Vairimorpha bombi genome and annotation

All quality-filtered and non-bumblebee Nanopore reads were assembled using Canu version 2.2 with parameters corOutCoverage = 100, corMhapSensitivity = high, minInputCoverage = 0, corMinCoverage = 0, and the precited genome size as 10 Mb, which is approximately the same length of the other two bee-infecting microsporidia – V. apis (8.5 Mb) and V. ceranae (7.9 – 8.8 Mb). We trimmed adapter sequences from the Illumina reads using Trimmomatic and aligned them to the draft Nanopore assembly using BWA-mem. We down sampled and normalised the combined aligned reads to ~120 X coverage using bbnorm from the BBTools suite version 39.01) and then iteratively polished the assembly three times using Pilon version 1.24.