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Open Access Research article

Genomic sequence, organization and characteristics of a new nucleopolyhedrovirus isolated from Clanis bilineata larva

Shan-Ying Zhu1, Jian-Ping Yi2, Wei-De Shen3, Li-Qun Wang1, Hua-Gang He4, Yong Wang4, Bing Li3 and Wen-Bing Wang1*

Author Affiliations

1 Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, PR China

2 Shanghai Entry-Exit Inspection and Quarantine Bureau, Shanghai 200135, PR China

3 School of Life Sciences, Soochow University, Suzhou 215123, PR China

4 School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China

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BMC Genomics 2009, 10:91  doi:10.1186/1471-2164-10-91

Published: 25 February 2009

Abstract

Background

Baculoviruses are well known for their potential as biological agents for controlling agricultural and forest pests. They are also widely used as expression vectors in molecular cloning studies. The genome sequences of 48 baculoviruses are currently available in NCBI databases. As the number of sequenced viral genomes increases, it is important for the authors to present sufficiently detailed analyses and annotations to advance understanding of them. In this study, the complete genome of Clanis bilineata nucleopolyhedrovirus (ClbiNPV) has been sequenced and analyzed in order to understand this virus better.

Results

The genome of ClbiNPV contains 135,454 base pairs (bp) with a G+C content of 37%, and 139 putative open reading frames (ORFs) of at least 150 nucleotides. One hundred and twenty-six of these ORFs have homologues with other baculovirus genes while the other 13 are unique to ClbiNPV. The 30 baculovirus core genes are all present in ClbiNPV. Phylogenetic analysis based on the combined pif-2 and lef-8 sequences places ClbiNPV in the Group II Alphabaculoviruses. This result is consistent with the absence of gp64 from the ClbiNPV genome and the presence instead of a fusion protein gene, characteristic of Group II. Blast searches revealed that ClbiNPV encodes a photolyase-like gene sequence, which has a 1-bp deletion when compared with photolyases of other baculoviruses. This deletion disrupts the sequence into two small photolyase ORFs, designated Clbiphr-1 and Clbiphr-2, which correspond to the CPD-DNA photolyase and FAD-binding domains of photolyases, respectively.

Conclusion

ClbiNPV belongs to the Group II Alphabaculoviruses and is most closely related to OrleNPV, LdMNPV, TnSNPV, EcobNPV and ChchNPV. It contains a variant DNA photolyase gene, which only exists in ChchNPV, TnSNPV and SpltGV among the baculoviruses.