scholarly journals Gene organization and sequencing of the Choristoneura fumiferana defective nucleopolyhedrovirus genome

2005 ◽  
Vol 86 (4) ◽  
pp. 945-961 ◽  
Author(s):  
Hilary A. M. Lauzon ◽  
Peter B. Jamieson ◽  
Peter J. Krell ◽  
Basil M. Arif
Keyword(s):  
Choristoneura Fumiferana ◽  
Amino Acid Identity ◽  
Gene Organization ◽  
Open Reading Frames ◽  
Anticarsia Gemmatalis ◽  
Orgyia Pseudotsugata ◽  
Eastern Spruce Budworm ◽  
Group I ◽  
Average Amino Acid Identity ◽  
Late Expression

Two distinct nucleopolyhedrovirus species of the eastern spruce budworm, Choristoneura fumiferana, exist in a symbiont-like relationship. C. fumiferana defective nucleopolyhedrovirus (CfDEFNPV) only infects C. fumiferana larvae per os in the presence of C. fumiferana nucleopolyhedrovirus Ireland strain (CfMNPV), but is infective when injected into the haemolymph. CfDEFNPV synergizes CfMNPV in per os infections and CfMNPV is always the predominant progeny. This study was undertaken to report the genomic makeup and organization of CfDEFNPV in an attempt to identify its defect and understand its synergistic role. The genome was mapped, sequenced, characterized and compared to other baculoviruses. The CfDEFNPV genome was 131 160 nt long with 149 putative open reading frames (ORFs) and a G+C content of 45·8 mol%. Homologues of all 62 conserved lepidopteran baculovirus genes were found including those implicated in per os infectivity, p74, per os infectivity factor (pif) and pif-2. Although no obvious deletions were observed to explain the defect, two ORFs, Cfdef79 and Cfdef99 (inhibitor of apoptosis-4), contained potential deletions. Cfdef50 (late expression factor-10)/Cfdef51 (vp1054) and Cfdef76/Cfdef77 (telokin-like protein) had large overlaps and a potential homologue to ac105/he65 was split. Four baculovirus repeat ORFs were present, as were two unique genes, but no enhancins were identified. CfDEFNPV contained 13 homologous regions, each with one to five palindromes. Comparison with fully sequenced baculovirus genomes identified CfDEFNPV as a group I NPV with the closest average amino acid identity to Epiphyas postvittana NPV, followed by Orgyia pseudotsugata MNPV and CfMNPV, with its closest matches being to individual Anticarsia gemmatalis MNPV gene sequences.

scholarly journals Genome of the most widely used viral biopesticide: Anticarsia gemmatalis multiple nucleopolyhedrovirus

2006 ◽  
Vol 87 (11) ◽  
pp. 3233-3250 ◽  
Author(s):  
Juliana Velasco de Castro Oliveira ◽  
José Luiz Caldas Wolff ◽  
Alejandra Garcia-Maruniak ◽  
Bergmann Morais Ribeiro ◽  
Maria Elita Batista de Castro ◽  
...  
Keyword(s):  
Choristoneura Fumiferana ◽  
Heliothis Zea ◽  
Control Programme ◽  
Open Reading Frames ◽  
Anticarsia Gemmatalis ◽  
Coding Regions ◽  
Orgyia Pseudotsugata ◽  
Multiple Nucleopolyhedrovirus ◽  
Group I ◽  
Overlapping Open Reading Frames

The genome of Anticarsia gemmatalis multiple nucleopolyhedrovirus isolate 2D (AgMNPV-2D), which is the most extensively used virus pesticide in the world, was completely sequenced and shown to have 132 239 bp (G+C content 44.5 mol%) and to be capable of encoding 152 non-overlapping open reading frames (ORFs). Three ORFs were unique to AgMNPV-2D, one of which (ag31) had similarity to eukaryotic poly(ADP-ribose) polymerases. The lack of chiA and v-cath may explain some of the success and growth of the AgMNPV biological control programme, as it may explain the high recovery of polyhedra sequestered inside dead larvae in the field, which are collected and used for further application as biological pesticides in soybean fields. The genome organization was similar to that of the Choristoneura fumiferana defective MNPV (CfDefNPV). Most of the variation between the two genomes took place near highly repetitive regions, which were also closely associated with bro-coding regions. The separation of the NPVs into groups I and II was supported by: (i) a phenogram of the complete genomes of 28 baculovirus and Heliothis zea virus 1, (ii) the most parsimonious reconstruction of gene content along the phenograms and (iii) comparisons of genomic features. Moreover, these data also reinforced the notion that group I of the NPVs can be split further into the AgMNPV lineage (AgMNPV, CfDefNPV, Epiphyas postvittana NPV, Orgyia pseudotsugata MNPV and C. fumiferana MNPV), sharing eight defining genes, and the Autographa californica MNPV (AcMNPV) lineage (AcMNPV, Rachiplusia ou NPV and Bombyx mori NPV), sharing nine defining genes.

scholarly journals Analysis of the Choristoneura fumiferana nucleopolyhedrovirus genome

2005 ◽  
Vol 86 (4) ◽  
pp. 929-943 ◽  
Author(s):  
Jondavid G. de Jong ◽  
Hilary A. M. Lauzon ◽  
Cliff Dominy ◽  
Arkadi Poloumienko ◽  
Eric B. Carstens ◽  
...  
Keyword(s):  
Amino Acid ◽  
Choristoneura Fumiferana ◽  
Amino Acid Identity ◽  
Open Reading Frames ◽  
Acid Identity ◽  
Orgyia Pseudotsugata ◽  
Double Stranded Dna ◽  
Enhancing Factor ◽  
Group I ◽  
Reading Frames

The double-stranded DNA genome of Choristoneura fumiferana nucleopolyhedrovirus (CfMNPV) was sequenced and analysed in the context of other group I nucleopolyhedroviruses (NPVs). The genome consists of 129 593 bp with a G+C content of 50·1 mol%. A total of 146 open reading frames (ORFs) of greater than 150 bp, and with no or minimal overlap were identified. In addition, five homologous regions were identified containing 7–10 repeats of a 36 bp imperfect palindromic core. Comparison with other completely sequenced baculovirus genomes revealed that 139 of the CfMNPV ORFs have homologues in at least one other baculovirus and seven ORFs are unique to CfMNPV. Of the 117 CfMNPV ORFs common to all group I NPVs, 12 are exclusive to group I NPVs. Overall, CfMNPV is most similar to Orgyia pseudotsugata MNPV based on gene content, arrangement and overall amino acid identity. Unlike other group I baculoviruses, however, CfMNPV encodes a viral enhancing factor (vef) and has two copies of p26.

scholarly journals Gene organization and complete sequence of the Hyphantria cunea nucleopolyhedrovirus genome

2006 ◽  
Vol 87 (9) ◽  
pp. 2549-2562 ◽  
Author(s):  
Motoko Ikeda ◽  
Masamitsu Shikata ◽  
Noriko Shirata ◽  
Sudawan Chaeychomsri ◽  
Michihiro Kobayashi
Keyword(s):  
Choristoneura Fumiferana ◽  
Complete Sequence ◽  
Gene Organization ◽  
Open Reading Frames ◽  
Whole Genome Sequence ◽  
Hyphantria Cunea ◽  
Orgyia Pseudotsugata ◽  
Group I ◽  
Close Phylogenetic Relationship ◽  
Autographa Californica Mnpv

The whole-genome sequence of the Hyphantria cunea nucleopolyhedrovirus (HycuNPV) was analysed. The entire nucleotide sequence of the HycuNPV genome was 132 959 bp long, with a G+C content of 45.1 mol%. A total of 148 open reading frames (ORFs) consisting of more than 50 aa were encoded by the genome. HycuNPV shares more than 122 ORFs with other lepidopteran group I NPVs, including Autographa californica MNPV, Bombyx mori NPV, Choristoneura fumiferana MNPV (CfMNPV), Choristoneura fumiferana defective NPV, Epiphyas postvittana MNPV and Orgyia pseudotsugata MNPV (OpMNPV). Six ORFs are identified as being unique to HycuNPV. Most of the HycuNPV ORFs showed higher similarity to CfMNPV and OpMNPV ORFs than to those of the other group I NPVs. HycuNPV encodes two conotoxin-like homologues (ctls), which are observed only in OpMNPV in group I NPVs. HycuNPV encodes three inhibitors of apoptosis (iaps), hycu-iap-1, hycu-iap-2 and hycu-iap-3, a feature that it shares only with CfMNPV. In addition, six homologous regions (hrs) are identified in the HycuNPV genome. These hrs are located in regions similar to those of the OpMNPV hrs, but different from most of the CfMNPV hrs. Based on the close phylogenetic relationship and conservation of group I NPV-specific genes, such as gp64, ie-2 and ptp-1, it is concluded that HycuNPV belongs to the group I NPVs and is most similar to CfMNPV or OpMNPV.

scholarly journals Sequence analysis of the Choristoneura occidentalis granulovirus genome

2006 ◽  
Vol 87 (7) ◽  
pp. 1917-1933 ◽  
Author(s):  
Shannon R. Escasa ◽  
Hilary A. M. Lauzon ◽  
Amanda C. Mathur ◽  
Peter J. Krell ◽  
Basil M. Arif
Keyword(s):  
Amino Acid ◽  
Choristoneura Fumiferana ◽  
Cydia Pomonella ◽  
Amino Acid Identity ◽  
Open Reading Frames ◽  
Homologous Region ◽  
Choristoneura Occidentalis ◽  
Homologous Proteins ◽  
Group I ◽  
Apoptosis Inhibitor

The genome of the Choristoneura occidentalis granulovirus (ChocGV) isolated from the western spruce budworm, Choristoneura occidentalis, was sequenced completely. It was 104 710 bp long, with a 67.3 % A+T content and contained 116 potential open reading frames (ORFs) covering 88.4 % of the genome. Of these, 29 ORFs were conserved in all fully sequenced baculovirus genomes, 30 were GV-specific, 53 were present in some nucleopolyhedroviruses (NPVs) and/or GVs, three were common to ChocGV and Choristoneura fumiferana GV (ChfuGV) and one was so far unique. To date, ChocGV is the only GV identified that contains a homologue of the apoptosis inhibitor protein P35/P49, present in some group I NPVs. It is also the first GV without a Xestia c-nigrum GV ORF 26 homologue. Five homologous regions (hrs)/repeat regions, lacking typical NPV hr palindromes were identified. ChocGV hrs were similar to each other but not to other GV hrs. A 1.8 kb repeat region with a high A+T content (81 %) and multiple repeats of 21–210 bp was found between choc36 and 37. This area resembled the non-homologous region origin of DNA replication (non-hr ori) identified in Cryptophlebia leucotreta GV (CrleGV) and Cydia pomonella GV (CpGV). Based on the mean amino acid identities of homologous proteins, ChocGV was closest to fully sequenced genomes CpGV (52.3 %) and CrleGV (52.1 %). The closest amino acid identity was to individual ORFs from the partially sequenced ChfuGV genome (97.2 % in 38 ORFs). Phylogenetic analysis placed ChocGV in a clade with CrleGV and CpGV.

scholarly journals Genome sequence of Chrysodeixis chalcites nucleopolyhedrovirus, a baculovirus with two DNA photolyase genes

2005 ◽  
Vol 86 (7) ◽  
pp. 2069-2080 ◽  
Author(s):  
Monique M. van Oers ◽  
Marleen H. C. Abma-Henkens ◽  
Elisabeth A. Herniou ◽  
Joost C. W. de Groot ◽  
Sander Peters ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Evolutionary Relationship ◽  
Ring Finger ◽  
Amino Acid Identity ◽  
Open Reading Frames ◽  
Pyrimidine Dimer ◽  
Nuclear Antigen ◽  
Dna Photolyase ◽  
Group I ◽  
Group Ii

The complete genome sequence of a single nucleocapsid nucleopolyhedrovirus recently isolated from Chrysodeixis chalcites (ChchNPV) was determined. The viral genome has a size of 149 622 bp and an overall G+C content of 39·1 mol%. The sequence contains 151 predicted open reading frames (ORFs) with a minimal size of 50 codons. The similarity of these ORFs with those of other completely sequenced baculoviruses was calculated using a newly developed database, named gecco. Phylogenetic analysis of the whole genome confirmed the evolutionary relationship of ChchNPV with group II NPVs, as did the absence of the NPV group I-specific gp64 gene. It is the first group II NPV to encode proliferating cell nuclear antigen. Most noteworthy is the presence of two ORFs encoding a class II cyclobutane pyrimidine dimer DNA photolyase. These two ORFs share only 45 % amino acid identity and have different promoter motifs. Twenty-two additional unique baculovirus genes were identified, including a gene encoding a novel putative RING finger protein with a possible homologue in poxviruses.

scholarly journals Two Phages, phiIPLA-RODI and phiIPLA-C1C, Lyse Mono- and Dual-Species Staphylococcal Biofilms

2015 ◽  
Vol 81 (10) ◽  
pp. 3336-3348 ◽  
Author(s):  
Diana Gutiérrez ◽  
Dieter Vandenheuvel ◽  
Beatriz Martínez ◽  
Ana Rodríguez ◽  
Rob Lavigne ◽  
...  
Keyword(s):  
Phage Therapy ◽  
Gene Organization ◽  
Open Reading Frames ◽  
Group I Introns ◽  
High Similarity ◽  
Content Type ◽  
Staphylococcal Infections ◽  
Group I ◽  
Genes Encoding ◽  
Reading Frames

ABSTRACTPhage therapy is a promising option for fighting against staphylococcal infections. Two lytic phages, vB_SauM_phiIPLA-RODI (phiIPLA-RODI) and vB_SepM_phiIPLA-C1C (phiIPLA-C1C), belonging to theMyoviridaefamily and exhibiting wide host ranges, were characterized in this study. The complete genome sequences comprised 142,348 bp and 140,961 bp and contained 213 and 203 open reading frames, respectively. The gene organization was typical ofSpounavirinaemembers, with long direct terminal repeats (LTRs), genes grouped into modules not clearly separated from each other, and several group I introns. In addition, four genes encoding tRNAs were identified in phiIPLA-RODI. Comparative DNA sequence analysis showed high similarities with two phages, GH15 and 676Z, belonging to theTwort-like virusgenus (nucleotide identities of >84%); for phiIPLA-C1C, a high similarity with phage phiIBB-SEP1 was observed (identity of 80%). Challenge assays of phages phiIPLA-RODI and phiIPLA-C1C against planktonic staphylococcal cells confirmed their lytic ability, as they were able to remove 5 log units in 8 h. Exposure of biofilms to phages phiIPLA-RODI and phiIPLA-C1C reduced the amount of adhered bacteria to about 2 log units in both monospecies and dual-species biofilms, but phiIPLA-RODI turned out to be as effective as the mixture of both phages. Moreover, the frequencies of bacteriophage-insensitive mutants (BIMs) ofStaphylococcus aureusandS. epidermidiswith resistance to phiIPLA-RODI and phiIPLA-C1C were low, at 4.05 × 10−7± 2.34 × 10−9and 1.1 × 10−7± 2.08 × 10−9, respectively. Overall, a generally reduced fitness in the absence of phages was observed for BIMs, which showed a restored phage-sensitive phenotype in a few generations. These results confirm that lytic bacteriophages can be efficient biofilm-disrupting agents, supporting their potential as antimicrobials against staphylococcal infections.

scholarly journals The sequence of the Helicoverpa armigera single nucleocapsid nucleopolyhedrovirus genome

2001 ◽  
Vol 82 (1) ◽  
pp. 241-257 ◽  
Author(s):  
Xinwen Chen ◽  
Wilfred F. J. IJkel ◽  
Renato Tarchini ◽  
Xiulian Sun ◽  
Hans Sandbrink ◽  
...  
Keyword(s):  
Helicoverpa Armigera ◽  
Amino Acid Identity ◽  
Computer Assisted ◽  
Structural Genomic ◽  
Orgyia Pseudotsugata ◽  
Group I ◽  
Helicoverpa Armígera ◽  
Group Ii ◽  
Budded Virus ◽  
Assisted Analysis

The nucleotide sequence of the Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus (HaSNPV) DNA genome was determined and analysed. The circular genome encompasses 131403 bp, has a G+C content of 39·1 mol% and contains five homologous regions with a unique pattern of repeats. Computer-assisted analysis revealed 135 putative ORFs of 150 nt or larger; 100 ORFs have homologues in Autographa californica multicapsid NPV (AcMNPV) and a further 15 ORFs have homologues in other baculoviruses such as Lymantria dispar MNPV (LdMNPV), Spodoptera exigua MNPV (SeMNPV) and Xestia c-nigrum granulovirus (XcGV). Twenty ORFs are unique to HaSNPV without homologues in GenBank. Among the six previously sequenced baculoviruses, AcMNPV, Bombyx mori NPV (BmNPV), Orgyia pseudotsugata MNPV (OpMNPV), SeMNPV, LdMNPV and XcGV, 65 ORFs are conserved and hence are considered as core baculovirus genes. The mean overall amino acid identity of HaSNPV ORFs was the highest with SeMNPV and LdMNPV homologues. Other than three ‘baculovirus repeat ORFs’ (bro) and two ‘inhibitor of apoptosis’ (iap) genes, no duplicated ORFs were found. A putative ORF showing similarity to poly(ADP-ribose) glycohydrolases (parg) was newly identified. The HaSNPV genome lacks a homologue of the major budded virus (BV) glycoprotein gene, gp64, of AcMNPV, BmNPV and OpMNPV. Instead, a homologue of SeMNPV ORF8, encoding the major BV envelope protein, has been identified. GeneParityPlot analysis suggests that HaSNPV, SeMNPV and LdMNPV (group II) have structural genomic features in common and are distinct from the group I NPVs and from the granuloviruses. Cluster alignment between group I and group II baculoviruses suggests that they have a common ancestor.

scholarly journals A Nymphalid-Infecting Group I Alphabaculovirus Isolated from the Major Passion Fruit Caterpillar Pest Dione juno juno (Lepidoptera: Nymphalidae)

Viruses ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 602 ◽  
Author(s):  
Bergmann Morais Ribeiro ◽  
Ethiane Rozo dos Santos ◽  
Luana Beló Trentin ◽  
Leonardo Assis da Silva ◽  
Fernando Lucas de Melo ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Insect Pests ◽  
Open Reading Frames ◽  
Thymidylate Kinase ◽  
Orgyia Pseudotsugata ◽  
Group I ◽  
Reading Frames ◽  
Core Genes

Baculoviruses are capable of infecting a wide diversity of insect pests. In the 1990s, the Dione juno nucleopolyhedrovirus (DijuNPV) was isolated from larvae of the major passionfruit defoliator pest Dione juno juno (Nymphalidae) and described at ultrastructural and pathological levels. In this study, the complete genome sequence of DijuNPV was determined and analyzed. The circular genome presents 122,075 bp with a G + C content of 50.9%. DijuNPV is the first alphabaculovirus completely sequenced that was isolated from a nymphalid host and may represent a divergent species. It appeared closely related to Orgyia pseudotsugata multiple nucleopolyhedrovirus (OpMNPV) and other Choristoneura-isolated group I alphabaculoviruses. We annotated 153 open reading frames (ORFs), including a set of 38 core genes, 26 ORFs identified as present in lepidopteran baculoviruses, 17 ORFs unique in baculovirus, and several auxiliary genes (e.g., bro, cathepsin, chitinase, iap-1, iap-2, and thymidylate kinase). The thymidylate kinase (tmk) gene was present fused to a dUTPase (dut) gene in other baculovirus genomes. DijuNPV likely lost the dut portion together with the iap-3 homolog. Overall, the genome sequencing of novel alphabaculoviruses enables a wide understanding of baculovirus evolution.

scholarly journals Whole genome analysis of the Epiphyas postvittana nucleopolyhedrovirus

2002 ◽  
Vol 83 (4) ◽  
pp. 957-971 ◽  
Author(s):  
Otto Hyink ◽  
Ross A. Dellow ◽  
Michael J. Olsen ◽  
Katherine M. B. Caradoc-Davies ◽  
Kylie Drake ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Open Reading Frames ◽  
Data Sets ◽  
Epiphyas Postvittana ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Orgyia Pseudotsugata ◽  
Group I ◽  
Intergenic Regions ◽  
Reading Frames

The nucleotide sequence of the Epiphyas postvittana nucleopolyhedrovirus (EppoMNPV) genome has been determined and analysed. The circular dsDNA genome contains 118584 bp, making it the smallest group I NPV sequenced to date. The genome has a G+C content of 40·7% and encodes 136 predicted open reading frames (ORFs), five homologous repeat regions and one unique repeat region. Of the genome, 92·9% encodes predicted ORFs and 2·2% is in repeat regions; the remaining 4·9% of the genome comprises nonrepeat intergenic regions. EppoMNPV encodes homologues of 126 Orgyia pseudotsugata MNPV (OpMNPV) ORFs and 120 Autographa californica MNPV ORFs, with average identities of 64·7 and 53·5%, respectively. Between the four sequenced group I NPVs, 117 ORFs are conserved, whereas 86 ORFs are conserved between all fully sequenced NPVs. A total of 62 ORFs is present in all baculoviruses sequenced to date, with EppoMNPV lacking a homologue of the superoxide dismutase (sod) gene, which has been found in all other fully sequenced baculoviruses. Whole genome phylogenetic analyses of the ten fully sequenced baculoviruses using the sequences of the 62 shared genes, gene content and gene order data sets confirmed that EppoMNPV clusters tightly with OpMNPV in the group I NPVs. The main variation between EppoMNPV and OpMNPV occurs where extra clusters of genes are present in OpMNPV, with sod occurring in one such cluster. EppoMNPV encodes one truncated baculovirus repeated ORF (bro) gene. The only repeated ORFs are the four iap genes. Eight, randomly distributed, unique ORFs were identified on EppoMNPV, none of which show any significant homology to genes in GenBank.

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