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

E. Fung; K. Hill; K. Hogendoorn; R.V. Glatz; K.R. Napier; M.I. Bellgard; R.A. Barrero

doi:10.1016/j.jip.2018.01.002

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

Journal article

Peer reviewed

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

E. Fung, K. Hill, K. Hogendoorn, R.V. Glatz, K.R. Napier, M.I. Bellgard and R.A. Barrero

Journal of Invertebrate Pathology, Vol.152, pp.38-47

2018

DOI: https://doi.org/10.1016/j.jip.2018.01.002

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Abstract

Bee pollination is critical for improving productivity of one third of all plants or plant products consumed by humans. The health of honey bees is in decline in many countries worldwide, and RNA viruses together with other biological, environmental and anthropogenic factors have been identified as the main causes. The rapid genetic variation of viruses represents a challenge for diagnosis. Thus, application of deep sequencing methods for detection and analysis of viruses has increased over the last years. In this study, we leverage from the innate Dicer-2 mediated antiviral response against viruses to reconstruct complete viral genomes using virus-derived small interfering RNAs (vsiRNAs). Symptomatic A. mellifera larvae collected from hives free of Colony Collapse Disorder (CCD) and the parasitic Varroa mite (Varroa destructor) were used to generate more than 107 million small RNA reads. We show that de novo assembly of insect viral sequences is less fragmented using only 22 nt long vsiRNAs rather than a combination of 21–22 nt small RNAs. Our results show that A. mellifera larvae activate the RNAi immune response in the presence of Sacbrood virus (SBV). We assembled three SBV genomes from three individual larvae from different hives in a single apiary, with 1–2% nucleotide sequence variability among them. We found 3–4% variability between SBV genomes generated in this study and earlier published Australian variants suggesting the presence of different SBV quasispecies within the country.

Details

Title: De novo assembly of honey bee RNA viral genomes by tapping into the innate insect antiviral response pathway
Authors/Creators: E. Fung (Author/Creator) - The University of Adelaide
K. Hill (Author/Creator) - South Australian Research and Development Institute
K. Hogendoorn (Author/Creator) - The University of Adelaide
R.V. Glatz (Author/Creator) - The University of Adelaide
K.R. Napier (Author/Creator) - Murdoch University
M.I. Bellgard (Author/Creator) - Murdoch University
R.A. Barrero (Author/Creator) - Murdoch University
Publication Details: Journal of Invertebrate Pathology, Vol.152, pp.38-47
Publisher: Elsevier
Identifiers: 991005544362807891
Copyright: © 2018 Published by Elsevier Inc.
Murdoch Affiliation: Centre for Comparative Genomics
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.32 Entomology; 3.32.750 Bee Ecology
Web Of Science research areas: Zoology
ESI research areas: Plant & Animal Science