1887

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Volume 99, Issue 9

Baculovirus Kimura two-parameter species demarcation criterion is confirmed by the distances of 38 core gene nucleotide sequences Free

Abstract

Kimura two-parameter nucleotide distance comparisons based on polyhedrin/granulin (polh/gran), late expression factor 8 (lef-8) and late expression factor 9 (lef-9) are a widely applied method for species demarcation for lepidopteran-specific baculoviruses. Baculoviruses are considered to belong to the same species when a pairwise distance threshold of 0.015 is not exceeded and are considered as possibly belonging to the same species with a distance of up to 0.050. In the present work this method was revised and extended for 172 entirely sequenced lepidopteran, hymenopteran and dipteran baculovirus genomes by applying the nucleotide sequences of all 38 known baculovirus core genes for pairwise distance calculations. On the basis of this large dataset, the previously established standard thresholds for baculovirus species demarcation were adjusted for pairwise nucleotide distances estimated from the alignments of all 38 core genes. With the newly applied thresholds for the 38 core-gene dataset, a more sophisticated Kimura two-parameter method was established, avoiding the possible influence of the chimerical polh gene of the Autographa californica multiple nucleopolyhedrovirus. Based on the new dataset, the present classification of baculovirus species was confirmed. Thereby the Kimura two-parameter method for baculovirus demarcation was extended to include the information from all 38 Baculoviridae core genes, which represent the established standard information for baculovirus phylogeny to date.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Baculoviridae , barcoding , Kimura two-parameter , molecular phylogeny , species demarcation and whole genome sequencing
© 2018 The Authors
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2018-07-27
2024-04-16
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References

  1. Herniou EA, Arif BM, Becnel JJ, Blissard GW, Bonning BC et al.  Baculoviridae. In King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ. (editors) Virus Taxonomy Oxford: Elsevier; 2011 pp. 163–174
     [Google Scholar]
  2. Jehle JA, Lange M, Wang H, Hu Z, Wang Y et al. Molecular identification and phylogenetic analysis of baculoviruses from Lepidoptera. Virology 2006; 346:180–193 [View Article][PubMed]
     [Google Scholar]
  3. Jehle JA, Blissard GW, Bonning BC, Cory JS, Herniou EA et al. On the classification and nomenclature of baculoviruses: a proposal for revision. Arch Virol 2006; 151:1257–1266 [View Article][PubMed]
     [Google Scholar]
  4. Garavaglia MJ, Miele SA, Iserte JA, Belaich MN, Ghiringhelli PD. The ac53, ac78, ac101, and ac103 genes are newly discovered core genes in the family Baculoviridae. J Virol 2012; 86:12069–12079 [View Article][PubMed]
     [Google Scholar]
  5. Javed MA, Biswas S, Willis LG, Harris S, Pritchard C et al. Autographa californica multiple nucleopolyhedrovirus AC83 is a Per Os Infectivity Factor (PIF) protein required for occlusion-derived virus (ODV) and budded virus nucleocapsid assembly as well as assembly of the PIF complex in ODV envelopes. J Virol 2017; 91:e0211502116 [View Article][PubMed]
     [Google Scholar]
  6. Williams T, Bergoin M, van Oers MM. Diversity of large DNA viruses of invertebrates. J Invertebr Pathol 2017; 147:4–22 [View Article][PubMed]
     [Google Scholar]
  7. Kariithi HM, Meki IK, Boucias DG, Abd-Alla AM. Hytrosaviruses: current status and perspective. Curr Opin Insect Sci 2017; 22:71–78 [View Article][PubMed]
     [Google Scholar]
  8. Yang YT, Lee DY, Wang Y, Hu JM, Li WH et al. The genome and occlusion bodies of marine Penaeus monodon nudivirus (PmNV, also known as MBV and PemoNPV) suggest that it should be assigned to a new nudivirus genus that is distinct from the terrestrial nudiviruses. BMC Genomics 2014; 15:628 [View Article][PubMed]
     [Google Scholar]
  9. Jehle JA, Abd-Alla AM, Wang Y. Phylogeny and evolution of Hytrosaviridae. J Invertebr Pathol 2013; 112:S62–S67 [View Article][PubMed]
     [Google Scholar]
  10. Wang Y, Bininda-Emonds OR, Jehle JA. Nudivirus genomics and phylogeny. Viral Genomes-Molecular Structure, Diversity, Gene Expression Mechanisms and Host-Virus Interactions InTech; 2012
     [Google Scholar]
  11. Wennmann JT, Gueli Alletti G, Jehle JA. The genome sequence of Agrotis segetum nucleopolyhedrovirus B (AgseNPV-B) reveals a new baculovirus species within the Agrotis baculovirus complex. Virus Genes 2015; 50:260–276 [View Article][PubMed]
     [Google Scholar]
  12. Jakubowska AK, Peters SA, Ziemnicka J, Vlak JM, van Oers MM. Genome sequence of an enhancin gene-rich nucleopolyhedrovirus (NPV) from Agrotis segetum: collinearity with Spodoptera exigua multiple NPV. J Gen Virol 2006; 87:537–551 [View Article][PubMed]
     [Google Scholar]
  13. Yin F, Zhu Z, Liu X, Hou D, Wang J et al. The complete genome of a new betabaculovirus from Clostera anastomosis. PLoS One 2015; 10:e0132792 [View Article][PubMed]
     [Google Scholar]
  14. Li Q, Donly C, Li L, Willis LG, Theilmann DA et al. Sequence and organization of the Mamestra configurata nucleopolyhedrovirus genome. Virology 2002; 294:106–121 [View Article][PubMed]
     [Google Scholar]
  15. Li L, Donly C, Li Q, Willis LG, Keddie BA et al. Identification and genomic analysis of a second species of nucleopolyhedrovirus isolated from Mamestra configurata. Virology 2002; 297:226–244[PubMed]
     [Google Scholar]
  16. ICTV Virus Taxonomy: 2016 Release. Int Comm Taxon Viruses 2016 www.ictvonline.org/virustaxonomy.asp
     [Google Scholar]
  17. Xu YP, Ye ZP, Niu CY, Bao YY, Wang WB et al. Comparative analysis of the genomes of Bombyx mandarina and Bombyx mori nucleopolyhedroviruses. J Microbiol 2010; 48:102–110 [View Article][PubMed]
     [Google Scholar]
  18. Lange M, Wang H, Zhihong H, Jehle JA. Towards a molecular identification and classification system of lepidopteran-specific baculoviruses. Virology 2004; 325:36–47 [View Article][PubMed]
     [Google Scholar]
  19. Moser B, Becnel J, White S, Afonso C, Kutish G et al. Morphological and molecular evidence that Culex nigripalpus baculovirus is an unusual member of the family Baculoviridae. J Gen Virol 2001; 82:283–297 [View Article][PubMed]
     [Google Scholar]
  20. Wang M, Wang J, Yin F, Tan Y, Deng F et al. Unraveling the entry mechanism of baculoviruses and its evolutionary implications. J Virol 2014; 88:2301–2311 [View Article][PubMed]
     [Google Scholar]
  21. Miele SA, Garavaglia MJ, Belaich MN, Ghiringhelli PD. Baculovirus: molecular insights on their diversity and conservation. Int J Evol Biol 2011; 2011:1–15 [View Article][PubMed]
     [Google Scholar]
  22. Ayres MD, Howard SC, Kuzio J, Lopez-Ferber M, Possee RD. The complete DNA sequence of Autographa californica nuclear polyhedrosis virus. Virology 1994; 202:586–605 [View Article][PubMed]
     [Google Scholar]
  23. Ahrens CH, Russell RL, Funk CJ, Evans JT, Harwood SH et al. The sequence of the Orgyia pseudotsugata multinucleocapsid nuclear polyhedrosis virus genome. Virology 1997; 229:381–399 [View Article][PubMed]
     [Google Scholar]
  24. Ijkel WF, van Strien EA, Heldens JG, Broer R, Zuidema D et al. Sequence and organization of the Spodoptera exigua multicapsid nucleopolyhedrovirus genome. J Gen Virol 1999; 80:3289–3304 [View Article][PubMed]
     [Google Scholar]
  25. Hashimoto Y, Hayakawa T, Ueno Y, Fujita T, Sano Y et al. Sequence analysis of the Plutella xylostella granulovirus genome. Virology 2000; 275:358–372 [View Article][PubMed]
     [Google Scholar]
  26. Gomi S, Majima K, Maeda S. Sequence analysis of the genome of Bombyx mori nucleopolyhedrovirus. J Gen Virol 1999; 80:1323–1337 [View Article][PubMed]
     [Google Scholar]
  27. Kuzio J, Pearson MN, Harwood SH, Funk CJ, Evans JT et al. Sequence and analysis of the genome of a baculovirus pathogenic for Lymantria dispar. Virology 1999; 253:17–34 [View Article][PubMed]
     [Google Scholar]
  28. Chen X, Ijkel WF, Tarchini R, Sun X, Sandbrink H et al. The sequence of the Helicoverpa armigera single nucleocapsid nucleopolyhedrovirus genome. J Gen Virol 2001; 82:241–257 [View Article][PubMed]
     [Google Scholar]
  29. Luque T, Finch R, Crook N, O'Reilly DR, Winstanley D. The complete sequence of the Cydia pomonella granulovirus genome. J Gen Virol 2001; 82:2531–2547 [View Article][PubMed]
     [Google Scholar]
  30. Herniou EA, Luque T, Chen X, Vlak JM, Winstanley D et al. Use of whole genome sequence data to infer baculovirus phylogeny. J Virol 2001; 75:8117–8126 [View Article][PubMed]
     [Google Scholar]
  31. Herniou EA, Jehle JA. Baculovirus phylogeny and evolution. Curr Drug Targets 2007; 8:1043–1050 [View Article][PubMed]
     [Google Scholar]
  32. Simón O, Erlandson MA, Frayssinet M, Williams T, Theilmann DA et al. Lacanobia oleracea nucleopolyhedrovirus (LaolNPV): a new European species of alphabaculovirus with a narrow host range. PLoS One 2017; 12:e0176171 [View Article][PubMed]
     [Google Scholar]
  33. Harrison RL, Rowley DL, Mowery J, Bauchan GR, Theilmann DA et al. The complete genome sequence of a second distinct betabaculovirus from the true armyworm, Mythimna unipuncta. PLoS One 2017; 12:e0170510 [View Article][PubMed]
     [Google Scholar]
  34. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article][PubMed]
     [Google Scholar]
  35. Jehle JA. The mosaic structure of the polyhedrin gene of the Autographa californica nucleopolyhedrovirus (AcMNPV). Virus Genes 2004; 29:5–8 [View Article][PubMed]
     [Google Scholar]
  36. Krejmer M, Skrzecz I, Wasag B, Szewczyk B, Rabalski L. The genome of Dasychira pudibunda nucleopolyhedrovirus (DapuNPV) reveals novel genetic connection between baculoviruses infecting moths of the Lymantriidae family. BMC Genomics 2015; 16:759 [View Article][PubMed]
     [Google Scholar]
  37. Thumbi DK, Béliveau C, Cusson M, Lapointe R, Lucarotti CJ. Comparative genome sequence analysis of Choristoneura occidentalis Freeman and C. rosaceana Harris (Lepidoptera: Tortricidae) alphabaculoviruses. PLoS One 2013; 8:e68968 [View Article][PubMed]
     [Google Scholar]
  38. Harrison RL, Lynn DE. Genomic sequence analysis of a nucleopolyhedrovirus isolated from the diamondback moth, Plutella xylostella. Virus Genes 2007; 35:857–873 [View Article][PubMed]
     [Google Scholar]
  39. Kariuki CW, McIntosh AH. Infectivity studies of a new baculovirus isolate for the control of the Diamondback Moth (Plutellidae: Lepidoptera). J Econ Entomol 1999; 92:1093–1098 [View Article][PubMed]
     [Google Scholar]
  40. Kariuki CW, McIntosh AH, Goodman CL. In vitro host range studies with a new baculovirus isolate from the diamondback moth Plutella xylostella (L.) (Plutellidae: Lepidoptera). Vitro Cell Dev Biol-Anim 2000; 36:271–276 [View Article]
     [Google Scholar]
  41. Choi JB, Heo WI, Shin TY, Bae SM, Kim WJ et al. Complete genomic sequences and comparative analysis of Mamestra brassicae nucleopolyhedrovirus isolated in Korea. Virus Genes 2013; 47:133–151 [View Article][PubMed]
     [Google Scholar]
  42. Tanada Y. Descriptions and characteristics of a nuclear polyhedrosis virus and a granulosis virus of the armyworm Pseudaletia unipuncta (Haworth) (Lepidoptera, Noctuidae). J Insect Pathol 1959; 1:197–214
     [Google Scholar]
  43. de Los Ángeles Bivian-Hernández M, López-Tlacomulco J, Mares-Mares E, Ibarra JE, del Rincón-Castro MC. Genomic analysis of a Trichoplusia ni Betabaculovirus (TnGV) with three different viral enhancing factors and two unique genes. Arch Virol 2017; 162:3705–3715 [View Article][PubMed]
     [Google Scholar]
  44. van Regenmortel MH. Virus species, a much overlooked but essential concept in virus classification. Intervirology 1990; 31:241–254 [View Article][PubMed]
     [Google Scholar]
  45. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article][PubMed]
     [Google Scholar]
  46. Afonso CL, Tulman ER, Lu Z, Balinsky CA, Moser BA et al. Genome sequence of a baculovirus pathogenic for Culex nigripalpus. J Virol 2001; 75:11157–11165 [View Article][PubMed]
     [Google Scholar]
  47. Garcia-Maruniak A, Maruniak JE, Zanotto PM, Doumbouya AE, Liu JC et al. Sequence analysis of the genome of the Neodiprion sertifer nucleopolyhedrovirus. J Virol 2004; 78:7036–7051 [View Article][PubMed]
     [Google Scholar]
  48. Lauzon HA, Lucarotti CJ, Krell PJ, Feng Q, Retnakaran A et al. Sequence and organization of the Neodiprion lecontei nucleopolyhedrovirus genome. J Virol 2004; 78:7023–7035 [View Article][PubMed]
     [Google Scholar]
  49. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article][PubMed]
     [Google Scholar]
  50. Paradis E, Claude J, Strimmer K. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 2004; 20:289–290 [View Article][PubMed]
     [Google Scholar]
  51. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
     [Google Scholar]
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Baculovirus Kimura two-parameter species demarcation criterion is confirmed by the distances of 38 core gene nucleotide sequences
J. Gen. Virol. 99, 1307 (2018); https://doi.org/10.1099/jgv.0.001100
/content/journal/jgv/10.1099/jgv.0.001100
/content/journal/jgv/10.1099/jgv.0.001100
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