Serving the Society Since 1986
Advanced Search
Volume 32 Issue 2
April 2017
    Citation: Guo-Hua Huang, Dian-Hai Hou, Manli Wang, Xiao-Wen Cheng, Zhihong Hu. Genome analysis of Heliothis virescens ascovirus 3h isolated from China .VIROLOGICA SINICA, 2017, 32(2) : 147-154.  http://dx.doi.org/10.1007/s12250-016-3929-8
    shu

    Genome analysis of Heliothis virescens ascovirus 3h isolated from China

    Genome analysis of HvAV-3h

    cstr: 32224.14.s12250-016-3929-8
    • 1.

      State Key Laboratory of Virology, Microorganisms & Viruses Culture Collection Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China

    • 2.

      Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Institute of Virology, Hunan Agricultural University, Changsha, Hunan 410128, China

    • 3.

      Department of Microbiology, 32 Pearson Hall, Miami University, Oxford, Ohio 45056, USA

    • Corresponding author: Zhihong Hu, huzh@wh.iov.cn, ORCID: 0000-0002-1560-0928
    • Received Date: 08 December 2016
      Accepted Date: 15 February 2017
      Published Date: 30 March 2017
      Available online: 01 April 2017
    • 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.
    • 加载中
    • 10.1007s12250-016-3929-8.pdf

      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.
          doi: 10.1093/nar/25.17.3389

      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.
          doi: 10.1099/jgv.0.000677

      3. Asgari S, Davis J, Wood D, Wilson P, McGrath A. 2007. Sequence and organization of the Heliothisvirescens ascovirus genome. J Gen Virol. 88: 1120–1132.
          doi: 10.1099/vir.0.82651-0

      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, double-stranded DNA insect virus that manipulates apoptosis for viral reproduction. J Virol. 80: 11791–11805.
          doi: 10.1128/JVI.01639-06

      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.

      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.
          doi: 10.1371/journal.pone.0006397

      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.
          doi: 10.1099/0022-1317-81-12-3073

      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.
          doi: 10.1186/1752-0509-7-87

      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.
          doi: 10.1099/0022-1317-71-8-1661

      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.
          doi: 10.1006/jipa.1998.4763

      11. Huang GH, Garretson TA, Cheng XH, Holztrager MS, Li SJ, Wang X, Cheng XW. 2012a. Phylogenetic position and replication kinetics of Heliothisvirescens ascovirus 3h (HvAV-3h) isolated from Spodoptera exigua. PLoS ONE.7: e40225.
          doi: 10.1371/journal.pone.0040225

      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.
          doi: 10.1128/JVI.02342-12

      13. Jacob T, Broeke CVD, Favoreel HW. 2011.Viral Serine/Threonine Protein Kinases. J Virol. 85: 1158–1173.
          doi: 10.1128/JVI.01369-10

      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.
          doi: 10.1093/bioinformatics/btm404

      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.
          doi: 10.1038/srep21296

      16. Lindahl T. 1982. DNA repair enzymes. Annu Rev Biochem. 51: 61–87.
          doi: 10.1146/annurev.bi.51.070182.000425

      17. Long CM, Rohrmann GF, Merrill GF. 2009. The conserved baculovirus protein p33 (Ac92) is a flavin adenine dinucleotide-linked sulfhydryl oxidase. Virology. 388: 231–235.
          doi: 10.1016/j.virol.2009.04.006

      18. Parsons J. 1995. Miropeats: graphical DNA sequence comparisons. Comput Appl Biosci. 11: 615–619.

      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.
          doi: 10.1016/j.ympev.2014.12.013

      20. Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 19: 1572–1574.
          doi: 10.1093/bioinformatics/btg180

      21. Silvestro D, Michalak I. 2012. Raxml GUI: a graphical front-end for RAxML. Org Divers Evol. 12: 335–337.
          doi: 10.1007/s13127-011-0056-0

      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.
          doi: 10.1093/molbev/mst197

      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.
          doi: 10.1007/s00284-012-0236-y

      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.
          doi: 10.1016/j.virol.2006.06.029

      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.
          doi: 10.1016/j.jip.2014.08.003

      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.
          doi: 10.1128/JVI.06252-11

      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.
          doi: 10.1128/JVI.01598-10

    • 加载中

    Figures(4) / Tables(5)

    PDF

    Article Metrics

    Article views(9147) PDF downloads(27) Cited by()

    Related
    Proportional views

      Genome analysis of Heliothis virescens ascovirus 3h isolated from China

        Corresponding author: Zhihong Hu, huzh@wh.iov.cn
      • 1. State Key Laboratory of Virology, Microorganisms & Viruses Culture Collection Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
      • 2. Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Institute of Virology, Hunan Agricultural University, Changsha, Hunan 410128, China
      • 3. Department of Microbiology, 32 Pearson Hall, Miami University, Oxford, Ohio 45056, USA
      • Received Date: 08 December 2016
      • Accepted Date: 15 February 2017
      • Published Date: 30 March 2017

      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.

        HTML

        INTRODUCTION