Raw data were first processed through in-house Perl scripts and clean data (clean reads) were obtained. At the same time, Q20, Q30, GC-content, and sequence duplication levels of the clean data were calculated. All the downstream analyses were based on clean data with high quality. These post-sequencing analytical procedures were done as reported earlier [96]. The transcriptome was assembled based on the two pooled files for each sample using Trinity [97].
Gene function annotation was done according to NR (NCBI non-redundant protein sequences); Pfam (Protein family); KOG/COG/eggNOG (Clusters of Orthologous Groups of proteins) [98, 99]; Swiss-Prot (A manually annotated and reviewed protein sequence database) [100]; KEGG (Kyoto Encyclopedia of Genes and Genomes) [101]; and GO (Gene Ontology) [102] databases.
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