Single nucleotide polymorphism (SNP) frequencies and distribution reveal complex genetic composition of seven novel natural isolates of Cydia pomonella granulovirus

Fan, Jiangbin; Wennmann, Jörg T.; Wang, Dun; Jehle, Johannes A.

doi:10.1016/j.virol.2019.11.016

Cited by 17 publications

(20 citation statements)

References 42 publications

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“…The terminology of homogenous, heterogeneous and mixed isolates was first introduced for the Cydia pomonella granulovirus (CpGV), a baculovirus of the genus Betabaculovirus [ 25 , 42 ]. Similar to BmNPV-My, the Mexican and Canadian isolates CpGV-M and CpGV-S, respectively, were identified as highly pure in their genotype composition, since variable SNP positions were missing [ 25 , 43 ]. The English isolate CpGV-E2 was identified as highly heterogeneous, since a clear demarcation of a certain genotype was not possible ([ 25 , 28 ], whereas other CpGV isolates appeared to be mixtures of rather pure genotypes [ 25 , 28 ].…”

Section: Discussionmentioning

confidence: 99%

“…Another interesting observation was the detection of possible regions of recombination between these two major genotypes at around 5 kb, as well as 80 to 95 kb, where a drop in the alternative nucleotide frequencies, and therefore an increase of the reference nucleotide frequency, was noted, respectively. This hint for genome recombination based on SNP analysis was also previously described for isolate CpGV-R5 in multiple genome regions, and for CpGV-WW [ 25 , 28 , 43 ]. Besides the mixed character of BmNPV-De and BmNPV-Ja, a certain level of an overall genetic heterogeneity was also observed, underlining the complex genetic diversity within these BmNPV isolates.…”

Section: Discussionmentioning

confidence: 99%

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Patterns in Genotype Composition of Indian Isolates of the Bombyx mori Nucleopolyhedrovirus and Bombyx mori Bidensovirus

Gani

Senger

Lokanath

et al. 2021

Viruses

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The mulberry silkworm, Bombyx mori (L.), is a model organism of lepidopteran insects with high economic importance. The viral diseases of the silkworm caused by Bombyx mori nucleopolyhedrovirus (BmNPV) and Bombyx mori bidensovirus (BmBDV) inflict huge economic losses and significantly impact the sericulture industry of India and other countries. To understand the distribution of Indian isolates of the BmNPV and to investigate their genetic composition, an in-depth population structure analysis was conducted using comprehensive and newly developed genomic analysis methods. The seven new Indian BmNPV isolates from Anantapur, Dehradun, Ghumarwin, Jammu, Kashmir, Mysore and Salem grouped in the BmNPV clade, and are most closely related to Autographa californica multiple nucleopolyhedrovirus and Rachiplusia ou multiple nucleopolyhedrovirus on the basis of gene sequencing and phylogenetic analyses of the partial polh, lef-8 and lef-9 gene fragments. The whole genome sequencing of three Indian BmNPV isolates from Mysore (-My), Jammu (-Ja) and Dehradun (-De) was conducted, and intra-isolate genetic variability was analyzed on the basis of variable SNP positions and the frequencies of alternative nucleotides. The results revealed that the BmNPV-De and BmNPV-Ja isolates are highly similar in their genotypic composition, whereas the population structure of BmNPV-My appeared rather pure and homogenous, with almost no or few genetic variations. The BmNPV-De and BmNPV-Ja samples further contained a significant amount of BmBDV belonging to the Bidnaviridae family. We elucidated the genotype composition within Indian BmNPV and BmBDV isolates, and the results presented have broad implications for our understanding of the genetic diversity and evolution of BmNPV and co-occurring BmBDV isolates.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Patterns in Genotype Composition of Indian Isolates of the Bombyx mori Nucleopolyhedrovirus and Bombyx mori Bidensovirus

Gani

Senger

Lokanath

et al. 2021

Viruses

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“…2 ). Finally, we surveyed 22 baculovirus sequencing data sets produced as part of other studies ( Gueli Alletti, Eigenbrod, et al 2017 ; Gueli Alletti, Sauer, et al 2017 ; Gueli Alletti et al 2018 ; Fan, Jehle, et al 2020 ; Fan, Wennmann, et al 2020 ), including one data set of the Agrotis segetum granulovirus (AgseGV) purified from the turnip moth ( Agrotis segetum ), six data sets of the Agrotis segetum nucleopolyhedrovirus B (AgseNPV-B) purified from a cell line of the black cutworm ( A. ipsilon ), and 15 data sets of the Cydia pomonella granulovirus (CpGV) purified from the codling moth ( Cydia pomonella ) ( fig. 2 ).…”

Section: Resultsmentioning

confidence: 99%

Monitoring Insect Transposable Elements in Large Double-Stranded DNA Viruses Reveals Host-to-Virus and Virus-to-Virus Transposition

Loiseau

Peccoud

Bouzar

et al. 2021

Molecular Biology and Evolution

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The mechanisms by which transposable elements (TEs) can be horizontally transferred between animals are unknown, but viruses are possible candidate vectors. Here, we surveyed the presence of host-derived TEs in viral genomes in 35 deep sequencing datasets produced from eleven host-virus systems, encompassing nine arthropod host species (five lepidopterans, two dipterans and two crustaceans) and six different double-stranded (ds) DNA viruses (four baculoviruses and two iridoviruses). We found evidence of viral-borne TEs in 14 datasets, with frequencies of viral genomes carrying a TE ranging from 0.01 to 26.33% for baculoviruses and from 0.45 to 7.36% for iridoviruses. The analysis of viral populations separated by a single replication cycle revealed that viral-borne TEs originating from an initial host species can be retrieved after viral replication in another host species, sometimes at higher frequencies. Furthermore, we detected a strong increase in the number of integrations in a viral population for a TE absent from the hosts’ genomes, indicating that this TE has undergone intense transposition within the viral population. Finally, we provide evidence that many TEs found integrated in viral genomes (15/41) have been horizontally transferred in insects. Altogether, our results indicate that multiple large dsDNA viruses have the capacity to shuttle TEs in insects and they underline the potential of viruses to act as vectors of horizontal transfer of TEs. Furthermore, the finding that TEs can transpose between viral genomes of a viral species sets viruses as possible new niches in which TEs can persist and evolve.

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“…The deciphering and differentiation of two or multiple dominant genotypes within a sequenced baculovirus sample, as it was the case for CpGV-0006, is not always possible, because some isolates have been found to be highly variable in their genotype composition [ 12 ]. This was also the case for CpGV-E2, whose composition in genotypes was described to be highly heterogenous and complex and whose SNPs do not allow a clear differentiation [ 12 ]. However, the strength and the aim of bacsnp and its related workflow is the evaluation of a sequenced baculovirus population’s heterogeneity that genotype population studies or the analysis of biological functions of relevant individual SNPs can build on.…”

Section: Discussionmentioning

confidence: 99%

“…Three isolates of Cydia pomonella granulovirus (CpGV) were used: CpGV isolates CpGV-M (genome group A) and CpGV-S (genome group E) [ 11 ] were obtained from the virus collection at the Julius Kühn-Institut (JKI), Institute for Biological Control, in Darmstadt. These virus stocks were used for previous bioassay studies [ 12 , 13 , 14 ] and sequencing analysis [ 5 , 11 ]. The isolate CpGV-0006 derived from the commercial product MadexMAX (Andermatt Biocontrol, Stahlermatten, Switzerland) [ 6 , 15 ].…”

Section: Methodsmentioning

confidence: 99%

Bacsnp: Using Single Nucleotide Polymorphism (SNP) Specificities and Frequencies to Identify Genotype Composition in Baculoviruses

Wennmann

Fan

Jehle

2020

Viruses

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Natural isolates of baculoviruses (as well as other dsDNA viruses) generally consist of homogenous or heterogenous populations of genotypes. The number and positions of single nucleotide polymorphisms (SNPs) from sequencing data are often used as suitable markers to study their genotypic composition. Identifying and assigning the specificities and frequencies of SNPs from high-throughput genome sequencing data can be very challenging, especially when comparing between several sequenced isolates or samples. In this study, the new tool “bacsnp”, written in R programming langue, was developed as a downstream process, enabling the detection of SNP specificities across several virus isolates. The basis of this analysis is the use of a common, closely related reference to which the sequencing reads of an isolate are mapped. Thereby, the specificities of SNPs are linked and their frequencies can be used to analyze the genetic composition across the sequenced isolate. Here, the downstream process and analysis of detected SNP positions is demonstrated on the example of three baculovirus isolates showing the fast and reliable detection of a mixed sequenced sample.

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Single nucleotide polymorphism (SNP) frequencies and distribution reveal complex genetic composition of seven novel natural isolates of Cydia pomonella granulovirus

Cited by 17 publications

References 42 publications

Patterns in Genotype Composition of Indian Isolates of the Bombyx mori Nucleopolyhedrovirus and Bombyx mori Bidensovirus

Patterns in Genotype Composition of Indian Isolates of the Bombyx mori Nucleopolyhedrovirus and Bombyx mori Bidensovirus

Monitoring Insect Transposable Elements in Large Double-Stranded DNA Viruses Reveals Host-to-Virus and Virus-to-Virus Transposition

Bacsnp: Using Single Nucleotide Polymorphism (SNP) Specificities and Frequencies to Identify Genotype Composition in Baculoviruses

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