Virologica Sinica

, Volume 32, Issue 2, pp 147–154 | Cite as

Genome analysis of Heliothis virescens ascovirus 3h isolated from China

  • Guo-Hua Huang
  • Dian-Hai Hou
  • Manli Wang
  • Xiao-Wen Cheng
  • Zhihong Hu
Research Article

Abstract

No ascovirus isolated from China has been sequenced so far. Therefore, in this study, we aimed to sequence the genome of Heliothis virescens ascovirus 3h (HvAV-3h) using the 454 pyrosequencing technology. The genome was found to be 190,519-bp long with a G+C content of 45.5%. We also found that it encodes 185 hypothetical open reading frames (ORFs) along with at least 50 amino acids, including 181 ORFs found in other ascoviruses and 4 unique ORFs. Gene-parity plots and phylogenetic analysis revealed a close relationship between HvAV-3h and three other HvAV-3a strains and a distant relationship with Spodoptera frugiperda ascovirus 1a (SfAV-1a), Trichoplusia ni ascovirus 6a (TnAV-6a), and Diadromus pulchellus ascovirus 4a (DpAV-4a). Among the 185 potential genes encoded by the genome, 44 core genes were found in all the sequenced ascoviruses. In addition, 25 genes were found to be conserved in all ascoviruses except DpAV-4a. In the HvAV-3h genome, 24 baculovirus repeat ORFs (bros) were present, and the typical homologous repeat regions (hrs) were absent. This study supplies information important for understanding the conservation and functions of ascovirus genes as well as the variety of ascoviral genomes.

Keywords

Heliothis virescens ascovirus 3h (HvAV-3h) genome organization bro genes phylogenetic relationship 

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Genome analysis of Heliothis virescens ascovirus 3h isolated from China

References

  1. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res, 25: 3389–3402.CrossRefPubMedPubMedCentralGoogle Scholar
  2. Asgari S, Bideshi D, Bigot Y, Federici BA, Cheng XW, ICTV Report Consortium. 2017. ICTV Virus Taxonomy Profile: Ascoviridae. J Gen Virol, 98: 4–5.CrossRefPubMedPubMedCentralGoogle Scholar
  3. Asgari S, Davis J, Wood D, Wilson P, McGrath A. 2007. Sequence and organization of the Heliothis virescens ascovirus genome. J Gen Virol, 88: 1120–1132.CrossRefPubMedGoogle Scholar
  4. Bideshi DK, Demattei MV, Rouleux-Bonnin F, Stasiak K, Tan Y, Bigot S, Bigot Y, Federici BA. 2006. Genomic sequence of Spodoptera frugiperda ascovirus 1a, an enveloped, doublestranded DNA insect virus that manipulates apoptosis for viral reproduction. J Virol, 80: 11791–11805.CrossRefPubMedPubMedCentralGoogle Scholar
  5. Bigot Y, Asgari S, Bideshi DK, Cheng X, Federici BA, Renault S. 2011. Family Ascoviridae. In: Virus Taxonomy: Ninth Report of the International Committee on the Taxonomy of Viruses, third ed. King, AMQ., Adams, MJ, Carstens, EB, Lefkowitz, EJ (Eds.). London: Elsevier Inc. pp. 147–152.Google Scholar
  6. Bigot Y, Renault S, Nicolas J, Moundras C, Demattei MV, Samain S, Bideshi DK, Federici BA. 2009. Symbiotic virus at the evolutionary intersection of three types of large DNA viruses; iridoviruses, ascoviruses, and ichnoviruses. PLoS ONE, 4: e6397.CrossRefPubMedPubMedCentralGoogle Scholar
  7. Bigot Y, Stasiak K, Rouleux-Bonnin F, Federici BA. 2000. Characterization of repetitive DNA regions and methylated DNA in ascovirus genomes. J Gen Virol, 81: 3073–3082.CrossRefPubMedGoogle Scholar
  8. de Castro Oliveira JV, de Brito AF, Braconi CT, de Melo Freire CC, Iamarino A, de Andrade Zanotto PM. 2013. Modularity and evolutionary constraints in a baculovirus gene regulatory network. BMC Syst Biol, 7: 87.CrossRefGoogle Scholar
  9. Federici BA, Vlak JM, Hamm JJ. 1990. Comparative study of virion structure, protein composition and genomic DNA of three ascovirus isolates. J Gen Virol, 71: 1661–1668.CrossRefPubMedGoogle Scholar
  10. Hamm JJ, Styer EL, Federici BA. 1998. Comparison of field-collected ascovirus isolates by DNA hybridization, host range, and histopathology. J Invertebr Pathol, 72: 138–146.CrossRefPubMedGoogle Scholar
  11. Huang GH, Garretson TA, Cheng XH, Holztrager MS, Li SJ, Wang X, Cheng XW. 2012a. Phylogenetic position and replication kinetics of Heliothis virescensascovirus 3h (HvAV-3h) isolated from Spodoptera exigua. PLoS ONE, 7: e40225.CrossRefPubMedPubMedCentralGoogle Scholar
  12. Huang GH, Wang YS, Wang X, Garretson TA, Dai LY, Zhang CX, Cheng XW. 2012b. Genomic sequence of Heliothis virescens ascovirus 3g isolated from Spodoptera exigua. J Virol, 86: 12467–12468.CrossRefPubMedPubMedCentralGoogle Scholar
  13. Jacob T, Broeke CVD, Favoreel HW. 2011. Viral Serine/Threonine Protein Kinases. J Virol, 85: 1158–1173.CrossRefPubMedGoogle Scholar
  14. Larkin M A, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. 2007. Clustal W and Clustal X version 2.0. Bioinformatics, 23: 2947–2948.CrossRefPubMedGoogle Scholar
  15. Li SJ, Hopkins RJ, Zhao YP, Zhang YX, Hu J, Chen XY, Xu Z, Huang GH. 2016. Imperfection works: survival, transmission and persistence in the system of Heliothis virescens ascovirus 3h (HvAV-3h), Microplitis similis and Spodoptera exigua. Sci Rep, 6: 21296.CrossRefPubMedPubMedCentralGoogle Scholar
  16. Lindahl T. 1982. DNA repair enzymes. Annu Rev Biochem, 51: 61–87.CrossRefPubMedGoogle Scholar
  17. Long CM, Rohrmann GF, Merrill GF. 2009. The conserved baculovirus protein p33 (Ac92) is a flavin adenine dinucleotidelinked sulfhydryl oxidase. Virology, 388: 231–235.CrossRefPubMedGoogle Scholar
  18. Parsons J. 1995. Miropeats: graphical DNA sequence comparisons. Comput Appl Biosci, 11: 615–619.PubMedGoogle Scholar
  19. Piégu B, Asgari S, Bideshi D, Federici BA, Bigot Y. 2015. Evolutionary relationships of iridoviruses and divergence of ascoviruses from invertebrate iridoviruses in the superfamily Megavirales. Mol Phylogenet Evol, 84: 44–52.CrossRefPubMedGoogle Scholar
  20. Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19: 1572–1574.CrossRefPubMedGoogle Scholar
  21. Silvestro D, Michalak I. 2012. Raxml GUI: a graphical front-end for RAxML. Org Divers Evol, 12: 335–337.CrossRefGoogle Scholar
  22. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol, 30: 2725–2729.CrossRefPubMedPubMedCentralGoogle Scholar
  23. Tang Q, Li G, Yao Q, Chen L, Feng F, Yuan Y, Chen K. 2013. Bm65 is essential for the propagation of Bombyx mori nucleopolyhedrovirus. Curr Microbiol, 66: 22–29.CrossRefPubMedGoogle Scholar
  24. Wang LH, Xue JL, Seaborn CP, Arif BM, Cheng XW. 2006. Sequence and organization of the Trichoplusiani ascovirus 2c (Ascoviridae) genome. Virology, 354: 167–177.CrossRefPubMedGoogle Scholar
  25. Wei YL, Hu J, Li SJ, Chen ZS, Cheng XW, Huang GH. 2014. Genome sequence and organization analysis of Heliothis virescens ascovirus 3f isolated from a Helicoverpa zea larva. J Invertebr Pathol, 122: 40–43.CrossRefPubMedGoogle Scholar
  26. Wu W, Passarelli AL. 2012. The Autographa californica M nucleopolyhedrovirus ac79 gene encodes an early gene product with structural similarities to UvrC and intron-encoded endonucleases that is required for efficient budded virus production. J Virol, 86: 5614–5625.CrossRefPubMedPubMedCentralGoogle Scholar
  27. Wu W, Passarelli AL. 2010. Autographa californica multiple nucleopolyhedrovirus Ac92 (ORF92, P33) is required for budded virus production and multiply enveloped occlusion-derived virus formation. J Virol, 84: 12351–12361.CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Wuhan Institute of Virology, CAS and Springer Science+Business Media Singapore 2017

Authors and Affiliations

  • Guo-Hua Huang
    • 1
    • 2
  • Dian-Hai Hou
    • 1
  • Manli Wang
    • 1
  • Xiao-Wen Cheng
    • 3
  • Zhihong Hu
    • 1
  1. 1.State Key Laboratory of Virology, Microorganisms & Viruses Culture Collection Center, Wuhan Institute of VirologyChinese Academy of SciencesWuhan, HubeiChina
  2. 2.Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Institute of VirologyHunan Agricultural UniversityChangsha, HunanChina
  3. 3.Department of Microbiology, 32 Pearson HallMiami UniversityOxfordUSA

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