1887

Abstract

The genome of the most virulent among 22 Brazilian geographical isolates of nucleopolyhedrovirus, isolate 19 (SfMNPV-19), was completely sequenced and shown to comprise 132 565 bp and 141 open reading frames (ORFs). A total of 11 ORFs with no homology to genes in the GenBank database were found. Of those, four had typical baculovirus promoter motifs and polyadenylation sites. Computer-simulated restriction enzyme cleavage patterns of SfMNPV-19 were compared with published physical maps of other SfMNPV isolates. Differences were observed in terms of the restriction profiles and genome size. Comparison of SfMNPV-19 with the sequence of the SfMNPV isolate 3AP2 indicated that they differed due to a 1427 bp deletion, as well as by a series of smaller deletions and point mutations. The majority of genes of SfMNPV-19 were conserved in the closely related NPV (SeMNPV) and NPV (AgseMNPV-A), but a few regions experienced major changes and rearrangements. Synthenic maps for the genomes of group II NPVs revealed that gene collinearity was observed only within certain clusters. Analysis of the dynamics of gene gain and loss along the phylogenetic tree of the NPVs showed that group II had only five defining genes and supported the hypothesis that these viruses form ten highly divergent ancient lineages. Crucially, more than 60 % of the gene gain events followed a power-law relation to genetic distance among baculoviruses, indicative of temporal organization in the gene accretion process.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.83581-0
2008-05-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/jgv/89/5/1202.html?itemId=/content/journal/jgv/10.1099/vir.0.83581-0&mimeType=html&fmt=ahah

References

  1. Afonso C. L., Tulman E. R., Lu Z., Balinsky C. A., Moser B. A., Becnel J. J., Rock D. L., Kutish G. F. 2001; Genome sequence of a baculovirus pathogenic for Culex nigripalpus . J Virol 75:11157–11165 [CrossRef]
    [Google Scholar]
  2. Ahrens C. H., Russell R. L., Funk C. J., Evans J. T., Harwood S. H., Rohrmann G. F. 1997; The sequence of the Orgyia pseudotsugata multinucleocapsid nuclear polyhedrosis virus genome. Virology 229:381–399 [CrossRef]
    [Google Scholar]
  3. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. 1990; Basic local alignment search tool. J Mol Biol 215:403–410 [CrossRef]
    [Google Scholar]
  4. Ayres M. D., Howard S. C., Kuzio J., Lopez-Ferber M., Possee R. D. 1994; The complete DNA sequence of Autographa californica nuclear polyhedrosis virus. Virology 202:586–605 [CrossRef]
    [Google Scholar]
  5. Barreto M. E., Guimaraes C. T., Teixeira F. F., Paiva E., Valicente F. H. 2005; Effect of Baculovirus spodoptera isolates in Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae) larvae and their characterization by RAPD. Neotrop Entomol 34:67–75 [CrossRef]
    [Google Scholar]
  6. Berretta M. F., Rios M. L., de Sciocco C. A. 1998; Characterization of a nuclear polyhedrosis virus of Spodoptera frugiperda from Argentina. J Invertebr Pathol 71:280–282 [CrossRef]
    [Google Scholar]
  7. Blissard G. W., Rohrmann G. F. 1990; Baculovirus diversity and molecular biology. Annu Rev Entomol 35:127–155 [CrossRef]
    [Google Scholar]
  8. Blissard G. W., Black B., Crook N. E., Keddie B. A., Possee R. D., Rohrmann G. F., Theilmann D. A., Volkman L. E. 2000; Family Baculoviridae . In Virus Taxonomy: Seventh Report of the International Committee on Taxonomy of Viruses . pp 195–202Edited by Regenmortel M. H. V. Van, Fauquet C. M., Bishop D. H. L., Carstens E. B., Estes M. K., Lemon S. M., Maniloff J., Mayo M. A., McGeoch D. J., Pringle C. R., Wickner E. B. San Diego, CA: Academic Press;
  9. Broer R., Heldens J. G. M., Strien E. A., Zuidema D., Vlak J. M. 1998; Specificity of multiple homologous genomic regions in Spodoptera exigua nucleopolyhedrovirus DNA replication. J Gen Virol 79:1563–1572
    [Google Scholar]
  10. Bruno W. J., Socci N. D., Halpern A. L. 2000; Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction. Mol Biol Evol 17:189–197 [CrossRef]
    [Google Scholar]
  11. Bulach D. M., Kumar C. A., Zaia A., Liang B., Tribe D. E. 1999; Group II nucleopolyhedrovirus subgroups revealed by phylogenetic analysis of polyhedrin and DNA polymerase gene sequences. J Invertebr Pathol 73:59–73 [CrossRef]
    [Google Scholar]
  12. Carver T. J., Rutherford K. M., Berriman M., Rajandream M. A., Barrell B. G., Parkhill J. 2005; ACT: the Artemis comparison tool. Bioinformatics 21:3422–3423 [CrossRef]
    [Google Scholar]
  13. Duffy S. P., Young A. M., Morin B., Lucarotti C. J., Koop B. F., Levin D. B. 2006; Sequence analysis and organization of the Neodiprion abietis nucleopolyhedrovirus genome. J Virol 80:6952–6963 [CrossRef]
    [Google Scholar]
  14. Felsenstein J. 1989; phylip – phylogeny inference package (version 3.2). Cladistics 5:164–166
    [Google Scholar]
  15. Garcia-Maruniak A., Maruniak J. E., Zanotto P. M. A., Doumbouya A. E., Liu J. C., Merritt T. M., Lanoie J. S. 2004; Sequence analysis of the genome of the Neodiprion sertifer nucleopolyhedrovirus. J Virol 78:7036–7051 [CrossRef]
    [Google Scholar]
  16. Gomi S., Majima K., Maeda S. 1999; Sequence analysis of the genome of Bombyx mori nucleopolyhedrovirus. J Gen Virol 80:1323–1337
    [Google Scholar]
  17. Gonzalez M. A., Smith G. E., Summers M. D. 1989; Insertion of the SfMNPV polyhedrin gene into an AcMNPV polyhedrin deletion mutant during viral infection. Virology 170:160–175 [CrossRef]
    [Google Scholar]
  18. Guarino L. A., Gonzalez M. A., Summers M. D. 1986; Complete sequence and enhancer function of the homologous DNA regions of Autographa californica nuclear polyhedrosis virus. J Virol 60:224–229
    [Google Scholar]
  19. Hayakawa T., Ko R., Okano K., Seong S. I., Goto C., Maeda S. 1999; Sequence analysis of the Xestia c-nigrum granulovirus genome. Virology 262:277–297 [CrossRef]
    [Google Scholar]
  20. Heldens J. G., Broer R., Zuidema D., Goldbach R. W., Vlak J. M. 1997; Identification and functional analysis of a non- hr origin of DNA replication in the genome of Spodoptera exigua multicapsid nucleopolyhedrovirus. J Gen Virol 78:1497–1506
    [Google Scholar]
  21. Herniou E. A., Luque T., Chen X., Vlak J. M., Winstanley D., Cory J. S., O'Reilly D. R. 2001; Use of whole genome sequence data to infer baculovirus phylogeny. J Virol 75:8117–8126 [CrossRef]
    [Google Scholar]
  22. Herniou E. A., Olszewski J. A., Cory J. S., O'Reilly D. R. 2003; The genome sequence and evolution of baculoviruses. Annu Rev Entomol 48:211–234 [CrossRef]
    [Google Scholar]
  23. Hong T., Summers M. D., Braunagel S. C. 1997; N-terminal sequences from Autographa californica nuclear polyhedrosis virus envelope proteins ODV-E66 and ODV-E25 are sufficient to direct reporter proteins to the nuclear envelope, intranuclear microvesicles and the envelope of occlusion derived virus. Proc Natl Acad Sci U S A 94:4050–4055 [CrossRef]
    [Google Scholar]
  24. IJkel W. F., van Strien E. A., Heldens J. G., Broer R., Zuidema D., Goldbach R. W., Vlak J. M. 1999; Sequence and organization of the Spodoptera exigua multicapsid nucleopolyhedrovirus genome. J Gen Virol 80:3289–3304
    [Google Scholar]
  25. Jakubowska A. K., Peters S. A., Ziemnicka J., Vlak J. M., van Oers M. M. 2006; Genome sequence of an enhancin gene-rich nucleopolyhedrovirus (NPV) from Agrotis segetum : collinearity with Spodoptera exigua multiple NPV. J Gen Virol 87:537–551 [CrossRef]
    [Google Scholar]
  26. Jehle J. A., Blissard G. W., Bonning B. C., Cory J. S., Herniou E. A., Rohrmann G. F., Theilmann D. A., Thiem S. M., Vlak J. M. 2006; On the classification and nomenclature of baculoviruses: a proposal for revision. Arch Virol 151:1257–1266 [CrossRef]
    [Google Scholar]
  27. Knell J. D., Summers M. D. 1981; Investigation of genetic heterogeneity in wild isolates of Spodoptera frugiperda nuclear polyhedrosis virus by restriction endonuclease analysis of plaque-purified variants. Virology 112:190–197 [CrossRef]
    [Google Scholar]
  28. Kool M., Ahrens C. H., Vlak J. M., Rohrmann G. F. 1995; Replication of baculovirus DNA. J Gen Virol 76:2103–2118 [CrossRef]
    [Google Scholar]
  29. Lauzon H. A. M., Lucarotti C. J., Krell P. J., Feng Q., Retnakaran A., Arif B. M. 2004; Sequence and organization of the Neodiprion lecontei nucleopolyhedrovirus genome. J Virol 78:7023–7035 [CrossRef]
    [Google Scholar]
  30. Lauzon H. A. M., Jamieson P. B., Krell P. J., Arif B. M. 2005; Gene organization and sequencing of the Choristoneura fumiferana defective nucleopolyhedrovirus genome. J Gen Virol 86:945–961 [CrossRef]
    [Google Scholar]
  31. Leisy D. J., Rohrmann G. F. 1993; Characterization of the replication of plasmids containing hr sequences in baculovirus-infected Spodoptera frugiperda cells. Virology 196:722–730 [CrossRef]
    [Google Scholar]
  32. Leisy D. J., Rasmussen C., Kim H. T., Rohrmann G. F. 1995; The Autographa californica nuclear polyhedrosis virus homologous region 1a: identical sequences are essential for DNA replication activity and transcriptional enhancer function. Virology 208:742–752 [CrossRef]
    [Google Scholar]
  33. Li L., Donly C., Li Q., Willis L. G., Keddie B. A., Erlandson M. A., Theilmann D. A. 2002; Identification and genomic analysis of a second species of nucleopolyhedrovirus isolated from Mamestra configurata . Virology 297:226–244 [CrossRef]
    [Google Scholar]
  34. Liu J. C., Maruniak J. E. 1995; Nucleotide sequence and transcriptional analysis of the gp41 gene of Spodoptera frugiperda nuclear polyhedrosis virus. J Gen Virol 76:1443–1450 [CrossRef]
    [Google Scholar]
  35. Loh L. C., Hamm J. J., Huang E. S. 1981; Spodoptera frugiperda nuclear polyhedrosis virus genome: physical maps for restriction endonucleases Bam HI and Hin dIII. J Virol 38:922–931
    [Google Scholar]
  36. Loh L. C., Hamm J. J., Kawanishi C., Huang E. S. 1982; Analysis of the Spodoptera frugiperda nuclear polyhedrosis virus genome by restriction endonucleases and electron microscopy. J Virol 44:747–751
    [Google Scholar]
  37. Maruniak J. E., Brown S. E., Knudson D. L. 1984; Physical maps of SfMNPV baculovirus DNA and its genomic variants. Virology 136:221–234 [CrossRef]
    [Google Scholar]
  38. McLysaght A., Baldi P. F., Gaut B. S. 2003; Extensive gene gain associated with adaptive evolution of poxviruses. Proc Natl Acad Sci U S A 100:15655–15660 [CrossRef]
    [Google Scholar]
  39. Montague M. G., Hutchison C. A. III 2000; Gene content phylogeny of herpesviruses. Proc Natl Acad Sci U S A 97:5334–5339 [CrossRef]
    [Google Scholar]
  40. Oliveira J. V. de C., Wolff J. L. C., Garcia-Maruniak A., Ribeiro B. M., de Castro M. E. B., de Souza M. L., Moscardi F., Maruniak J. E., Zanotto P. M. de A. 2006; Genome of the most widely used viral biopesticide: Anticarsia gemmatalis multiple nucleopolyhedrovirus. J Gen Virol 87:3233–3250 [CrossRef]
    [Google Scholar]
  41. O'Reilly D. R., Miller L. K., Luckow V. A. 1992 Baculovirus Expression Vectors: a Laboratory Manual Salt Lake City, UT: W. H. Freeman;
    [Google Scholar]
  42. Pertsemlidis A., Fondon J. W. III 2001; Having a blast with bioinformatics (and avoiding blastphemy). Genome Biol 2:reviews2002.1–reviews2002.10
    [Google Scholar]
  43. Rutherford K., Parkhill J., Crook J., Horsnell T., Rice P., Rajandream M. A., Barrell B. 2000; Artemis: sequence visualization and annotation. Bioinformatics 16:944–945 [CrossRef]
    [Google Scholar]
  44. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual, 2nd edition. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  45. Shapiro D. I., Fuxa J. R., Braymer H. D., Pashley D. P. 1991; DNA restriction polymorphism in wild isolates of Spodoptera frugiperda nuclear polyhedrosis virus. J Invertebr Pathol 58:96–105 [CrossRef]
    [Google Scholar]
  46. Simon O., Chevenet F., Williams T., Caballero P., Lopez-Ferber M. 2005a; Physical and partial genetic map of Spodoptera frugiperda nucleopolyhedrovirus (SfMNPV) genome. Virus Genes 30:403–417 [CrossRef]
    [Google Scholar]
  47. Simon O., Gutierrez S., Williams T., Caballero P., Lopez-Ferber M. 2005b; Nucleotide sequence and transcriptional analysis of the pif gene of Spodoptera frugiperda nucleopolyhedrovirus (SfMNPV). Virus Res 108:213–220 [CrossRef]
    [Google Scholar]
  48. Sonnhammer E. L. L., Durbin R. 1995; A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene 167:GC1–GC10 [CrossRef]
    [Google Scholar]
  49. Stothard P., Wishart D. S. 2005; Circular genome visualization and exploration using CGView. Bioinformatics 21:537–539 [CrossRef]
    [Google Scholar]
  50. Tanada Y., Kaya H. K. 1992 Insect Pathology San Diego, CA: Academic Press;
    [Google Scholar]
  51. Theilmann D. A., Stewart S. 1992; Tandemly repeated sequence at the 3′ end of the IE-2 gene of the baculovirus Orgyia pseudotsugata multicapsid nuclear polyhedrosis virus is an enhancer element. Virology 187:97–106 [CrossRef]
    [Google Scholar]
  52. Tumilasci V. F., Leal E., Zanotto P. M., Luque T., Wolff J. L. 2003; Sequence analysis of a 5.1 kbp region of the Spodoptera frugiperda multicapsid nucleopolyhedrovirus genome that comprises a functional ecdysteroid UDP-glucosyltransferase ( egt ) gene. Virus Genes 27:137–144 [CrossRef]
    [Google Scholar]
  53. Vlak J. M., Smith G. E. 1982; Orientation of the genome of Autographa californica nuclear polyhedrosis virus: a proposal. J Virol 41:1118–1121
    [Google Scholar]
  54. Willis L. G., Siepp R., Stewart T. M., Erlandson M. A., Theilmann D. A. 2005; Sequence analysis of the complete genome of Trichoplusia ni single nucleopolyhedrovirus and the identification of a baculoviral photolyase gene. Virology 338:209–226 [CrossRef]
    [Google Scholar]
  55. Zanotto P. M., Kessing B. D., Maruniak J. E. 1993; Phylogenetic interrelationships among baculoviruses: evolutionary rates and host associations. J Invertebr Pathol 62:147–164 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.83581-0
Loading
/content/journal/jgv/10.1099/vir.0.83581-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error