Transcriptome assembly
After transcriptome sequencing we removed adaptor sequences and low-quality reads in multiple steps using TrimGalore! v. 0.6.6 (Krueger, 2019), while iteratively examining the quantity and quality of reads with FastQC v. 0.11.8 (Andrews, 2010). The cleaned reads were subjected to de novo transcriptome assembly with Agalma v. 2.0.0 (Dunn et al., 2013), which includes several filtering procedures and ribosomal RNA removal followed by assembly with Trinity v. 2.8.5 (Grabherr et al., 2011). We screened against the NCBI UniVec database to identify vector contaminants and rRNA transcripts. Subsequently, we performed a reference-free assessment of the quality and completeness of our de novo assemblies with TransRate v. 1.0.3 (Smith-Unna et al., 2016) combined with BUSCO v. 3.0.1 (Simão et al., 2015).