Dataset Information

Genome Sequencing and Analysis of Catopsilia pomona nucleopolyhedrovirus: A Distinct Species in Group I Alphabaculovirus.

ABSTRACT: The genome sequence of Catopsilia pomona nucleopolyhedrovirus (CapoNPV) was determined by the Roche 454 sequencing system. The genome consisted of 128,058 bp and had an overall G+C content of 40%. There were 130 hypothetical open reading frames (ORFs) potentially encoding proteins of more than 50 amino acids and covering 92% of the genome. Among all the hypothetical ORFs, 37 baculovirus core genes, 23 lepidopteran baculovirus conserved genes and 10 genes conserved in Group I alphabaculoviruses were identified. In addition, the genome included regions of 8 typical baculoviral homologous repeat sequences (hrs). Phylogenic analysis showed that CapoNPV was in a distinct branch of clade "a" in Group I alphabaculoviruses. Gene parity plot analysis and overall similarity of ORFs indicated that CapoNPV is more closely related to the Group I alphabaculoviruses than to other baculoviruses. Interesting, CapoNPV lacks the genes encoding the fibroblast growth factor (fgf) and ac30, which are conserved in most lepidopteran and Group I baculoviruses, respectively. Sequence analysis of the F-like protein of CapoNPV showed that some amino acids were inserted into the fusion peptide region and the pre-transmembrane region of the protein. All these unique features imply that CapoNPV represents a member of a new baculovirus species.

SUBMITTER: Wang J

PROVIDER: S-EPMC4864199 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Genome Sequencing and Analysis of Catopsilia pomona nucleopolyhedrovirus: A Distinct Species in Group I Alphabaculovirus.

Wang Jun J Zhu Zheng Z Zhang Lei L Hou Dianhai D Wang Manli M Arif Basil B Kou Zheng Z Wang Hualin H Deng Fei F Hu Zhihong Z

PloS one 20160511 5

The genome sequence of Catopsilia pomona nucleopolyhedrovirus (CapoNPV) was determined by the Roche 454 sequencing system. The genome consisted of 128,058 bp and had an overall G+C content of 40%. There were 130 hypothetical open reading frames (ORFs) potentially encoding proteins of more than 50 amino acids and covering 92% of the genome. Among all the hypothetical ORFs, 37 baculovirus core genes, 23 lepidopteran baculovirus conserved genes and 10 genes conserved in Group I alphabaculoviruses w ...[more]

PMID: 27166956

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Project description:BackgroundBaculoviruses act as effective biological control agents against the invasive pest Hyphantria cunea Drury. In this study, two Chinese Hyphantria cunea nucleopolyhedrovirus (HycuNPV) isolates, HycuNPV-BJ and HycuNPV-HB, were deep sequenced and compared with the Japanese isolate, HycuNPV-N9, to determine whole-genome level diversity and evolutionary history.ResultsThe divergence of the phylogenetic tree and the K2P distances based on 38 core-gene concatenated alignment revealed that two Chinese HycuNPV isolates were a novel species of Alphabaculovirus that infected Hyphantria cunea in China. The gene contents indicated significant differences in the HycuNPV genomes between the Chinese and Japanese isolates. The differences included gene deletions, acquisitions and structural transversions, but the main difference was the high number of single nucleotide polymorphisms (SNPs). In total, 10,393 SNPs, corresponding to approximately 8% of the entire HycuNPV-N9 genome sequence, were detected in the aligned reads. By analyzing non-synonymous variants, we found that hotspot mutation-containing genes had mainly unknown functions and most were early expressing genes. We found that the hycu78 gene which had early and late promoter was under positive selection. Biological activity assays revealed that the infectivity of HycuNPV-HB was greater than that of HycuNPV-BJ, and the killing speed of HycuNPV-HB was faster than that of HycuNPV-BJ. A comparison of molecular genetic characteristics indicated that the virulence differences between the two isolates were affected by SNP and structural variants, especially the homologous repeat regions.ConclusionsThe genomes of the two Chinese HycuNPV isolates were characterized, they belonged to a novel species of Alphabaculovirus that infected Hyphantria cunea in China. We inferred that the loss or gain of genetic material in the HycuNPV-HB and HycuNPV-BJ genomes resulted in new important adaptive capabilities to the H. cunea host. These results extend the current understanding of the genetic diversity of HycuNPV and will be useful for improving the applicability of this virus as a biological control agent.

Project description:Helicoverpa assulta is a pest that causes severe damage to tobacco, pepper and other cash crops. A local strain of HearNPV-BJ (formerly Helicoverpa assulta nucleopolyhedrovirus (HeasNPV-DJ0031)) was isolated from infected H. assulta larvae in Beijing, which had been regarded as a new kind of baculovirus in previous studies. Describing the biological characteristics of the strain, including its external morphology, internal structure and the pathological characteristics of the infection of various cell lines, can provide references for the identification and function of the virus. HearNPV-BJ virion was defined as a single-nucleocapsid nucleopolyhedrovirus by scanning electron microscopy. QB-Ha-E-5 (H. armigera) and BCIRL-Hz-AM1 (H. zea) cell lines were sensitive to HearNPV-BJ. Undoubtedly modern developed sequencing technology further facilitates the increasing understanding of various strains. The whole genome sequence of the HearNPV-BJ was sequenced and analyzed. The HearNPV-BJ isolate genome was 129, 800 bp nucleotides in length with a G + C content of 38.87% and contained 128 open reading frames (ORFs) encoding predicted proteins of 50 or over 50 amino acids, 67 ORFs in the forward orientation and 61 ORFs in the reverse orientation, respectively. The genome shared 99% sequence identity with Helicoverpa armigera nucleopolyhedrovirus C1 strain (HearNPV-C1), and 103 ORFs had very high homology with published HearNPV sequences. Two bro genes and three hrs were found to be dispersed along the HearNPV-BJ genome. Three of the highest homologs, ORFs with HearNPV, were smaller due to the earlier appearance of the stop codon with unknown functions. P6.9 of HearNPV-BJ, a structural protein, is distinctly different from that of Autographa californica nucleopolyhedrovirus (AcMNPV); its homology with the corresponding gene in HearNPV-C1 was 93.58%. HearNPV-BJ contains 38 core genes identified in other baculoviruses, and phylogenetic analysis indicates HearNPV-BJ belongs to Alphabaculovirus Group II, same as HearNPV-C1. The resulting data provide a better understanding of virion structure, gene function and character of infection. By supplementing the whole-genome sequencing data and Kimura-2 model index, there is more evidence to indicate that HearNPV-BJ may be a variant of Helicoverpa armigera nucleopolyhedrovirus, which also deepens our understanding of the virus species demarcation criteria.

Dataset Information

Genome Sequencing and Analysis of Catopsilia pomona nucleopolyhedrovirus: A Distinct Species in Group I Alphabaculovirus.

Publications

Genome Sequencing and Analysis of Catopsilia pomona nucleopolyhedrovirus: A Distinct Species in Group I Alphabaculovirus.

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