Analysis of bulk RNA-seq

Bulk RNA-seq libraries were paired-end-sequenced. FastQC software (version 0.11.9) was used for quality control. Adapters were trimmed off with the Trimmomatic program (version 0.39) (Bolger et al., 2014). After filtering, the paired reads were aligned to the honeybee reference genome (assembly Amel_HAv3.1) using STAR software (version 2.7.9a) (Dobin et al., 2013). The STAR mapping produced reads were accurately quantified by the RSEM program (version 1.3.1) (Li and Dewey, 2011) to obtain count matrices about gene expression. The count matrices were processed by DEseq2 (version 1.32.0) (Love et al., 2014) R package.