Genomic diversity in a population of Spodoptera frugiperda nucleopolyhedrovirus

Masson, Tomás; Fabre, María Laura; Pidre, Matías L.; Niz, José María; Berretta, Marcelo Facundo; Romanowski, Vı́ctor; Ferrelli, María Leticia

doi:10.1016/j.meegid.2021.104749

Cited by 10 publications

(18 citation statements)

References 69 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Thus far, the genome description of BmNPV isolates was mainly restricted to consensus sequences that reflected the majority nucleotide composition of an isolate [ 9 , 40 ]. New approaches in baculovirus genomics have aimed to decipher the genetic composition of isolates and allowed the differentiation and bioinformatic presentation of complex genotype mixtures [ 25 , 26 , 37 , 41 ]. Here, this approach was successfully transferred to an alphabaculovirus in the example of BmNPV.…”

Section: Discussionmentioning

confidence: 99%

“…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. The complexity of alphabaculovirus genome populations within single isolates was further reflected by sequencing approaches on AcMNPV-WP10, as well as an Argentinian isolate of the Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV-ARG-M) [ 24 , 26 ]. For SfMNPV-ARG-M, a number of 704 highly variable SNP positions were detected [ 26 ], describing this isolate as heterogeneous without a differentiation of major or minor genotypes.…”

Section: Discussionmentioning

confidence: 99%

“…The complexity of alphabaculovirus genome populations within single isolates was further reflected by sequencing approaches on AcMNPV-WP10, as well as an Argentinian isolate of the Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV-ARG-M) [ 24 , 26 ]. For SfMNPV-ARG-M, a number of 704 highly variable SNP positions were detected [ 26 ], describing this isolate as heterogeneous without a differentiation of major or minor genotypes. For AcMNPV-WP10, an ultra-deep sequencing approach was followed, where an average read depth of >124 k was achieved, which resulted in the detection of 3242 SNP positions, most of which with nucleotide frequencies ranging between 10% < ƒ < 50% [ 24 ].…”

Section: Discussionmentioning

confidence: 99%

“…Thus far, whole genome analysis of BmNPV/BomaNPV and BmBDV allowed the establishment of consensus genomes of these viruses that reflect the entity of the sequenced virus populations. Recent analyses focusing on the population structure of baculoviruses showed that the genotypic composition of single virus isolates can be rather complex [ 24 , 25 , 26 ]. Genetic diversity was determined by detecting single nucleotide polymorphisms (SNPs) and the frequencies of alternative occurring nucleotide variants in these positions, which allowed for the differentiation of homogeneous, heterogeneous and mixed isolates [ 24 , 25 , 26 ].…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

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

Gani

Senger

Lokanath

et al. 2021

Viruses

View full text Add to dashboard Cite

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.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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

Gani

Senger

Lokanath

et al. 2021

Viruses

View full text Add to dashboard Cite

show abstract

“…One of the main reasons for the differences in virulence is the variations in some of the genes that make up the genomes of the different isolates [78,121,122]. Aside from the core genes that most baculoviruses share, variations arising from insertions and deletions and single nucleotide polymorphisms in parts of the genome have been reported among different isolates [76,123,124]. In addition, the virulence of SfMNPV isolates also depends on the S. frugiperda strains present in the field.…”

Section: Sfmnpv: the Most Promising Viral Candidate For The Biological Control Of Fawmentioning

confidence: 99%

Viruses of the Fall Armyworm Spodoptera frugiperda: A Review with Prospects for Biological Control

Hussain

Wennmann

Goergen

et al. 2021

Viruses

View full text Add to dashboard Cite

The fall armyworm (FAW), Spodoptera frugiperda, is a native pest species in the Western hemisphere. Since it was first reported in Africa in 2016, FAW has spread throughout the African continent and is now also present in several countries in Asia as well as Australia. The invasion of FAW in these areas has led to a high yield reduction in crops, leading to huge economic losses. FAW management options in the newly invaded areas are limited and mainly rely on the use of synthetic pesticides. Since there is a risk of resistance development against pesticides in addition to the negative environmental and human health impacts, other effective, sustainable, and cost-efficient control alternatives are desired. Insect pathogenic viruses fulfil these criteria as they are usually effective and highly host-specific with no significant harmful effect on beneficial insects and non-target organisms. In this review, we discuss all viruses known from FAW and their potential to be used for biological control. We specifically focus on baculoviruses and describe the recent advancements in the use of baculoviruses for biological control in the native geographic origin of FAW, and their potential use in the newly invaded areas. Finally, we identify current knowledge gaps and suggest new avenues for productive research on the use of viruses as a biopesticide against FAW.

show abstract

Haplotype determination of the Bombyx mori nucleopolyhedrovirus by Nanopore sequencing and linkage of single nucleotide variants

Wennmann,

Lim,

Senger

et al. 2024

Journal of General Virology

View full text Add to dashboard Cite

Naturally occurring isolates of baculoviruses, such as the Bombyx mori nucleopolyhedrovirus (BmNPV), usually consist of numerous genetically different haplotypes. Deciphering the different haplotypes of such isolates is hampered by the large size of the dsDNA genome, as well as the short read length of next generation sequencing (NGS) techniques that are widely applied for baculovirus isolate characterization. In this study, we addressed this challenge by combining the accuracy of NGS to determine single nucleotide variants (SNVs) as genetic markers with the long read length of Nanopore sequencing technique. This hybrid approach allowed the comprehensive analysis of genetically homogeneous and heterogeneous isolates of BmNPV. Specifically, this allowed the identification of two putative major haplotypes in the heterogeneous isolate BmNPV-Ja by SNV position linkage. SNV positions, which were determined based on NGS data, were linked by the long Nanopore reads in a Position Weight Matrix. Using a modified Expectation–Maximization algorithm, the Nanopore reads were assigned according to the occurrence of variable SNV positions by machine learning. The cohorts of reads were de novo assembled, which led to the identification of BmNPV haplotypes. The method demonstrated the strength of the combined approach of short- and long-read sequencing techniques to decipher the genetic diversity of baculovirus isolates.

show abstract

Genomic diversity in a population of Spodoptera frugiperda nucleopolyhedrovirus

Cited by 10 publications

References 69 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

Viruses of the Fall Armyworm Spodoptera frugiperda: A Review with Prospects for Biological Control

Haplotype determination of the Bombyx mori nucleopolyhedrovirus by Nanopore sequencing and linkage of single nucleotide variants

Contact Info

Product

Resources

About