The authors present a comprehensive transcriptome dataset for Schistocephalus solidus, of which the genome assembly is available as part of the 50helminth genome projects. Authors de novo assembled these data through the standard trinity pipeline and reported some basic results of these data.

Comment 1:
Line 142: Bioanalyzer profile: Author should consult the Sanger parasite genomics for Bioanalyzer profile from several cestode transcriptome projects they are currently working on. I am sure they are happy to provide it as means of personal communication. It is not good enough to safely assume the samples are cestode specific.

Comment 2: Section on Comparison with gene prediction models
It is well known that de novo assemblies of transcriptomes give an overestimate of gene models (as a result of failing to collapse transcripts or misassembly). Such metric can be assessed if an assembly is available, The authors correctly pointed out that their transcriptome is only a subset of life cycles but failed to use a mapping approach to check 1) how many / % of genes in the assemblies have evidence of expression , and 2) the mappability of their RNAseq dataset? It's great if over than 90% of reads can be aligned back to the assembly, but if not, what could be contributing it (goes back to comment 1)?

Line 232: It seems to me that a median of 92% suggest either that there are two very different S. solidus strains or a long tail in distribution in matchings. Could the authors plot the distribution of similarity matches and identify the mode to clarify?

Comment 3:
This phylogeny has poor choice of outgroup. If you look at http://www.nature.com/nature/journal/vaop/ncurrent/fig_tab/nature16994_F1.html, there are way too many species that have been classified as "parasitic nematodes" which is frankly wrong. I recommend use one or two trematode species as outgroup that are more closely related to cestodes like the ones here: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0510-3 . The authors could also include the proteomes of the wormbase of S. solidus to assess how related are the two strains.

Comment 4: Please revise the title. The word "reference" in the title should not be used since it's only a subset of the life cycle and there were no other means to determine whether they are more accurate than the current predicted proteome. And no biological insights have been revealed throughout the manuscript other than confirming the phylogenetic position of S. solidus.

Minor comments:
de novo should be italicized throughout

line 189: although obvious, there's no direction of threshold (i.e., to include / exclude transcript of CPM >10). Please clarify.
line 240-242: How do the authors know that the S. solidus prediction in 50HG is based on C. elegans prediction? As far as I know it's based on many species including existing parasites. Please clarify.

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