De novo assembly of honey bee RNA viral genomes by tapping into the innate insect antiviral response pathway

Fung, Elisabeth; Hill, Kelly; Hogendoorn, Katja; Glatz, Richard; Napier, Kathryn R.; Bellgard, M.; Barrero, Roberto A.

doi:10.1016/j.jip.2018.01.002

Cited by 15 publications

(11 citation statements)

References 63 publications

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“…Investigating viral reads generated by oligo (dT), RNAseq is not the only method to assess whether samples are harboring true infections [38,39]. Nonetheless, this method will reveal high read counts, full-genome coverage, and assembled full genomes, suggesting that DWV is replicating in at least some samples from each species.…”

Section: Discussionmentioning

confidence: 99%

RNAseq Analysis Reveals Virus Diversity within Hawaiian Apiary Insect Communities

Brettell

Schroeder

Martin

2019

Viruses

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Deformed wing virus (DWV) is the most abundant viral pathogen of honey bees and has been associated with large-scale colony losses. DWV and other bee-associated RNA viruses are generalists capable of infecting diverse hosts. Here, we used RNAseq analysis to test the hypothesis that due to the frequency of interactions, a range of apiary pest species would become infected with DWV and/or other honey bee-associated viruses. We confirmed that DWV-A was the most prevalent virus in the apiary, with genetically similar sequences circulating in the apiary pests, suggesting frequent inter-species transmission. In addition, different proportions of the three DWV master variants as indicated by BLAST analysis and genome coverage plots revealed interesting DWV-species groupings. We also observed that new genomic recombinants were formed by the DWV master variants, which are likely adapted to replicate in different host species. Species groupings also applied when considering other viruses, many of which were widespread in the apiaries. In social wasps, samples were grouped further by site, which potentially also influenced viral load. Thus, the apiary invertebrate community has the potential to act as reservoirs of honey bee-associated viruses, highlighting the importance of considering the wider community in the apiary when considering honey bee health.

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Section: Discussionmentioning

confidence: 99%

RNAseq Analysis Reveals Virus Diversity within Hawaiian Apiary Insect Communities

Brettell

Schroeder

Martin

2019

Viruses

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“…A pioneering work of Kreuze et al (2009) and the follow-up studies listed in Supplementary Tables S1 , S2 and discussed below have established that both RNA and DNA viruses as well as viral satellites and viroids can be identified and their genomes partially or fully reconstructed by deep sequencing and bioinformatic analysis of small RNA population (small RNA-ome) from an infected plant. Likewise, small RNA deep sequencing can be used for virus detection and assembly of viral genomes from fungi ( Vainio et al, 2015 ; Yaegashi et al, 2016 ; Donaire and Ayllón, 2017 ; Velasco et al, 2018 ) and from invertebrate animals ( Wu et al, 2010 ; Aguiar et al, 2015 ; Fung et al, 2018 ), including insect vectors of the plant viruses transmitted in a propagative manner ( Xu et al, 2012 ; Fletcher et al, 2016 ; de Haro et al, 2017 ). Such universality of the small RNA-omics approach for virus diagnostics is based on evolutionary conservation of the small RNA-generating RNA interference (RNAi) and gene silencing machinery that regulates gene expression and defends against invasive nucleic acids such as transposons, transgenes and viruses in most eukaryotes ( Ghildiyal and Zamore, 2009 ; Nayak et al, 2013 ; tenOever, 2016 ).…”

Section: Introductionmentioning

confidence: 99%

Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization

Pooggin

2018

Front. Microbiol.

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RNA interference (RNAi)-based antiviral defense generates small interfering RNAs that represent the entire genome sequences of both RNA and DNA viruses as well as viroids and viral satellites. Therefore, deep sequencing and bioinformatics analysis of small RNA population (small RNA-ome) allows not only for universal virus detection and genome reconstruction but also for complete virome reconstruction in mixed infections. Viral infections (like other stress factors) can also perturb the RNAi and gene silencing pathways regulating endogenous gene expression and repressing transposons and host genome-integrated endogenous viral elements which can potentially be released from the genome and contribute to disease. This review describes the application of small RNA-omics for virus detection, virome reconstruction and antiviral defense characterization in cultivated and non-cultivated plants. Reviewing available evidence from a large and ever growing number of studies of naturally or experimentally infected hosts revealed that all families of land plant viruses, their satellites and viroids spawn characteristic small RNAs which can be assembled into contigs of sufficient length for virus, satellite or viroid identification and for exhaustive reconstruction of complex viromes. Moreover, the small RNA size, polarity and hotspot profiles reflect virome interactions with the plant RNAi machinery and allow to distinguish between silent endogenous viral elements and their replicating episomal counterparts. Models for the biogenesis and functions of small interfering RNAs derived from all types of RNA and DNA viruses, satellites and viroids as well as endogenous viral elements are presented and discussed.

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“…With the development of RNAi, the applications of dsRNA delivery into honey bees and other insects have been increasingly improved ( Jarosch and Moritz, 2011 ; Jarosch et al, 2011 ; Hassani et al, 2012 ). Recently experimental evidence confirmed that RNAi immune response was triggered by Dicer-2 when honey bees were infected by SBV ( Fung et al, 2018 ).…”

Section: Introductionmentioning

confidence: 93%

Diverse Factors Affecting Efficiency of RNAi in Honey Bee Viruses

Yang

Zhao³

et al. 2018

Front. Genet.

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Infection and transmission of honey bee viruses pose a serious threat to the pollination services of crops and wild plants, which plays a vital role in agricultural economy and ecology. RNA interference (RNAi) is an effective defense mechanism against commonly occurring viral infections of animals and plants. However, recent studies indicate that the effects of RNAi on the honey bee can induce additional impacts and might not always be effective in suppressing the virus. Moreover, the RNAi responses differed in relation to the developmental stage of the insect and the target tissue used, even though the same method of delivery was used. These results indicate that further analysis and field experiments should be performed to characterize the varying effectiveness of RNAi-based methods for treating honey bee viral infections. In this review, we provide an overview of the current knowledge and the recent progress in RNAi-based anti-viral treatments for honey bees, focusing in particular highlight the role of the dsRNA-delivery method used and its effect on RNAi efficiency and demonstrate the potential practical value of this tool for controlling the virus. We conclude studying the gene function and disease control of honey bee by RNAi technology requires a complex consideration from physiology, genetics to environment.

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De novo assembly of honey bee RNA viral genomes by tapping into the innate insect antiviral response pathway

Cited by 15 publications

References 63 publications

RNAseq Analysis Reveals Virus Diversity within Hawaiian Apiary Insect Communities

RNAseq Analysis Reveals Virus Diversity within Hawaiian Apiary Insect Communities

Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization

Diverse Factors Affecting Efficiency of RNAi in Honey Bee Viruses

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