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Genome dynamics in three different geographical isolates of white spot syndrome virus (WSSV)

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Abstract

White spot syndrome virus (WSSV), the sole member of the monotypic family Nimaviridae, is considered an extremely lethal shrimp pathogen. Despite its impact, some essential biological characteristics related to WSSV genome dynamics, such as the synonymous codon usage pattern and selection pressure in genes, remain to be elucidated. The results show that compositional limitations and mutational pressure determine the codon usage bias and base composition in WSSV. Furthermore, different forces of selective pressure are acting across various regions of the WSSV genome. Finally, this study points out the possible occurrence of two major recombination events.

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References

  1. De La Peña LD, Lavilla-Pitogo CR, Villar CBR, Paner MG, Sombito CD, Capulos GC (2007) Prevalence of white spot syndrome virus (WSSV) in wild shrimp Penaeus monodon in the Philippines. Dis Aquat Organ 77:175–179

    Article  PubMed  Google Scholar 

  2. Vlak JM, Bonami JR, Flegel TW, Kou GH, Lightner DV, Lo CF, Loh PC, Walker PW (2004) Nimaviridae. In: VIIIth report of the International Committee on Taxonomy of Viruses. Elsevier, Amsterdam, The Netherlands, pp 187–192

  3. Chou HY, Huang CY, Lo CF, Kou GH (1998) Studies on transmission of white spot syndrome associated baculovirus (WSBV) in Penaeus monodon and P. japonicus via waterborne contact and oral ingestion. Aquaculture 164:263–276

    Article  Google Scholar 

  4. Marks H, van Duijse JJA, Zuidema D, van Hulten MCW, Vlak JM (2005) Fitness and virulence of an ancestral white spot syndrome virus isolate from shrimp. Virus Res 110:9–20

    Article  PubMed  CAS  Google Scholar 

  5. Wang CH, Lo CF, Leu JH, Chou CM, Yeh PY, Chou HY, Tung MC, Chang CF, Su MS, Kou GH (1995) Purification and genomic analysis of baculovirus associated with white spot syndrome (WSBV) of Penaeus monodon. Dis Aquat Org 23:239–242

    Article  Google Scholar 

  6. van Hulten MCW, Witteveldt J, Peters S, Kloosterboer N, Tarchini R, Fiers M, Sandbrink H, Lankhorst RK, Vlak JM (2001) The white spot syndrome virus DNA genome sequence. Virology 286:7–22

    Article  PubMed  Google Scholar 

  7. Yang F, He J, Lin X, Li Q, Pan D, Zhang X, Xu X (2001) Complete genome sequence of the shrimp white spot bacilliform virus. J Virol 75:11811–11820

    Article  PubMed  CAS  Google Scholar 

  8. Sharp PM, Emery LR, Zeng K (2010) Forces that influence the evolution of codon bias. Philos Trans R Soc Lond 365B:1203–1212

    Article  Google Scholar 

  9. Ding J, Doorbar J, Li B, Zhou F, Gu W, Zhao L, Saunders NA, Frazer IH, Zhao KN (2010) Expression of papillomavirus L1 proteins regulated by authentic gene codon usage is favoured in G2/M-like cells in differentiating keratinocytes. Virology 399:46–58

    Article  PubMed  CAS  Google Scholar 

  10. Wong E, Smith D, Rabadan R, Peiris M, Poon L (2010) Codon usage bias and the evolution of influenza A viruses. Codon usage biases of influenza virus. BMC Evol Biol 10:253

    Article  PubMed  Google Scholar 

  11. Harrison RJ, Charlesworth B (2011) Biased gene conversion affects patterns of codon usage and amino acid usage in the Saccharomyces sensu stricto group of yeasts. Mol Biol Evol 28:117–129

    Article  PubMed  CAS  Google Scholar 

  12. Chiari Y, Dion K, Colborn J, Parmakelis A, Powell JR (2010) On the possible role of tRNA base modifications in the evolution of codon usage: queuosine and Drosophila. J Mol Evol 70:339–345

    Article  PubMed  CAS  Google Scholar 

  13. Liu X, Wu C, Chen AYH (2010) Codon usage bias and recombination events for neuraminidase and hemagglutinin genes in Chinese isolates of influenza A virus subtype H9N2. Arch Virol 155:685–693

    Article  PubMed  CAS  Google Scholar 

  14. Froissart R, Roze D, Uzest M, Galibert L, Blanc S, Michalakis Y (2005) Recombination every day: abundant recombination in a virus during a single multi-cellular host infection. PLoS Biol 3:e89

    Article  PubMed  Google Scholar 

  15. Martin DP, Van Der Walt E, Posada D, Rybicki EP (2005) The evolutionary value of recombination is constrained by genome modularity. PLoS Genet 1:e51

    Article  PubMed  Google Scholar 

  16. Domingo E (2010) Mechanisms of viral emergence. Vet Res 41:38

    Article  PubMed  Google Scholar 

  17. Worobey M, Holmes EC (1999) Evolutionary aspects of recombination in RNA viruses. J Gen Virol 80:2535–2543

    PubMed  CAS  Google Scholar 

  18. Lin YCJ, Evans DH (2010) Vaccinia virus particles mix inefficiently, and in a way that would restrict viral recombination, in coinfected cells. J Virol 84:2432–2443

    Article  PubMed  CAS  Google Scholar 

  19. Lefeuvre P, Lett JM, Varsani A, Martin DP (2009) Widely conserved recombination patterns among single-stranded DNA viruses. J Virol 83:2697–2707

    Article  PubMed  CAS  Google Scholar 

  20. Chen R, Holmes EC (2006) Avian influenza virus exhibits rapid evolutionary dynamics. Mol Biol Evol 23:2336–2341

    Article  PubMed  CAS  Google Scholar 

  21. Wright F (1990) The “effective number of codons” used in a gene. Gene 87:23–29

    Article  PubMed  CAS  Google Scholar 

  22. Sablok G, Nayak K, Vazquez F, Tatarinova TV (2011) Synonymous codon usage, GC3 and Evolutionary patterns across plastomes of three pooid model species—Emerging grass genome models for monocots. Mol. Biotechnol 49:116–128

    Article  PubMed  CAS  Google Scholar 

  23. Sharp PM, Li WH (1986) Codon usage in regulatory genes in Escherichia coli does not reflect selection for “rare” codons. Nucleic Acids Res 14:7737–7749

    Article  PubMed  CAS  Google Scholar 

  24. Grocock RJ, Sharp PM (2001) Synonymous codon usage in Cryptosporidium parvum: identification of two distinct trends among genes. Int J Parasitol 31:402–412

    Article  PubMed  CAS  Google Scholar 

  25. Sánchez-Paz A (2010) White spot syndrome virus: an overview on an emergent concern. Vet Res 41:43

    Article  PubMed  Google Scholar 

  26. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    Article  PubMed  CAS  Google Scholar 

  27. Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P (2010) RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26:2462

    Article  PubMed  CAS  Google Scholar 

  28. Sharp PM, Li WH (1987) The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15:1281–1295

    Article  PubMed  CAS  Google Scholar 

  29. Aragonès L, Guix S, Ribes E, Bosch A, Pintó RM (2010) Fine-tuning translation kinetics selection as the driving force of codon usage bias in the hepatitis A virus capsid. PLoS pathog 6:e1000797

    Article  PubMed  Google Scholar 

  30. Irwin B, Heck JD, Hatfield G (1995) Codon pair utilization biases influence translational elongation step times. J Biol Chem 270:22801–22806

    Article  PubMed  CAS  Google Scholar 

  31. Mueller S, Papamichail D, Coleman JR, Skiena S, Wimmer E (2006) Reduction of the rate of poliovirus protein synthesis through large-scale codon deoptimization causes attenuation of viral virulence by lowering specific infectivity. J Virol 80:9687–9696

    Article  PubMed  CAS  Google Scholar 

  32. Hughes AL, Westover K, Da Silva J, O’Connor DH, Watkins DI (2001) Simultaneous positive and purifying selection on overlapping reading frames of the tat and vpr genes of simian immunodeficiency virus. J Virol 75:7966–7972

    Article  PubMed  CAS  Google Scholar 

  33. Marks H, Goldbach RW, Vlak JM, Van Hulten MCW (2004) Genetic variation among isolates of white spot syndrome virus. Arch Virol 149:673–697

    Article  PubMed  CAS  Google Scholar 

  34. Tsai MF, Yu HT, Tzeng HF, Leu JH, Chou CM, Huang CJ, Wang CH, Lin JY, Kou GH, Lo CF (2000) Identification and characterization of a shrimp white spot syndrome virus (WSSV) gene that encodes a novel chimeric polypeptide of cellular-type thymidine kinase and thymidylate kinase. Virology 277:100–110

    Article  PubMed  CAS  Google Scholar 

  35. Zwart MP, Dieu BTM, Hemerik L, Vlak JM (2010) Evolutionary trajectory of white spot syndrome virus (WSSV) genome shrinkage during spread in Asia. PLoS One 5:e13400

    Article  PubMed  Google Scholar 

  36. Rokyta D, Badgett MR, Molineux IJ, Bull JJ (2002) Experimental genomic evolution: extensive compensation for loss of DNA ligase activity in a virus. Mol Biol Evol 19:230–238

    Article  PubMed  CAS  Google Scholar 

  37. Gilbertson RL, Sudarshana M, Jiang H, Rojas MR, Lucas WJ (2003) Limitations on geminivirus genome size imposed by plasmodesmata and virus-encoded movement protein: insights into DNA trafficking. Plant Cell 15:2578–2591

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

XMW thanks ShenYang Agricultural University for computational facilities. Part of this work was funded by the Consejo Nacional de Ciencia y Tecnología (CONACyT), México, for grant 102744 (to ASP). Thanks are also due to the supportive staff of the Laboratorio de Sanidad Acuícola (CIBNOR, Hermosillo), particularly to MVZ Fernando Mendoza, Daniel Coronado Molina and to Dr. Adriana Muhlia for careful reading and critical review of this manuscript.

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Authors and Affiliations

  1. Fondazione Edmund Mach, Centro Ricerca ed Innovazione, Via Mach 2, 38010, San Michele all’Adige, TN, Italy

    Gaurav Sablok

  2. Laboratorio de Sanidad Acuícola, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), S.C. (Campus Hermosillo), Calle Hermosa No. 101. Col. Los Angeles, 83106, Hermosillo, Sonora, Méjico

    Arturo Sánchez-Paz

  3. School of Biological Science and Technology, ShenYang Agricultural University, ShenYang, 110866, LiaoNing, People’s Republic of China

    XianMing Wu

  4. Fondazione Edmund Mach, Centro Ricerca ed Innovazione, Via Mach 2, 38010, San Michele all’Adige, TN, Italy

    Jayant Ranjan

  5. Department of Planning and Research, National Museum of Marine Biology and Aquarium, Pingtung 944, Taiwan

    Jimmy Kuo

  6. Universität Greifswald, Institut für Mathematik und Informatik, Walther-Rathenau-Straße 47, 17487, Greifswald, Germany

    Ingo Bulla

Authors
  1. Gaurav Sablok
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  2. Arturo Sánchez-Paz
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  3. XianMing Wu
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  4. Jayant Ranjan
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  5. Jimmy Kuo
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  6. Ingo Bulla
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Corresponding authors

Correspondence to Gaurav Sablok or Arturo Sánchez-Paz.

Additional information

G. Sablok, A. Sánchez-Paz and X. Wu contributed equally to work.

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Sablok, G., Sánchez-Paz, A., Wu, X. et al. Genome dynamics in three different geographical isolates of white spot syndrome virus (WSSV). Arch Virol 157, 2357–2362 (2012). https://doi.org/10.1007/s00705-012-1395-7

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  • DOI: https://doi.org/10.1007/s00705-012-1395-7

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