Mapping and polyhedrin gene analysis of the Epiphyas postvittana nucleopolyhedrovirus genome.

Hyink, Otto; Graves, Sally; Fairbairn, Fiona M; Ward, Vernon K.

doi:10.1099/0022-1317-79-11-2853

Cited by 30 publications

(47 citation statements)

References 29 publications

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“…Although the genomes of many of the viruses that fall into group I have not been completely sequenced, many are known to be variants of, or closely related to, those of AcMNPV and OpMNPV (see, e.g., reference 14). All the NPVs that have been completely sequenced, analyzed phylogenetically, and classified as group II viruses lack gp64 (5,13,14,43). However, although GVs have not been placed in group II, based on their lack of gp64, they also appear to be members of this category.…”

Section: Discussionmentioning

confidence: 99%

“…In addition to their presence in AcMNPV, homologs of gp64 have been found in a number of relatively closely related baculoviruses including OpMNPV (3), Choristoneura fumiferana MNPV (12), Anagrapha falcipera MNPV (6), Epiphyas postvittana NPV (14), Bombyx mori NPV (8), and Anticarsia gemmatalis MNPV (27). In all these viruses the predicted GP64 proteins are over 74% identical at the amino acid level.…”

Section: Discussionmentioning

confidence: 99%

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Identification of the Lymantria dispar Nucleopolyhedrovirus Envelope Fusion Protein Provides Evidence for a Phylogenetic Division of the Baculoviridae

Pearson

Groten

Rohrmann

2000

J Virol

144

132

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The complete genome sequences of a number of diverse members of the Baculoviridae including both nucleopolyhedroviruses (NPVs) and granuloviruses (GVs) revealed that they lack a homolog of GP64, the envelope fusion protein of the budded form of Autographa californica multinucleocapsid NPV (AcMNPV) and its close relatives. Computer-assisted analyses of the genome of one of these viruses, Lymantria dispar MNPV The Baculoviridae are a large family of occluded, rod-shaped viruses with circular, supercoiled, double-stranded DNA genomes of 100 to 180 kb depending on the virus strain. Two baculovirus genera have been described; the nucleopolyhedroviruses (NPVs) (34) have multiple virions present in large polyhedron-shaped occlusion bodies, whereas the granuloviruses (GVs) (42) normally display a single nucleocapsid embedded in a small granular occlusion body. NPVs are characterized by the production of two virion forms, or phenotypes (40). Occlusion-derived virions are found in occlusion bodies and initiate infection in midgut cells upon ingestion by susceptible hosts. In contrast, the budded virus (BV) form is not occluded, is produced early in infection, and spreads the infection within the infected insect prior to occlusion body production. Although the nucleocapsids for the two virion forms appear to have similar polypeptide contents, the compositions and structures of their envelopes appear to be distinct (7). BV infection by both Autographa californica multinucleocapsid NPV (AcMNPV) and Orgyia pseudotsugata MNPV (OpMNPV) has been investigated, and a glycoprotein called GP64 has been found to be associated with the BV form of both these viruses (3, 39, 41). GP64 is expressed both early and late in infection and is transported to and incorporated into the cell membrane. As nucleocapsids bud through the cell membrane and exit the cell, they become enveloped in the GP64-modified cell membrane. GP64 appears to be required for the spread of the infection to other cells and for the virus to exit from an infected cell (23,26,28). BV enters cells via an endocytic pathway, and, upon acidification of the endocytic vesicle, the structure of GP64 is altered and fusion of the viral and endosomal membranes occurs (17,20,22). This results in the release of the nucleocapsid into the cytoplasm. Surprisingly, GP64 is closely related to the envelope fusion protein of the Thogoto virus genus of the Orthomyxoviridae, which are minus strand RNA viruses (24,25).Recently the sequences of the 161-kb Lymantria dispar MNPV (LdMNPV) (18), 136-kb Spodoptera exigua MNPV (15), and 178-kb Xestia c-Nigrum GV (XcGV) (11) genomes have been reported. A striking feature of these genomes is the lack of an identifiable homolog to gp64. The fact that the life cycle of LdMNPV is similar to those of AcMNPV and OpMNPV suggested that it must express a different envelope fusion protein. Computer-assisted analyses of the LdMNPV genome identified a single 676-amino-acid product of LdMNPV open reading frame (ORF) 130 (ld130), which was predicted to have both a ...

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Identification of the Lymantria dispar Nucleopolyhedrovirus Envelope Fusion Protein Provides Evidence for a Phylogenetic Division of the Baculoviridae

Pearson

Groten

Rohrmann

2000

J Virol

144

132

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“…One of the unusual aspects of viral genomes is that they exhibit high sequence divergence [7,11]. Several works have attempted to infer viral phylogeny from their whole genomes [1,2,4,8,[12][13][14][15][16][17][18][19]. Among these studies of genome trees, the alignment-free methods proposed by Gao and Qi [1], Wu et al [2], Gao et al [12] and Stuart et al [16] seem to be sufficiently powerful to resolve the phylogeny of viruses at large evolutionary distance.…”

Section: Introductionmentioning

confidence: 99%

Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model

Chu

et al. 2010

BMC Evol Biol

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BackgroundThe vast sequence divergence among different virus groups has presented a great challenge to alignment-based analysis of virus phylogeny. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignment could not be directly applied to the whole-genome comparison and phylogenomic studies of viruses. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among the alignment-free methods, a dynamical language (DL) method proposed by our group has successfully been applied to the phylogenetic analysis of bacteria and chloroplast genomes.ResultsIn this paper, the DL method is used to analyze the whole-proteome phylogeny of 124 large dsDNA viruses and 30 parvoviruses, two data sets with large difference in genome size. The trees from our analyses are in good agreement to the latest classification of large dsDNA viruses and parvoviruses by the International Committee on Taxonomy of Viruses (ICTV).ConclusionsThe present method provides a new way for recovering the phylogeny of large dsDNA viruses and parvoviruses, and also some insights on the affiliation of a number of unclassified viruses. In comparison, some alignment-free methods such as the CV Tree method can be used for recovering the phylogeny of large dsDNA viruses, but they are not suitable for resolving the phylogeny of parvoviruses with a much smaller genome size.

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Section: Introductionmentioning

confidence: 99%

“…In the meantime there are several other attempts to infer viral phylogeny from their whole genomes [12,[20][21][22][23][24][25] to avoid the problem of gene rearrangement, gene loss, gene duplication and lateral gene transfer. However, some of them infer the majority consensus tree of the many trees of individual genes or use the combined sequences of many shared genes [12,21,22]. Some of them employ gene content [12,22,23] and gene order [12,22] method, but the former has to correct for the genome size effect [26] and the latter can be hindered by a lack of synteny conservation or the variation of the evolving rate of synteny between taxa [12,26].…”

Section: Introductionmentioning

confidence: 99%

Whole genome molecular phylogeny of large dsDNA viruses using composition vector method

Gao

2007

BMC Evol Biol

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Background: One important mechanism by which large DNA viruses increase their genome size is the addition of modules acquired from other viruses, host genomes or gene duplications. Phylogenetic analysis of large DNA viruses, especially using methods based on alignment, is often difficult due to the presence of horizontal gene transfer events. The recent composition vector approach, not sensitive to such events, is applied here to reconstruct the phylogeny of 124 large DNA viruses.

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Mapping and polyhedrin gene analysis of the Epiphyas postvittana nucleopolyhedrovirus genome.

Abstract: The light brown apple moth, Epiphyas postvittana, is a major insect pest of a variety of fruit crops grown in New Zealand and we are studying a nucleopolyhedrovirus, EppoNPV, isolated from this insect. Restriction endonuclease analysis of EppoNPV

Cited by 30 publications

References 29 publications

Identification of the Lymantria dispar Nucleopolyhedrovirus Envelope Fusion Protein Provides Evidence for a Phylogenetic Division of the Baculoviridae

Identification of the Lymantria dispar Nucleopolyhedrovirus Envelope Fusion Protein Provides Evidence for a Phylogenetic Division of the Baculoviridae

Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model

Whole genome molecular phylogeny of large dsDNA viruses using composition vector method

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