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.