Library preparation, transcriptome sequencing and bioinformatics analysis

Total RNA was isolated from the materials using a TRIzol kit (Invitrogen, USA) and purified to enrich messenger RNA (mRNA). Quantification and qualification RNA was checked to meet the standards for library construction. A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext^® Ultra™ RNA Library Prep Kit for Illumina^® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated. Raw data (raw reads) were filtered to obtain the clean reads to ensure the quality of the information analysis. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.