Mansour et al have undertaken substantial re-analysis and revisions to their previous submission and I would like to thank them for their time and careful consideration.

I have a few additional comments that I think would be worth addressing prior to formal acceptance of this manuscript for publication.

First, the authors explain in their response to review that "they decided to use relaxed assembly parameters in the original assembly to increase transcript sensitivity at the cost of potentially including some erroneous assemblies in order to uncover rare transcripts". This is a reasonable explanation, but unfortunately is not explicitly stated in the present draft. I recommend including this point into the background so that readers are made aware of this choice.

Second, I still have some remaining disagreement with the background justification for this study. On page 3, line 23 authors state that previous transcriptome studies have focused only on the adult stage. In fact, the first published coral transcriptome was developed for a larval coral (A. millepora - (Meyer et al. 2009). An additional assembly for this species incorporated multiple life history stages for the exact reasons mentioned by the authors - to explore the onset of calcification - (Moya et al. 2012). This statement should either be removed or qualified to reflect that only adults were used in the prior P. astreoides assembly.

On page 4, line 5-7 authors state that the availability of larvae without a skeleton make P. astreoides an ideal species for studying molecular basis of calcification. All corals undergo this same larval phase lacking a skeleton - why would P. astreoides be any better or worse? Furthermore, as stated above, such a multi-life-stage resource already exists for Acropora millepora. Suggest revising or removing this point.

Meyer, E., G. Aglyamova, S. Wang, J. Buchanan-Carter, D. Abrego, J. K. Colbourne, B. L. Willis, and M. Matz. 2009. Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics 10:doi:10.1186/1471-2164-1110-1219.

Moya, A., L. Huisman, E. E. Ball, D. C. Hayward, L. C. Grasso, C. M. Chua, H. N. Woo, J. P. Gattuso, S. Foret, and D. J. Miller. 2012. Whole transcriptome analysis of the coral Acropora millepora reveals compex responses to CO2-driven acidification during the initiation of calcification. Molecular Ecology 21:2440-2454.

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Authors response to reviews: (https://static-content.springer.com/openpeerreview/art%3A10.1186%2Fs13742-016-0138-1/13742_2016_138_AuthorComment_V2.pdf)