Laszlo Stipkovits
    • 2
  • Susan Szathmary
    • 2
  • Zygmunt Pejsak
    • 3
  • Yong-sheng Liu
    • 1
  1. 1.State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference LaboratoryLanzhou Veterinary Research Institute, Chinese Academy of Agricultural SciencesLanzhouPeople’s Republic of China
  2. 2.RT-Europe CenterBudapestHungary
  3. 3.Department of Swine DiseasesNational Veterinary Research InstitutePuławyPoland