2.2. Transcriptome de novo Assembly, ORF Prediction, and Protein Domain Mapping

RNA-seq reads were trimmed for the presence of adaptor sequences, and for quality, using TrimGalore! [50], allowing for a maximum of two ambiguous bases and a quality threshold of PHRED20. Trimmed reads were de novo assembled using CLC Genomic Workbench v.10 (Qiagen, Hilden, Germany), setting automatic word and bubble sizes, and a minimal contig length of 200 bp. The resulting contigs were subjected to open reading frame (ORF) prediction, using the transdecoder tool included in the Trinity suite [51], applying a minimal ORF length of 100 codons. HMMer v.3.1 [52] was used to identify the presence of conserved protein domains (Pfam-A models, v.29 [53], applying a cut-off E-value of 10⁻⁵.