A well described report of an excellent new resource for this field. The authors have a good sampling strategy, with comprehensive replication, covering parasites at different life stages. All of the related data is available in a usable format and is described fully. The bioinformatic pipeline is available on GitHub.

The transcriptome data provides important evidence and support for gene models in this species - the limitations of relying on gene prediction algorithms alone are nicely recognised in the text.

I recommend publication after the following points are addressed:

Major points:

• Figures 1 and 2 both need to be altered to comply with copyright as the worm illustrations in incorporated into these figures are from Tsai and Zarowiecki et al 2013. http://www.nature.com/nature/journal/v496/n7443/full/nature12031.html. These aspects of the figures need to be either removed or replaced with the author's own.

Very minor points:

• References for WormBase (Howe et al 2015) should be included.

• Would prefer the sentence line 84, to be altered as innovation in the field has not been
  ongoing for 200 yrs. Suggestion "Despite complex parasite life cycles being first described
  200 years ago.. etc."

• Line 90. Sentence does not quite make sense, as the transcriptome is not (at least the
  primary) direct interface between the host and parasite at a molecular level (this is most
  usually at the protein level). Change or remove last part of sentence.

• Line 125. at four and 16 weeks post-exposure. (clarity)

• Line 136. Specify how the worms were cut - with a scalpel?

• Line 148. 14 RNA samples from individual worms were used to produce sequencing
  libraries. (make it clearer that samples were one worm per libary and weren't combined).

• Line 270. each of which are potential players... (being -> are)

• Figure 1. Numbers included at end of pipeline. Specifiy "77% of unigenes are annotated with
  a protein name" or even "77% of unigenes with protein annotation" (at the moment it says
  "77% of annotated unigenes" and sentence meaning is unclear).

Level of interest

Please indicate how interesting you found the manuscript:
An article of importance in its field

Quality of written English

Please indicate the quality of language in the manuscript:
Acceptable

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Authors' response to reviews: (http://www.gigasciencejournal.com/imedia/1164912975201205_comment.pdf)