Illumina deep sequencing reads map.

RNA was extracted from samples by using TRIzol method (Invitrogen) and its degradation and contamination were monitored on 1% agarose gels. The cDNA synthesis was performed with 3 μg of total RNA using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following the manufacturer's recommendations. The Deep Seq transcriptome sequencing analysis was carried out using polyA selected RNA at 30M PE reads per sample in an Illumina NextSeq500 sequencer. Reference genomes and gene model annotation files were used from TriTryp database. Raw sequencing reads (raw data) were processed and the read counts were extracted. The raw reads were then filtered to remove low-quality sequences and empty reads to gain clean reads. All subsequent analyses were based on the clean reads with high quality.