Construction of RNA-seq libraries and transcriptome data analysis
21-day-old transgenic hairy roots (G5O14) and control roots (ATCC) were collected from three biological replicates and used for total RNA extraction. 3 μg RNA of each sample was used to construct Illumina sequencing libraries using the Illumina PE150 platform (Novogene, China.). Three biological replicates were used for each sample.
The reference genome and gene model annotation files were downloaded from genome websites (Xu et al. , 2016). Genes with an adjustedP -value<0.05 and |fold-change|≥2 were considered significantly differentially expressed. GO Slim enrichment was evaluated using the GOseq R package (Young et al. , 2010). Significantly enriched KEGG pathways were identified with KOBAS 2.0 (Maoet al. , 2005).