Fig. 1

De novo assembly method used in the construction of a reference transcriptome for Schistocephalus solidus. Sequencing libraries from three developmental stages of S. solidus, non-infective plerocercoid, infective plerocercoid and adult, were trimmed (PHRED > 2, read length > 60 nucl.), concatenated and assembled de novo (1 library per stage). Next, the three libraries initially used to produce the de novo assembly, in addition to 11 libraries spanning the same three developmental stages (non-infective plerocercoid = 6 libraries, infective plerocercoid = 3 libraries, adult = 2 libraries) were aligned back to the de novo assembly. corset was used on the resulting alignment to eliminate redundancy by creating clusters of similar sequences, called ‘unigenes’. Transcripts were finally annotated through the Trinotate pipeline and transcripts poorly supported by protein-coding evidence were discarded, along with transcripts showing a low average coverage, i.e. CPM < 10 in 50 % of the samples in one group. The final transcriptome contains 24,765 transcripts accounting for 10,285 unigenes, of which 77 % could be annotated