“…This database consisted of the five bacterial pathogens Melissococcus plutonius (GCF_000747585.1), Paenibacillus larvae (GCF_002003265.1), Serratia marcescens (GCF_000513215.1), Spiroplasma apis (GCF_000500935.1), and Spiroplasma melliferum (GCF_000236085.2), the chalkbrood fungus Ascosphaera apis (GCA_000149775.1), the three stonebrood fungi Aspergillus fumigatus (GCF_000002655.1), A. flavus (GCF_000006275.2), and A. niger (GCF_000002855.3), and the nine honey bee viruses Acute bee paralysis virus (GCF_000856345.1), Apis mellifera filamentous virus (GCF_001308775.1), Black queen cell virus (GCF_000851425.1), Chronic bee paralysis virus (GCF_000875145.1), Deformed wing virus (GCF_000852585.1), Israel acute paralysis virus (GCF_000870485.1), Kashmir bee virus (GCF_000853385.1), Sacbrood virus (GCF_000847625.1), and Slow bee paralysis virus (GCF_000887395.1). This list, while not exhaustive, should capture the majority of possible pathogens expected to be present in appreciable frequency (Brutscher et al 2016;Evison & Jensen 2016;Funfhaus et al 2018). When genomes were represented by multiple scaffolds, we concatenated them into a single sequence for mapping.…”