Virologica Sinica

, Volume 30, Issue 6, pp 417–424 | Cite as

Genome sequencing and analysis of a granulovirus isolated from the Asiatic rice leafroller, Cnaphalocrocis medinalis

  • Shan Zhang
  • Zheng Zhu
  • Shifeng Sun
  • Qijin Chen
  • Fei DengEmail author
  • Kai YangEmail author
Research Article


The complete genome of Cnaphalocrocis medinalis granulovirus (CnmeGV) from a serious migratory rice pest, Cnaphalocrocis medinalis (Lepidoptera: Pyralidae), was sequenced using the Roche 454 Genome Sequencer FLX system (GS FLX) with shotgun strategy and assembled by Roche GS De Novo assembler software. Its circular double-stranded genome is 111,246 bp in size with a high A+T content of 64.8% and codes for 118 putative open reading frames (ORFs). It contains 37 conserved baculovirus core ORFs, 13 unique ORFs, 26 ORFs that were found in all Lepidoptera baculoviruses and 42 common ORFs. The analysis of nucleotide sequence repeats revealed that the CnmeGV genome differs from the rest of sequenced GVs by a 23 kb and a 17kb gene block inversions, and does not contain any typical homologous region (hr) except for a region of non-hr-like sequence. Chitinase and cathepsin genes, which are reported to have major roles in the liquefaction of the hosts, were not found in the CnmeGV genome, which explains why CnmeGV infected insects do not show the phenotype of typical liquefaction. Phylogenetic analysis, based on the 37 core baculovirus genes, indicates that CnmeGV is closely related to Adoxophyes orana granulovirus. The genome analysis would contribute to the functional research of CnmeGV, and would benefit to the utilization of CnmeGV as pest control reagent for rice production.


baculovirus granulovirus Cnaphalocrocis medinalis granulovirus (CnmeGV) genome sequencing 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Supplementary material

12250_2015_3658_MOESM1_ESM.pdf (265 kb)
Supplementary material, approximately 265 KB.


  1. Chai HN, Du YZ, Qiu BL, Zhai BP. 2011. Detection and phylogenetic analysis of Wolbachia in the Asiatic rice leafroller, Cnaphalocrocis medinalis, in Chinese populations. J Insect Sci, 11: 123.PubMedPubMedCentralCrossRefGoogle Scholar
  2. Choi J, Guarino LA. 1995. The baculovirus transactivator IE1 binds to viral enhancer elements in the absence of insect cell factors. J Virol, 69: 4548–4551.PubMedPubMedCentralGoogle Scholar
  3. Conant GC, Wolfe KH. 2008. GenomeVx: simple web-based creation of editable circular chromosome maps. Bioinformatics, 24: 861–862.PubMedCrossRefGoogle Scholar
  4. Federici BA. 1997. Baculovirus Pathogenesis. In: The Baculoviruses. Miller LK (ed.) PLENUM PRESS, pp. 33–59.CrossRefGoogle Scholar
  5. Ferrelli ML, Berretta MF, Belaich MN, Ghiringhelli PD, Sciocco CA. 2012. The baculoviral genome, viral genomes-molecular structure, diversity, gene expression mechanisms and host-virus interactions.Google Scholar
  6. Ferrelli ML, Salvador R, Biedma ME, Berretta MF, Haase S, Sciocco-Cap A, Ghiringhelli PD, Romanowski V. 2012. Genome of Epinotia aporema granulovirus (EpapGV), a polyorganotropic fast killing betabaculovirus with a novel thymidylate kinase gene. BMC Genomics, 13: 548.PubMedPubMedCentralCrossRefGoogle Scholar
  7. Guarino LA, Gonzalez MA, Summers MD. 1986. Complete Sequence and Enhancer Function of the Homologous DNA Regions of Autographa californica Nuclear Polyhedrosis Virus. J Virol, 60: 224–229.PubMedPubMedCentralGoogle Scholar
  8. Hawtin RE, Zarkowska T, Arnold K, Thomas CJ, Gooday GW, King LA, Kuzio JA, Possee RD. 1997. Liquefaction of Autographa californica nucleopolyhedrovirus-infected insects is dependent on the integrity of virus-encoded chitinase and cathepsin genes. Virology, 238: 243–253.PubMedCrossRefGoogle Scholar
  9. Herniou EA, Olszewski JA, Cory JS, O'Reilly DR. 2003. The genome sequence and evolution of baculoviruses. Annu Rev Entomol, 48: 211–234.PubMedCrossRefGoogle Scholar
  10. Hilton S, Winstanley D. 2008. The origins of replication of granuloviruses. Arch Virol, 153: 1527–1535.PubMedCrossRefGoogle Scholar
  11. Hu ZH, Arif BM, Jin F, Martens JW, Chen XW, Sun JS, Zuidema D, Goldbach RW, Vlak JM. 1998. Distinct gene arrangement in the Buzura suppressaria single-nucleocapsid nucleopolyhedrovirus genome. J Gen Virol, 79: 2841–2851.PubMedCrossRefGoogle Scholar
  12. Jehle JA, Blissard GW, Bonning BC, Cory JS, Herniou EA, Rohrmann GF, Theilmann DA, Thiem SM, Vlak JM. 2006. On the classification and nomenclature of baculoviruses: a proposal for revision. Arch Virol, 151: 1257–1266.PubMedCrossRefGoogle Scholar
  13. Jones DT, Taylor WR, Thornton JM. 1992. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci, 8: 275–282.PubMedGoogle Scholar
  14. Kool M, Voeten JT, Goldbach RW, Tramper J, Vlak JM. 1993. Identification of seven putative origins of Autographa californica multiple nucleocapsid nuclear polyhedrosis virus DNA replication. J Gen Virol, 74: 2661–2668.PubMedCrossRefGoogle Scholar
  15. Lange M, Jehle JA. 2003. The genome of the Cryptophlebia leucotreta granulovirus. Virology, 317: 220–236.PubMedCrossRefGoogle Scholar
  16. Liu D, Li Y, Zhao J, Deng F, Duan X, Kou C, Wu T, Li Y, Wang Y, Ma J, Yang J, Hu Z, Zhang F, Zhang Y, Sun S. 2014. Fine epitope mapping of the central immunodominant region of nucleoprotein from Crimean-Congo hemorrhagic fever virus (CCHFV). PLoS One, 9: e108419.PubMedPubMedCentralCrossRefGoogle Scholar
  17. Lu A, Krell PJ, Vlak JM, Rohrmann GF. 1997. Baculovirus DNA replication. In: The Baculoviruses, Miller LK (ed.). New York: Plenum press, pp. 171–192.CrossRefGoogle Scholar
  18. Lu A, Miller LK. 1997. Regulation of baculovirus late and very late gene expression. In: The Baculoviruses, Miller LK (ed.). New York: Plenum press, pp. 193–216.CrossRefGoogle Scholar
  19. Luque T, Finch R, Crook N, O'Reilly DR, Winstanley D. 2001. The complete sequence of the Cydia pomonella granulovirus genome. J Gen Virol, 82: 2531–2547.PubMedCrossRefGoogle Scholar
  20. O'Reilly DR. 1997. Auxiliary genes of baculoviruses. In: The Baculoviruses, Miller LK (ed.). New York: Plenum press, pp. 276–300.Google Scholar
  21. O'Reilly DR, Miller LK, Luckow VA. 1992. Baculovirus Expression Vector: A Laboratory Manual. New York: W. H. Freeman & Company, pp. 368.Google Scholar
  22. Pang Y, Lai Y, Liu J. 1981. A new granulovirus from naturally infected Asiatic rice leafroller, Cnaphalocrocis medinalis (Guenee). Microbiology China, 02: 103–104.Google Scholar
  23. Rodems SM, Friesen PD. 1995. Transcriptional enhancer activity of hr5 requires dual-palindrome half sites that mediate binding of a dimeric form of the baculovirus transregulator IE1. J Virol, 69: 5368–5375.PubMedPubMedCentralGoogle Scholar
  24. Rohrmann GF. 2013. In: Baculovirus Molecular Biology, Third Edition. Available: 24479205.Google Scholar
  25. Sanderson MJ, Wojciechowski MF. 2000. Improved bootstrap confidence limits in large-scale phylogenies, with an example from Neo-Astragalus (Leguminosae). Syst Biol, 49: 671–685.PubMedCrossRefGoogle Scholar
  26. Slack JM, Kuzio J, Faulkner P. 1995. Characterization of v-cath, a cathepsin L-like proteinase expressed by the baculovirus Autographa californica multiple nuclear polyhedrosis virus. J Gen Virol, 76: 1091–1098.PubMedCrossRefGoogle Scholar
  27. Solovyev VV, Salamov AA. 1999. INFOGENE: a database of known gene structures and predicted genes and proteins in sequences of genome sequencing projects. Nucleic Acids Res, 27: 248–250.PubMedPubMedCentralCrossRefGoogle Scholar
  28. Taha A, Nour-El-Din A, Croizier L, Ferber ML, Croizier G. 2000. Comparative analysis of the granulin regions of the Phthorimaea operculella and Spodoptera littoralis granuloviruses. Virus Genes, 21: 147–155.PubMedCrossRefGoogle Scholar
  29. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol, 28: 2731–2739.PubMedPubMedCentralCrossRefGoogle Scholar
  30. Winstanley D, Crook NE. 1993. Replication of Cydia pomonella granulosis virus in cell cultures. J Gen Virol, 74: 1599–1609.PubMedCrossRefGoogle Scholar
  31. Wormleaton S, Kuzio J, Winstanley D. 2003. The complete sequence of the Adoxophyes orana granulovirus genome. Virology, 311: 350–365.PubMedCrossRefGoogle Scholar
  32. 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.PubMedPubMedCentralCrossRefGoogle Scholar
  33. Wu Y, Carstens EB. 1996. Initiation of baculovirus DNA replication: early promoter regions can function as infection-dependent replicating sequences in a plasmid-based replication assay. J Virol, 70: 6967–6972.PubMedPubMedCentralGoogle Scholar
  34. Yin F, Zhu Z, Liu X, Hou D, Wang J, Zhang L, Wang M, Kou Z, Wang H, Deng F, Hu Z. 2015. The Complete Genome of a New Betabaculovirus from Clostera anastomosis. PLoS One, 10: e0132792.PubMedPubMedCentralCrossRefGoogle Scholar
  35. Zemskov EA, Kang W, Maeda S. 2000. Evidence for nucleic acid binding ability and nucleosome association of Bombyx mori nucleopolyhedrovirus BRO proteins. J Virol, 74: 6784–6789.PubMedPubMedCentralCrossRefGoogle Scholar
  36. Zhang S, Jia XW, Sun SF, Pang Y, Chen QJ, Yang K. 2014. Phylogenetic analysis and epidemiologic investigation of a Cnaphalocrocis medinalis granulovirus strain. Journal of Environmental Entomology, 36: 756–762.Google Scholar
  37. Zhang X, Liang Z, Yin X, Wang J, Shao X. 2014. Complete genome sequence of Agrotis segetum granulovirus Shanghai strain. Arch Virol, 159: 1869–1872.PubMedCrossRefGoogle Scholar
  38. Zhou JB, Li XQ, De-Eknamkul W, Suraporn S, Xu JP. 2012. Identification of a new Bombyx mori nucleopolyhedrovirus and analysis of its bro gene family. Virus Genes, 44: 539–547.PubMedCrossRefGoogle Scholar

Copyright information

© Wuhan Institute of Virology, CAS and Springer Science+Business Media Singapore Pte Ltd 2015

Authors and Affiliations

  1. 1.State Key Laboratory of BiocontrolSun Yat-sen UniversityGuangzhouChina
  2. 2.State Key Laboratory of Virology and China Center for Virus Culture Collection, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
  3. 3.Guangdong Haina Agriculture Co., LtdHuizhouChina

Personalised recommendations