Alignments and trees from No detectable effect of <i>Wolbachia w</i>Mel on the prevalence and abundance of the RNA virome of <i>Drosophila melanogaster</i>

<i>Wolbachia</i> is an endosymbiotic bacterium that can block viral infections in arthropods, generating interest in its potential to control the spread of mosquito-borne disease. <i>Drosophila melanogaster</i> is model organism for <i>Wolbachia</i> infection, and the <i>w</i>Mel strain of <i>Wolbachia</i> can improve host survival following viral infection. However, it is unclear whether <i>w</i>Mel induces anti-viral blocking against the broader native virome of <i>D. melanogaster</i>, or whether the major effect of <i>Wolbachia</i> is a reduction in viral abundance rather than viral clearance. We examined the effect of <i>Wolbachia</i> on viral abundance by comparing the total transcriptome of <i>w</i>Mel-positive and <i>w</i>Mel-negative <i>D. melanogaster</i> populations sampled from six locations in Australia. In addition, we examined the impact of <i>w</i>Mel on individual flies by obtaining transcriptome data from 20 <i>w</i>Mel-positive and 20 <i>w</i>Mel-negative <i>D. melanogaster</i> from the location (Melbourne) with highest density of <i>w</i>Mel. These data revealed high viral abundance in both <i>Wolbachia</i>-positive and -negative populations and individuals. Notably, none of the viral species identified, representing RNA viruses from at least nine families/floating genera, showed evidence of protection by <i>w</i>Mel. Although the viral loads of picorna-like viruses are reduced by <i>w</i>Mel under experimental conditions, we observed no such effect here. These data show that <i>D. melanogaster</i> can harbour abundant RNA viruses regardless of its <i>Wolbachia</i> status and imply that the interaction between <i>Wolbachia</i> and viruses in nature is more complex than simple blocking.