The quality of the raw RNA-seq data was assessed with FastQC v0.11.5. Paired-end reads were subsequently trimmed and de novo assembled into transcripts with Trinity v2.4.0 (34, 35). Post-assembly quality control and taxonomic partitioning were done with BlobTools (36, 37) and phyloFlash (38). We did not find any substantial contamination. Transcript abundance was estimated with the RSEM (RNA-Seq by Expectation Maximization) method using the normalized expression values TPM (transcripts per kilobase million) and FPKM (fragments per kilobase million). Candidate coding regions were identified with TransDecoder v5.1.0. Completeness of the transcriptome was assessed with BUSCO v3.0.2b (39, 40) and compared to other available flatworm transcriptomes (fig. S13) (41). The transcriptome was annotated using the Trinotate v3.1.1 annotation pipeline (42), which includes blastx and blastp homology searches to the BLAST+/SwissProt databases (data files S1 and S2), protein domain identification with HMMER/Pfam, signal peptide and transmembrane domain prediction with signalP/tmHMM, and functional annotation against eggNOG/GO/KEGG databases.

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