Differential gene expression analysis

All libraries (30 in total) were mapped to the combined transcriptome assembly using kallisto software (Bray, Pimentel, Melsted, & Pachter, 2016) with one hundred bootstrap replicates. The averages of bootstrap replicates of Transcript per Million (TPM) (Li, Ruotti, Stewart, Thomson, & Dewey, 2010) values were used as counts for differential gene expression analysis. We imported the count tables to R by tximport package (Soneson, Love, & Robinson, 2015). Principal Component Analysis of all samples, both for combined and for each genotype separately was carried out using plotPCA command in DESeq2 and using rgl package (Adler, Nenadic, & Zucchini, 2017) for 3D plot and ggplot2 (Wickham H, 2016) for 2D plots. We analyzed the samples at genotype and phenotype levels (Res, Sus and Res_vs_Sus) by DESeq2 (Love, Huber, & Anders, 2014) to obtain differentially expressed genes.