First analysis of synonymous codon usage in porcine circovirus

Archives of Virology

Volumn 159, Issue 8, 2014, Pages 2145-2151

  Chen, Ye ^a   Sun, Jingchen ^a   Tong, Xiong ^a   Xu, Jian ^a   Deng, Hongjuan ^a   Jiang, Zhiguo ^a   Jiang, Chengfeng ^a   Duan, Junli ^a   Li, Jingcong ^a   Zhou, Pei ^a   Wang, Chong ^a  

^a SOUTH CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CIRCOVIRUS; PORCINE CIRCOVIRUS; SUIDAE;

CODON;

ANIMAL; CIRCOVIRIDAE INFECTION; CIRCOVIRUS; CLASSIFICATION; CODON; GENETICS; ISOLATION AND PURIFICATION; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MUTATION; NUCLEOTIDE SEQUENCE; SWINE; SWINE DISEASE; VETERINARY; VIROLOGY; VIRUS GENOME;

ANIMALS; BASE SEQUENCE; CIRCOVIRIDAE INFECTIONS; CIRCOVIRUS; CODON; EVOLUTION, MOLECULAR; GENOME, VIRAL; MOLECULAR SEQUENCE DATA; MUTATION; SWINE; SWINE DISEASES;

EID: 84905215407     PISSN: 03048608     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00705-014-2015-5     Document Type: Article

References (23)

1. Allan G, Krakowka S, Ellis J, Charreyre C (2012) Discovery and evolving history of two genetically related but phenotypically different viruses, porcine circoviruses 1 and 2. Virus Res 164: 4-9.
2. Cortey M, Segalés J (2012) Low levels of diversity among genomes of Porcine circovirus type 1 (PCV1) points to differential adaptive selection between Porcine circoviruses. Virology 422: 161-164.
3. Meng XJ (2013) Porcine Circovirus Type 2 (PCV2): Pathogenesis and interaction with the immune system. Annu Rev Anim Biosci 1: 43-64.
4. Olvera A, Cortey M, Segales J (2007) Molecular evolution of porcine circovirus type 2 genomes: phylogeny and clonality. Virology 357: 175-185.
5. Lyoo K, Joo H, Caldwell B, Kim H, Davies PR, Torrison J (2011) Comparative efficacy of three commercial PCV2 vaccines in conventionally reared pigs. Vet J 189: 58-62.
6. Seo HW, Han K, Oh Y, Kang I, Park C, Chae C (2013) Comparison of three commercial one-dose porcine circovirus type 2 (PCV2) vaccines on PCV2 shedding in semen from experimentally infected boars. Vet Microbiol 164: 145-149.
7. van Wezel AL, van Steenis G, van der Marel P, Osterhaus AD (1984) Inactivated poliovirus vaccine: current production methods and new developments. Rev Infect Dis 6(Suppl 2): S335-S340.
8. Shen HG, Zhou JY, Huang ZY, Guo JQ, Xing G, He JL, Yan Y, Gong LY (2008) Protective immunity against porcine circovirus 2 by vaccination with ORF2-based DNA and subunit vaccines in mice. J Gen Virol 89: 1857-1865.
9. Martelli P, Ferrari L, Morganti M, De Angelis E, Bonilauri P, Guazzetti S, Caleffi A, Borghetti P (2011) One dose of a porcine circovirus 2 subunit vaccine induces humoral and cell-mediated immunity and protects against porcine circovirus-associated disease under field conditions. Vet Microbiol 149: 339-351.
10. Chen Y (2013) A comparison of synonymous codon usage bias patterns in DNA and RNA virus genomes: quantifying the relative importance of mutational pressure and natural selection. BioMed Res Int 2013: 10.
11. Cutler RW, Chantawannakul P (2008) Synonymous codon usage bias dependent on local nucleotide context in the class Deinococci. J Mol Evol 67: 301-314.
12. Liu YS, Zhou JH, Chen HT, Ma LN, Pejsak Z, Ding YZ, Zhang J (2011) The characteristics of the synonymous codon usage in enterovirus 71 virus and the effects of host on the virus in codon usage pattern. Infect Genet Evol 11: 1168-1173.
13. Shi SL, Jiang YR, Liu YQ, Xia RX, Qin L (2013) Selective pressure dominates the synonymous codon usage in parvoviridae. Virus Genes 46: 10-19.
14. Zhou JH, Zhang J, Chen HT, Ma LN, Liu YS (2010) Analysis of synonymous codon usage in foot-and-mouth disease virus. Vet Res Commun 34: 393-404.
15. Hu Y, Zhou H, Yu Z, Chen H, Jin M (2009) Characterization of the genes encoding complete US10, SORF3, and US2 proteins from duck enteritis virus. Virus Genes 38: 295-301.
16. Fuglsang A (2003) The effective number of codons for individual amino acids: some codons are more optimal than others. Gene 320: 185-190.
17. Fu M (2010) Codon usage bias in herpesvirus. Arch Virol 155: 391-396.
18. Gupta S, Ghosh T (2001) Gene expressivity is the main factor in dictating the codon usage variation among the genes in Pseudomonas aeruginosa. Gene 273: 63-70.
19. Tao P, Dai L, Luo M, Tang F, Tien P, Pan Z (2009) Analysis of synonymous codon usage in classical swine fever virus. Virus Genes 38: 104-112.
20. Zhou T, Gu W, Ma J, Sun X, Lu Z (2005) Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses. Biosystems 81: 77-86.
21. Haegeman B, Weitz JS (2012) A neutral theory of genome evolution and the frequency distribution of genes. BMC Genomics 13: 196.
22. Steiner UK, Tuljapurkar S (2012) Neutral theory for life histories and individual variability in fitness components. Proc Natl Acad Sci 109: 4684-4689.
23. Subramanian S (2008) Nearly neutrality and the evolution of codon usage bias in eukaryotic genomes. Genetics 178: 2429-2432.