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Open Access Highly Accessed Research article

Population-genomic variation within RNA viruses of the Western honey bee, Apis mellifera, inferred from deep sequencing

Robert Scott Cornman15*, Humberto Boncristiani16, Benjamin Dainat12, Yanping Chen1, Dennis vanEngelsdorp3, Daniel Weaver4 and Jay D Evans1

Author Affiliations

1 Bee Research Laboratory, USDA-ARS, Beltsville, MD, 20705, USA

2 Swiss Bee Research Centre, Agroscope-Liebefeld-Posieux Research Station, Bern, 3003, Switzerland

3 Department of Entomology, University of Maryland, College Park, MD, 20742, USA

4 Bee Power, LP, Navasota, TX, 77868, USA

5 Current address: Leetown Science Center, USGS, Leetown, Kearneysville, WV, 23540, USA

6 Current address: Department of Biology, University of North Carolina, Greensboro, NC, 27402, USA

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BMC Genomics 2013, 14:154  doi:10.1186/1471-2164-14-154

Published: 7 March 2013

Abstract

Background

Deep sequencing of viruses isolated from infected hosts is an efficient way to measure population-genetic variation and can reveal patterns of dispersal and natural selection. In this study, we mined existing Illumina sequence reads to investigate single-nucleotide polymorphisms (SNPs) within two RNA viruses of the Western honey bee (Apis mellifera), deformed wing virus (DWV) and Israel acute paralysis virus (IAPV). All viral RNA was extracted from North American samples of honey bees or, in one case, the ectoparasitic mite Varroa destructor.

Results

Coverage depth was generally lower for IAPV than DWV, and marked gaps in coverage occurred in several narrow regions (< 50 bp) of IAPV. These coverage gaps occurred across sequencing runs and were virtually unchanged when reads were re-mapped with greater permissiveness (up to 8% divergence), suggesting a recurrent sequencing artifact rather than strain divergence. Consensus sequences of DWV for each sample showed little phylogenetic divergence, low nucleotide diversity, and strongly negative values of Fu and Li’s D statistic, suggesting a recent population bottleneck and/or purifying selection. The Kakugo strain of DWV fell outside of all other DWV sequences at 100% bootstrap support. IAPV consensus sequences supported the existence of multiple clades as had been previously reported, and Fu and Li’s D was closer to neutral expectation overall, although a sliding-window analysis identified a significantly positive D within the protease region, suggesting selection maintains diversity in that region. Within-sample mean diversity was comparable between the two viruses on average, although for both viruses there was substantial variation among samples in mean diversity at third codon positions and in the number of high-diversity sites. FST values were bimodal for DWV, likely reflecting neutral divergence in two low-diversity populations, whereas IAPV had several sites that were strong outliers with very low FST.

Conclusions

This initial survey of genetic variation within honey bee RNA viruses suggests future directions for studies examining the underlying causes of population-genetic structure in these economically important pathogens.

Keywords:
Apis mellifera; Deformed wing virus; Israel acute paralysis virus; Single nucleotide polymorphism; Population genomics