Next Generation Sequencing Technologies for Insect Virus Discovery

Liu, Sijun; Vijayendran, Diveena; Bonning, Bryony C.

doi:10.3390/v3101849

Cited by 118 publications

(98 citation statements)

References 90 publications

(94 reference statements)

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“…However, in the past decade, the development of high-throughput next-generation sequencing (NGS) technologies and bioinformatics applications has provided new opportunities for discovering viruses in many organisms, including humans (4-7), arthropods , and plants (30)(31)(32)(33)(34)(35)(36)(37)(38)(39)(40)(41)(42)(43)(44)(45). In addition to transcriptome sequencing (RNA-seq) (15,18,28), deep sequencing of small RNAs (sRNAs) and the subsequent assembly of the sRNAs have been proven to be promising approaches for the discovery of both RNA and DNA viruses in plant and insect hosts (9,41,42,(46)(47)(48)(49)(50).…”

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confidence: 99%

Diverse Array of New Viral Sequences Identified in Worldwide Populations of the Asian Citrus Psyllid (Diaphorina citri) Using Viral Metagenomics

Nouri

Salem

Nigg

et al. 2016

J Virol

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The Asian citrus psyllid, Diaphorina citri, is the natural vector of the causal agent of Huanglongbing (HLB), or citrus greening disease. Together; HLB and D. citri represent a major threat to world citrus production. As there is no cure for HLB, insect vector management is considered one strategy to help control the disease, and D. citri viruses might be useful. In this study, we used a metagenomic approach to analyze viral sequences associated with the global population of D. citri. By sequencing small RNAs and the transcriptome coupled with bioinformatics analysis, we showed that the virus-like sequences of D. citri are diverse. We identified novel viral sequences belonging to the picornavirus superfamily, the Reoviridae, Parvoviridae, and Bunyaviridae families, and an unclassified positive-sense single-stranded RNA virus. Moreover, a Wolbachia prophage-related sequence was identified. This is the first comprehensive survey to assess the viral community from worldwide populations of an agricultural insect pest. Our results provide valuable information on new putative viruses, some of which may have the potential to be used as biocontrol agents. IMPORTANCEInsects have the most species of all animals, and are hosts to, and vectors of, a great variety of known and unknown viruses. Some of these most likely have the potential to be important fundamental and/or practical resources. In this study, we used highthroughput next-generation sequencing (NGS) technology and bioinformatics analysis to identify putative viruses associated with Diaphorina citri, the Asian citrus psyllid. D. citri is the vector of the bacterium causing Huanglongbing (HLB), currently the most serious threat to citrus worldwide. Here, we report several novel viral sequences associated with D. citri. Viruses are the most abundant microbes on our planet (1) and are found in all types of organisms. Insects are the largest and most diverse taxonomic class among animals, representing perhaps half of known animals, with more than one million species recognized worldwide (2). Insects are known to be hosts to viruses belonging to various viral taxa, including the Baculoviridae, Parvoviridae, Flaviviridae, Ascoviridae, Togaviridae, Bunyaviridae, and Rhabdoviridae (3). However, the number of currently described viral species infecting insects is relatively low compared to the number of viruses that have been discovered among prokaryotes, plants, and vertebrates. Furthermore, most of the insect viruses described to date have been discovered because of their pathogenic effects on their insect hosts or because they are pathogens of humans, other vertebrates, or economically important plants. Traditional viral detection methods that require prior knowledge of genome sequences may not be suitable for the discovery of new viruses and, in particular, viruses with a high level of genetic diversity. However, in the past decade, the development of high-throughput next-generation sequencing (NGS) technologies and bioinformatics applications has provided ne...

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mentioning

confidence: 99%

Diverse Array of New Viral Sequences Identified in Worldwide Populations of the Asian Citrus Psyllid (Diaphorina citri) Using Viral Metagenomics

Nouri

Salem

Nigg

et al. 2016

J Virol

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“…The number of described iflaviruses is relatively low, probably due to the lack of severe effects produced by most of these viruses (Van Oers, 2008). Only recently, the application of massive parallel sequencing methods has revealed, through the occurrence of expression sequence tags (ESTs) with homology to iflaviruses, the existence of new members of this family that were previously undetected (Liu, Vijayendran & Bonning, 2011;Pascual et al, 2012;Oliveira et al, 2010). The Spodoptera exigua iflavirus 1 (SeIV1) was the first iflavirus described in S. exigua.…”

Section: Introductionmentioning

confidence: 99%

Iflavirus increases its infectivity and physical stability in association with baculovirus

2016

Draw Science

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Virus transmission and the prevalence of infection depend on multiple factors, including the interaction with other viral pathogens infecting the same host. In this study, active replication of an iflavirus, Spodoptera exigua iflavirus 1 (order Picornavirales) was observed in the offspring of insects that survived following inoculation with a pathogenic baculovirus, Spodoptera exigua multiple nucleopolyhedrovirus. Tracking the origin of the iflavirus suggested the association of this virus with the occlusion bodies of the baculovirus. Here we investigated the effect of this association on the stability and infectivity of both viruses. A reduction in baculovirus pathogenicity, without affecting its infectivity and productivity, was observed when associated with the iflavirus. In contrast, viral association increased the infectivity of the iflavirus and its resistance to ultraviolet radiation and high temperature, two of the main factors affecting virus stability in the field. In addition, electron microscopy analysis revealed the presence of particles resembling iflavirus virions inside the occlusion bodies of the baculovirus, suggesting the possible co-occlusion of both viruses. Results reported here are indicative of facultative phoresis of a virus and suggest that virus-virus interactions may be more common than currently recognized, and may be influential in the ecology of baculovirus and host populations and in consequence in the use of baculoviruses as biological insecticides.

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“…In particular, deep sequencing of small RNA families such as short interfering RNAs (siRNAs) can be used to identify and reconstruct any DNA or RNA virus genome and its microvariants with the help of bioinformatics tools [155,157]. Furthermore, the application of NGS can be extended to insect vectors for discovery and characterization of insect viruses [109].…”

Section: Disease Diagnostics and Monitoringmentioning

confidence: 99%

“…However, there are substantial shotgun metagenome sequencing studies that investigate microbial communities in soil and plants and other environmental samples [105,[107][108][109]. The challenges of analysis are being addressed gradually [55,104].…”

Section: Metagenomicsmentioning

confidence: 99%

Perspectives on the Application of Next-generation Sequencing to the Improvement of Africa’s Staple Food Crops

Gedil¹,

Ferguson²,

Girma³

et al. 2016

Next Generation Sequencing - Advances, Applications and Challenges

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The persistent challenge of insufficient food, unbalanced nutrition, and deteriorating natural resources in the most vulnerable nations, characterized by fast population growth, calls for utilization of innovative technologies to curb constraints of crop production. Enhancing genetic gain by using a multipronged approach that combines conventional and genomic technologies for the development of stress-tolerant varieties with high yield and nutritional quality is necessary. The advent of nextgeneration sequencing (NGS) technologies holds the potential to dramatically impact the crop improvement process. NGS enables whole-genome sequencing (WGS) and re-sequencing, transcriptome sequencing, metagenomics, as well as high-throughput genotyping, which can be applied for genome selection (GS). It can also be applied to diversity analysis, genetic and epigenetic characterization of germplasm and pathogen detection, identification, and elimination. High-throughput phenotyping, integrated data management, and decision support tools form the necessary supporting environment for effective utilization of genome sequence information. It is important that these opportunities for mainstreaming innovative breeding strategies, enabled by cutting-edge "Omics" technologies, are seized in Africa; however, several constraints must be addressed before the benefit of NGS can be fully realized. African breeding programs must have access to high-throughput genotyping facilities, capacity in the application of genome selection and marker-assisted breeding must be built and supported by capacity in genomic analysis and bioinformatics. This chapter demonstrates how interventions with NGS-enabled innovative strategies can be applied to increase genetic gain with insights from the Consortium of International

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Next Generation Sequencing Technologies for Insect Virus Discovery

Cited by 118 publications

References 90 publications

Diverse Array of New Viral Sequences Identified in Worldwide Populations of the Asian Citrus Psyllid (Diaphorina citri) Using Viral Metagenomics

Diverse Array of New Viral Sequences Identified in Worldwide Populations of the Asian Citrus Psyllid (Diaphorina citri) Using Viral Metagenomics

Iflavirus increases its infectivity and physical stability in association with baculovirus

Perspectives on the Application of Next-generation Sequencing to the Improvement of Africa’s Staple Food Crops

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