Genomic sequencing and analyses of Lymantria xylina multiple nucleopolyhedrovirus

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Nai, Yu Shin ^a   Wu, Chih Yu ^a   Wang, Tai Chuan ^a   Chen, Yun Ru ^a   Lau, Wei Hong ^c   Lo, Chu Fang ^a   Tsai, Meng Feng ^b   Wang, Chung Hsiung ^a  

^a NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^b DA YEH UNIVERSITY   (Taiwan)

^c UNIVERSITY PUTRA MALAYSIA   (Malaysia)

Author keywords

[No Author keywords available]

Indexed keywords

GAG PROTEIN; HOST RANGE FACTOR 1; UNCLASSIFIED DRUG; VIRUS DNA; VIRUS PROTEIN;

ANIMAL CELL; ARTICLE; BACULOVIRUS; CONTROLLED STUDY; GENE STRUCTURE; GENOME ANALYSIS; GENOME SIZE; INFECTION SENSITIVITY; LEPIDOPTERA; LYMANTRIA XYLINA; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; POLYHEDROSIS VIRUS; PROMOTER REGION; RNA VIRUS INFECTION; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; VIRUS GENOME; VIRUS VIRULENCE; ANIMAL; CLASSIFICATION; COMPARATIVE GENOMIC HYBRIDIZATION; CONSENSUS SEQUENCE; DNA BASE COMPOSITION; DNA SEQUENCE; DUPLICATE GENE; GENE ORDER; GENETICS; INVERTED REPEAT; MOTH; PHYLOGENY; VIROLOGY; VIRUS GENE;

LEPIDOPTERA; LYMANTRIA DISPAR MNPV; LYMANTRIA XYLINA; LYMANTRIIDAE; NUCLEOPOLYHEDROVIRUS;

ANIMALS; BASE COMPOSITION; COMPARATIVE GENOMIC HYBRIDIZATION; CONSENSUS SEQUENCE; DNA, VIRAL; GENE ORDER; GENES, DUPLICATE; GENES, VIRAL; GENOME, VIRAL; INVERTED REPEAT SEQUENCES; MOTHS; NUCLEOPOLYHEDROVIRUS; OPEN READING FRAMES; PHYLOGENY; PROMOTER REGIONS, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 77649137106     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-116     Document Type: Article

References (84)

1. Theilmann DA, Blissard GW, Bonning B, Jehle JA, O'Reilly DR, Rohrmann GF, Thiem S, Valk JM. Family Baculoviridae. Virus Taxonomy: Eighth Report of the International Committee on Taxonomy of Viruses 2005, 1129-1185. Springer, New York, Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA.
2. Jehle JA, Blissard GW, Bonning BC, Cory JS, Herniou EA, Rohrmann GF, Theilmann DA, Thiem SM, Vlak JM. On the classification and nomenclature of baculoviruses: A proposal for revision. Arch Virol 2006, 151:1257-1266. 10.1007/s00705-006-0763-6, 16648963.
3. Zanotto PMD, Kessing BD, Maruniak JE. Phylogenetic interrelationships among baculoviruses evolutionary rates and host associations. J Invertebr Pathol 1993, 62:147-164. 10.1006/jipa.1993.1090, 8228320.
4. Bulach DM, Kumar CA, Zaia A, Liang BF, Tribe DE. Group II nucleopolyhedrovirus subgroups revealed by phylogenetic analysis of polyhedrin and DNA polymerase gene sequences. J Invertebr Pathol 1999, 73:59-73. 10.1006/jipa.1998.4797, 9878291.
5. Afonso CL, Tulman ER, Lu Z, Balinsky CA, Moser BA, Becnel JJ, Rock DL, Kutish GF. Genome sequence of a baculovirus pathogenic for Culex nigripalpus. J Virol 2001, 75:11157-11165. 10.1128/JVI.75.22.11157-11165.2001, 114695, 11602755.
6. Garcia-Maruniak A, Maruniak JE, Zanotto PMA, Doumbouya AE, Liu JC, Merritt TA, Lanoie JS. Sequence analysis of the genome of the Neodiprion sertifer nucleopolyhedrovirus. J Virol 2004, 78:7036-7051. 10.1128/JVI.78.13.7036-7051.2004, 421636, 15194780.
7. Lauzon HAM, Lucarotti CJ, Krell PJ, Feng QL, Retnakaran A, Arif BM. Sequence and organization of the Neodiprion lecontei nucleopolyhedrovirus genome. J Virol 2004, 78:7023-7035. 10.1128/JVI.78.13.7023-7035.2004, 421645, 15194779.
8. Duffy SP, Young AM, Morin B, Lucarotti CJ, Koop BF, Levin DB. Sequence analysis and organization of the Neodiprion abietis nucleopolyhedrovirus genome. J Virol 2006, 80:6952-6963. 10.1128/JVI.00187-06, 1489044, 16809301.
9. Shen TC, Shae YS, Liu CS, Tan CW, Hwang SY. Relationships Between Egg Mass Size and Egg Number per Egg Mass in the Casuarina Moth, Lymantria xylina (Lepidoptera: Lymantriidae). Environ Entomol 2003, 32:752-755.
10. Shen TC, Tseng CM, Guan LC, Hwang SY. Performance of Lymantria xylina (Lepidoptera: Lymantriidae) on artificial and host plant diets. J Econ Entomol 2006, 99:714-721. 10.1603/0022-0493-99.3.714, 16813303.
11. Chao JT, Schaefer PW, Fan YB, Lu SS. Host plants and infestation of casuarina moth Lymantria xylina (Lepidoptera: Lymantriidae) in Taiwan. Quart J Chinese Forest 1996, 11:23-28. (In Chinese).
12. Nai YS, Wang TC, Chen YR, Lo CF, Wang CH. A new nucleopolyhedrovirus strain (LdMNPV-like virus) with a defective fp25 gene from Lymantria xylina (Lepidoptera: Lymantriidae) in Taiwan. J Invertebr Pathol 2009, 102:110-119. 10.1016/j.jip.2009.07.004, 19616553.
13. Xiao GR. Forest insects of China. 1991, 1362. China Forestry Publishing House, 2, (in Chinese).
14. Kuzio J, Pearson MN, Harwood SH, Funk CJ, Evans JT, Slavicek JM, Rohrmann GF. Sequence and analysis of the genome of a baculovirus pathogenic for Lymantria dispar. Virology 1999, 253:17-34. 10.1006/viro.1998.9469, 9887315.
15. Nealis VG, Erb S. A sourcebook for management of the gypsy moth. Ministry of Nature Resources, Forestry Canada 1993, 47.
16. Wu CY, Wang CH. Characterization and polyhedron gene cloning of Lymantria xylina multiple nucleopolyhedrovirus. J Invertebr Pathol 2005, 88:238-246. 10.1016/j.jip.2005.01.012, 15955343.
17. Yu CC, Kao HH, Chao JT, Lu SS, Wang CH. The characterization of Lymantria xylina nucleopolyhedrovirus (LyxyMNPV) and the establishment of in vitro multiplication of LyxyMNPV. Chinese J Entomol 1997, 17:23-32. (in Chinese).
18. Wu CY, Wang CH. New cell lines from Lymantria xylina (Lepidoptera: Lymantriidae): characterization and susceptibility to baculoviruses. J Invertebr Pathol 2006, 93:186-191. 10.1016/j.jip.2006.08.003, 16989856.
19. Goodwin RH, Tropkins FJ, McCawley P. Gypsy moth cell lines divergent in viral susceptibility. In Vitro 1978, 14:485-494. 10.1007/BF02616088, 79542.
20. Bradford MB, Blissard GW, Rohrmann GF. Characterization of the infection cycle of the Orgyia pseudotsugata multicapsid nuclear polyhedrosis virus in Lymantria dispar cells. J Gen Virol 1990, 71:2841-2846. 10.1099/0022-1317-71-12-2841, 2273385.
21. Chou CM, Huang CJ, Lo CF, Kou GH, Wang CH. Characterization of Perina nuda Nucleopolyhedrovirus (PenuNPV) Polyhedrin Gene. J Invertebr Pathol 1996, 67:259-266. 10.1006/jipa.1996.0041, 8812607.
22. Ayres MD, Howard SC, Kuzio J, Lopez-ferber M, Possee RD. The complete DNA sequence of Autograha californica nuclear polyhedrosis virus. Virology 1994, 202:586-605. 10.1006/viro.1994.1380, 8030224.
23. Ahrens CH, Russell RLQ, Funk CJ, Evans JT, Harwood SH, Rohrmann GF. The sequence of the Orgyia pseudotsugata multinucleocapsid nuclear polyhedrosis virus genome. Virology 1997, 229:381-399. 10.1006/viro.1997.8448, 9126251.
24. Chen YR, Wu CY, Lee ST, Wu YJ, Lo CF, Tsai MF, Wang CH. Genomic and host range studies of Maruca vitrata nucleopolyhedrovirus. J Gen Virol 2008, 89:2315-2330. 10.1099/vir.0.2008/001412-0, 18753242.
25. Vlak JM, Smith GE. Orientation of the genome of Autographa californica nuclear polyhedrosis virus: a proposal. J Virol 1982, 41:1118-1121. 256854, 16789218.
26. Herniou EA, Olszewski JA, Cory JS, O'Reilly DR. The genome sequence and evolution of baculoviruses. Annu Rev Entomol 2003, 48:211-234. 10.1146/annurev.ento.48.091801.112756, 12414741.
27. McCarthy CB, Theilmann DA. AcMNPV ac143 (odv-e18) is essential for mediating budded virus production and is the 30th baculovirus core gene. Virology 2008, 375:277-291. 10.1016/j.virol.2008.01.039, 18328526.
28. Kool M, Vlak JM. The structural and functional organization of the Autographa californica nuclear polyhedrosis virus genome. Arch Virol 1993, 130:1-16. 10.1007/BF01318992, 8389114.
29. O'Reilly DR, Miller LK, Luckow VA. Gene organization, regulation, and function. Baculovirus Expression Vectors (A Laboratory Manual) 1994, 12-23. Oxford University Press, New York.
30. IJkel WFJ, van Strien EA, Heldens JGM, Broer R, Zuidema D, Goldbach RW, Vlak JM. Sequence and organization of the Spodoptera exigua multicapsid nucleopolyhedrovirus genome. J Gen Virol 1999, 80:3289-304.
31. 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.
32. Harrison RL, Bonning BC. Comparative analysis of the genomes of Rachiplusia ou and Autographa californica multiple nucleopolyhedrovirus. J Gen Virol 2003, 84:1827-1842. 10.1099/vir.0.19146-0, 12810877.
33. Hayakawa T, Ko R, Okano K, Seong SI, Goto C, Maeda S. Sequence analysis of the Xestia c-nigrum granulovirus genome. Virology 1999, 262:277-297. 10.1006/viro.1999.9894, 10502508.
34. Gomi S, Majima K, Maeda S. Sequence analysis of the genome of Bombyx mori nucleopolyhedrovirus. J Gen Virol 1999, 80:1323-1337.
35. Hyink O, Dellow RA, Olsen MJ, Caradoc-Davies KMB, Drake K, Herniou EA, Cory JS, O'Reilly DR, Ward VK. Whole genome analysis of the Epiphyas postvittana nucleopolyhedrovirus. J Gen Virol 2002, 83:957-971.
36. IJkel WFJ, Westenberg M, Goldbach RW, Blissard GW, Vlak JM. A novel baculovirus envelope fusion protein with a proprotein convertase cleavage site. Virology 2000, 275:30-41. 10.1006/viro.2000.0483, 11017785.
37. Pearson MN, Groten C, Rohrmann GF. Identification of the Lymantria dispar nucleopolyhedrovirus envelope fusion protein provides evidence for a phylogenetic division of the Baculoviridae. J Virol 2000, 74:6126-6131. 10.1128/JVI.74.13.6126-6131.2000, 112111, 10846096.
38. Pearson MN, Russell RLQ, Rohrmann GF. Characterization of a baculovirus-encoded protein that is associated with infected-cell membranes and budded virions. Virology 2001, 291:22-31. 10.1006/viro.2001.1191, 11878873.
39. Braunagel SC, He H, Ramamurthy P, Summers MD. Transcription, translation, and cellular localization of three Autographa californica nuclear polyhedrosis virus structural proteins: ODV-E18, ODV-E35, and ODV-EC27. Virology 1996, 222:100-114. 10.1006/viro.1996.0401, 8806491.
40. Lu A, Miller LK. Regulation of baculovirus late and very late gene expression. The Baculoviruses 1997, 193-216. Plenum Press, New York, Miller LK.
41. Rapp JC, Wilson JA, Miller LK. Nineteen baculovirus open reading frames, including LEF-12, support late gene expression. J Virol 1998, 72:10197-10206. 110566, 9811761.
42. Friesen PD. Regulation of baculovirus early gene expression. The Baculoviruses 1997, 141-170. Plenum Press, New York, Miller LK.
43. Lu A, Krell P, Vlak J, Rohrmann G. Baculovirus DNA replication. The Baculoviruses 1997, 171-192. Plenum Press, New York, Miller LK.
44. Mikhailov VS, Mikhailova AL, Iwanaga M, Gomi S, Maeda S. Bombyx mori nucleopolyhedrovirus encodes a DNA-binding protein capable of destabilizing duplex DNA. J Virol 1998, 72:3107-3116. 109761, 9525636.
45. Lange M, Jehle JA. The genome of Cryptophlebia leucotreta granulovirus. Virology 2003, 317:220-236. 10.1016/S0042-6822(03)00515-4, 14698662.
46. Kool M, Ahren CH, Goldbach RW, Rohrmann GF, Vlak JM. Identification of genes involved in DNA replication of the Autographa californica baculovirus. Proc Natl Acad Sci USA 1994, 91:11212-11216. 10.1073/pnas.91.23.11212, 45197, 7972036.
47. O'Reilly D. Auxiliary genes of baculoviruses. The Baculoviruses 1997, 267-300. Plenum Press, New York, Miller LK.
48. Olivera BM, Miljanich GP, Ramachandran J, Adams ME. Calcium channel diversity and neurotransmitter release: The omega-conotoxins and omega-agatoxins. Annu Rev Biochem 1994, 63:823-867. 10.1146/annurev.bi.63.070194.004135, 7979255.
49. Eldridge R, O'Reilly DR, Hammock BD, Miller LK. Insecticidal properties of genetically engineered baculoviruses expressing an insect juvenile hormone esterase gene. Appl Environ Microbiol 1992, 58:1583-1591. 195644, 1622228.
50. Derksen ACG, Granados RR. Alteration of a lepidopteran peritrophic membrane by baculoviruses and enhancement of viral infectivity. Virology 1988, 167:242-250. 10.1016/0042-6822(88)90074-8, 3055665.
51. Hashimoto Y, Corsaro BG, Granados RR. Location and nucleotide sequence of the gene encoding the viral enhancing factor of the Trichoplusia ni granulosis virus. J Gen Virol 1991, 72:2645-2651. 10.1099/0022-1317-72-11-2645, 1940861.
52. Bischoff DS, Slavicek JM. Molecular analysis of an enhancin gene in the Lymantria dispar nuclear polyhedrosis virus. J Virol 1997, 71:8133-8140. 192269, 9343163.
53. Popham HJR, Bischoff DS, Slavicek JM. Both Lymantria dispar nucleopolyhedrovirus enhancin genes contribute to viral potency. J Virol 2001, 75:8639-8648. 10.1128/JVI.75.18.8639-8648.2001, 115109, 11507209.
54. Crook NE, Clem RJ, Miller LK. An apoptosis-inhibiting baculovirus gene with a zinc-finger like motif. J Virol 1993, 67:2168-2174. 240327, 8445726.
55. Pang Y, Yu JX, Wang LH, Hu XH, Bao WD, Li G, Chen C, Han H, Hu SN, Yang HM. Sequence analysis of the Spodoptera litura multicapsid nucleopolyhedrovirus genome. Virology 2001, 287:391-404. 10.1006/viro.2001.1056, 11531416.
56. Birnbaum MJ, Clem RJ, Miller LK. An apoptosis inhibiting gene from a nuclear polyhedrosis virus encoding a polypeptide with Cys/His sequence motifs. J Virol 1994, 68:2521-2528. 236730, 8139034.
57. Seshagiri S, Miller LK. Baculovirus inhibitors of apoptosis (IAPs) block activation of Sf-caspase-1. Proc Natl Acad Sci USA 1997, 94:13606-13611. 10.1073/pnas.94.25.13606, 28353, 9391073.
58. Bideshi DK, Renault S, Stasiak K. Phylogenetic analysis and possible function of bro-like genes, a multigene family widespread among large double-stranded DNA viruses of invertebrates and bacteria. J Gen Virol 2003, 84:2531-2544. 10.1099/vir.0.19256-0, 12917475.
59. Zemskov EA, Kang W, Maeda S. Evidence for nucleic acid binding ability and nucleosome association of Bombyx mori nucleopolyhedrovirus BRO proteins. J Virol 2000, 74:6784-6789. 10.1128/JVI.74.15.6784-6789.2000, 112195, 10888617.
60. Li LL, Li OJ, Willis LG, Erlandson M, Theilmann DA, Donly C. Complete comparative genomic analysis of two field isolates of Mamestra configurata nucleopolyhedrovirus-A. J Gen Virol 2002, 86:91-105.
61. Garcia-Maruniak A, Pavan OHO, Maruniak JE. A variable region of Anticarsia gemmatalis nuclear polyhedrosis virus contains tandemly repeated DNA sequences. Virus Res 1996, 41:123-132. 10.1016/0168-1702(95)01264-8, 8738171.
62. Hilton S, Winstanley D. Identification and functional analysis of the origins of DNA replication in the Cydia pomonella granulovirus genome. J Gen Virol 2007, 88:1496-1504. 10.1099/vir.0.82760-0, 17412979.
63. Theilmann DA, Stewart S. Tandemly repeated sequence at the 3' end of the IE-2 gene of the baculovirus Orgyia pseudosugata multicapsid nuclear polyhedrosis virus is an enhancer element. Virology 1992, 187:97-106. 10.1016/0042-6822(92)90298-4, 1736547.
64. Carstens EB, Wu Y. No single homologous repeat region is essential for DNA replication of the baculovirus Autographa californica multiple nucleopolyhedrovirus. J Gen Virol 2007, 88:114-122. 10.1099/vir.0.82384-0, 17170443.
65. Garner KJ, Slavicek JM. Identification of a non-LTR retrotransposon from the gypsy moth. Insect molecular biology 1999, 8(2):231-242. 10.1046/j.1365-2583.1999.820231.x, 10380107.
66. Bess JW, Powell PJ, Issaq HJ, Schumack LJ, Grimes MK, Henderson LE, Arthur LO. Tightly Bound Zinc in Human Immunodeficiency Virus Type 1, Human T-Cell Leukemia Virus Type I, and Other Retroviruses. J Virol 1992, 66:840-847. 240784, 1731111.
67. Oliveira JVC, Wolff JLC, Garcia-Maruniak A, Ribeiro BM, de Castro MEB, de Souza ML, Moscardi F, Maruniak JE, Zanotto PMA. Genome of the most widely used viral biopesticide: Anticarsia gemmatalis multiple nucleopolyhedrovirus. J Gen Virol 2006, 87:3233-3250. 10.1099/vir.0.82161-0, 17030857.
68. Hilton S, Winstanley D. Genomic sequence and biological characterization of a nucleopolyhedrovirus isolated from the summer fruit tortrix, Adoxophyes orana. J Gen Virol 2008, 89:2898-2980. 10.1099/vir.0.2008/002881-0, 18931089.
69. Means JC, Penabaz T, Clem RJ. Identification and functional characterization of AMVp33, a novel homolog of the baculovirus caspase inhibitor p35 found in Amsacta moorei entomopoxvirus. Virology 2006, 358:436-437. 10.1016/j.virol.2006.08.043, 2582192, 17010407.
70. Ishikawa H, Ikeda M, Alves CAF, Thiem SM, Kobayashi M. Host range factor 1 from Lymantria dispar nucleopolyhedrovirus (NPV) is an essential viral factor required for productive infection of NPVs in IPLB-Ld652Y cells derived from L. dispar. J Virol 2004, 78:12703-12708. 10.1128/JVI.78.22.12703-12708.2004, 525096, 15507661.
71. Chen CJ, Quentin ME, Brenna LA, Kukel C, Thiem SM. Lymantria dispar nucleopolyhedrovirus hrf-1 expands the larval host range of Autographa californica nucleopolyhedrovirus. J Virol 1998, 72:2526-2531. 109557, 9499118.
72. Summers MD, Smith GE. A manual of methods for baculovirus vectors and insect cell culture procedures. Texas Agricul Exp Station Bull 1987, 1555:5.
73. Hink WF, Strauss E. Growth of the Trichoplusia ni (TN-368) cell line in suspension culture. Invertebrate Tissue Culture, Applications in Medicine, Biology, and Agriculture 1976, 297-300. Academic Press, New York, Kurstak E, Maramorosch K.
74. Ewing B, Green P. Base-calling of automated sequencer traces using PHRED. II. Error probabilities. Genome Res 1998, 8:186-194.
75. Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using PHRED. I. Accuracy assessment. Genome Res 1998, 8:175-185.
76. Bonfield JK, Smith KF, Staden R. A new DNA sequence assembly program. Nucleic Acids Res 1995, 23:4992-4999. 10.1093/nar/23.24.4992, 307504, 8559656.
77. Wheeler DL, Church DM, Federhen S, Lash AE, Madden TL, Pontious JU, Schuler GD, Schriml LM, Sequeira E, Tatusova TA, Wagner L. Database resources of the National Center for Biotechnology. Nucleic Acids Res 2003, 31:28-33. 10.1093/nar/gkg033, 165480, 12519941.
78. Xing K, Deng R, Wang J, Feng J, Huang M, Wang X. Analysis and prediction of baculovirus promoter sequences. Virus Research 2005, 113:64-71. 10.1016/j.virusres.2005.04.016, 15908030.
79. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
80. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997, 25:4876-4882. 10.1093/nar/25.24.4876, 147148, 9396791.
81. Benson G. Tandem repeats finder: a program to analyse DNA sequences. Nucleic Acids Research 1999, 27(2):573-580. 10.1093/nar/27.2.573, 148217, 9862982.
82. Hu ZH, Arif BM, Jin F, Martens JWM, Chen XW, Sun JS, Zuidema D, Goldbach RW, Vlak JM. Distinct gene arrangement in the Buzura suppressaria single-nucleocapsid nucleopolyhedrovirus genome. J Gen Virol 1998, 79:2841-2851.
83. Kumar S, Tamura K, Nei M. MEGA 3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 2004, 5:150-163. 10.1093/bib/5.2.150, 15260895.
84. Possee RD, Rohrmann GF. Baculovirus genome organization and evolution. The Baculoviruses 1997, 109-140. Plenum Press, New York, Miller LK.