Genome analysis of a novel Group I alphabaculovirus obtained from Oxyplax ochracea

Wang, Jun; Hou, Dianhai; Wang, Qianran; Kuang, Wenhua; Zhang, Lei; Shěn, Shū; Deng, Fei; Wang, Hualin; Hú, Zhìhóng

doi:10.1371/journal.pone.0192279

Cited by 10 publications

(13 citation statements)

References 65 publications

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“…In contrast, the gene order was significantly divergent with NeseNPV and CuniNPV (Figure 3). Consistent with previous studies [33,44,45], a conserved lepidopteran baculovirus collinear region was found in ArdiNPV, which contained 20 core genes, 5 genes conserved in lepidopteran baculovirus, and 3 other baculoviral genes (Figure 1).…”

Section: Resultssupporting

confidence: 91%

Genome Analysis of a Novel Clade II.b Alphabaculovirus Obtained from Artaxa digramma

Duan

Wang

Zhang

et al. 2019

Viruses

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Artaxa digramma is a lepidopteran pest distributed throughout southern China, Myanmar, Indonesia, and India. Artaxa digramma nucleopolyhedrovirus (ArdiNPV) is a specific viral pathogen of A. digramma and deemed as a promising biocontrol agent against the pest. In this study, the complete genome sequence of ArdiNPV was determined by deep sequencing. The genome of ArdiNPV contains a double-stranded DNA (dsDNA) of 161,734 bp in length and 39.1% G+C content. Further, 149 hypothetical open reading frames (ORFs) were predicted to encode proteins >50 amino acids in length, covering 83% of the whole genome. Among these ORFs, 38 were baculovirus core genes, 22 were lepidopteran baculovirus conserved genes, and seven were unique to ArdiNPV, respectively. No typical baculoviral homologous regions (hrs) were identified in the genome. ArdiNPV had five multi-copy genes including baculovirus repeated ORFs (bros), calcium/sodium antiporter B (chaB), DNA binding protein (dbp), inhibitor of apoptosis protein (iap), and p26. Interestingly, phylogenetic analyses showed that ArdiNPV belonged to Clade II.b of Group II Alphabaculoviruses, which all contain a second copy of dbp. The genome of ArdiNPV was the closest to Euproctis pseudoconspersa nucleopolyhedrovirus, with 57.4% whole-genome similarity. Therefore, these results suggest that ArdiNPV is a novel baculovirus belonging to a newly identified cluster of Clade II.b Alphabaculoviruses.

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Section: Resultssupporting

confidence: 91%

Genome Analysis of a Novel Clade II.b Alphabaculovirus Obtained from Artaxa digramma

Duan

Wang

Zhang

et al. 2019

Viruses

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“…They were used as query in a BLAST search against the Ref Seq protein database from all organisms deposited in GenBank ( https://blast.ncbi.nlm.nih.gov/Blast.cgi ). ORFs that encoded at least 50 amino acids and had a minimal overlap with the neighboring ORFs were selected for further characterization [ 45 ]. We set the polyhedrin start codon as the genome start position.…”

Section: Methodsmentioning

confidence: 99%

“…To evaluate the intra-populational diversity, each sequence dataset of the Chinese isolates was mapped against its respective representative genome for the individual-based analysis, and the SNPs were identified using the above method. Based on the gene-function classifications of AcMNPV and other related baculoviruses [ 45 , 52 , 53 ], all the SNPs identified in ORFs were grouped into the following six functional groups: auxiliary, replication, transcriptional, oral infection, structural and unknown function. The genetic diversity was estimated using NSSP (non-synonymous substitutions per base pair) values [ 30 ], and the result was plotted using the R statistical programming language.…”

Section: Methodsmentioning

confidence: 99%

Genomic analysis of two Chinese isolates of hyphantria cunea nucleopolyhedrovirus reveals a novel species of alphabaculovirus that infects hyphantria cunea drury (lepidoptera: arctiidae)

Peng

Zhang²,

Lei

et al. 2022

BMC Genomics

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Background Baculoviruses 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. Results The 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. Conclusions The 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.

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“…Genomes of baculoviruses range from 80-180 kbp in size, encoding 90-180 genes. Approximately 37 genes are conserved across different genera of baculoviruses and have been assigned as "Core genes", involving in viral DNA replication and packaging, transcription, architecture and assembly (Herniou, Olszewski et al 2003, Herniou and Jehle 2007, van Oers and Vlak 2007, Miele, Garavaglia et al 2011, Wang, Hou et al 2018. Baculoviruses confer high degree of host specificity and insecticidal activity, thus various NPVs are being studied and developed as environmentalfriendly biological pesticides that can be effectively used for pest management in agriculture and forestry (Szewczyk, Rabalski et al 2009).…”

Section: Introductionmentioning

confidence: 99%

Molecular Evolution of Alphabaculovirus genomes: Evidence of Mutational bias and Natural selection

Mahapattanakul

Rajbhandari

Rodpothong

2021

Preprint

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Codon usage is a reflection of evolutionary adaptation to environmental pressure. The pattern of usage may be unique to species of viruses, genomes of the same species or genes within the same genome. Here we have analysed the overall nucleotide composition and the nucleotides at different codon positions in the genomes of 6 Alphabaculoviruses. Principle Component Analysis (PCA) based on Relative Synonymous Codon Usage (RSCU) of all Open Reading Frames (ORFs) was employed to investigate the pattern of the codon usage. The results suggest the Alphabaculovirus genomes, except that of Agrotis Ipsilon mNPV (AgipNPV), are predominantly under an influence of a neutral mutation that bias toward A/T. The majority of the ORFs, except those of the AgipNPV, cluster at the same location in the 2-dimensional PCA map with one prominent outlier that has been identified as a P6.9 gene. The six Alpha-baculovirus P6.9 genes have a high G/C content, dissimilar to the majority of the ORFs. The G/C content is found to be significantly high at the 2 nd codon position, suggesting the influence of natural selection and perhaps reflecting its functional conservation in DNA packaging as well as its evolutionary relation to Protamine.

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Genome analysis of a novel Group I alphabaculovirus obtained from Oxyplax ochracea

Cited by 10 publications

References 65 publications

Genome Analysis of a Novel Clade II.b Alphabaculovirus Obtained from Artaxa digramma

Genome Analysis of a Novel Clade II.b Alphabaculovirus Obtained from Artaxa digramma

Genomic analysis of two Chinese isolates of hyphantria cunea nucleopolyhedrovirus reveals a novel species of alphabaculovirus that infects hyphantria cunea drury (lepidoptera: arctiidae)

Molecular Evolution of Alphabaculovirus genomes: Evidence of Mutational bias and Natural selection

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