Apis Mellifera metatranscriptomic sequencing
Total RNA was treated with DNase I and its integrity was assessed by determining the RNA Integrity Number (RIN) using the Agilent Bioanalyzer platform (Agilent). From each apiary, 100 ng of total RNA was processed by applying a ribosomal RNA (rRNA) depletion protocol using the Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit (Illumina) optimized with a spike-in of 86 probes specific (Table 1S) for A. mellifera rRNA designed on the reference genomes available in EnsemblMetazoa (Amel_HAv3.1; https://metazoa.ensembl.org). Sequencing libraries were prepared and sequenced on the high-throughput NovaSeq 6000 platform (Illumina) in 2x150 paired-end mode, with sequencing output designed to target 100 million reads per sample