Reviewer name and names of any other individual's who aided in reviewer	Yang Zhou
Do you understand and agree to our policy of having open and named reviews, and having your review included with the published papers. (If no, please inform the editor that you cannot review this manuscript.)	Yes
Is the language of sufficient quality?	Yes
Please add additional comments on language quality to clarify if needed
Are all data available and do they match the descriptions in the paper?	Yes
Additional Comments
Are the data and metadata consistent with relevant minimum information or reporting standards? See GigaDB checklists for examples <a href="http://gigadb.org/site/guide" target="_blank">http://gigadb.org/site/guide</a>	Yes
Additional Comments
Is the data acquisition clear, complete and methodologically sound?	Yes
Additional Comments
Is there sufficient detail in the methods and data-processing steps to allow reproduction?	Yes
Additional Comments
Is there sufficient data validation and statistical analyses of data quality?	Yes
Additional Comments
Is the validation suitable for this type of data?	Yes
Additional Comments
Is there sufficient information for others to reuse this dataset or integrate it with other data?	Yes
Additional Comments
Any Additional Overall Comments to the Author	This is a fascinating study on the assembly of the first deep-sea scleractinian coral, Lophelia pertusa. The manuscript is well-written and easy to follow. I have gone through your manuscript and would like you to address the following concerns/comments before publication. Line 47: 1.2 454 pyrosequencing reads means 1.2Gb 454 pyrosequencing reads? Line 51-52: Please add some references. Line 72: As far as I know, the DNA extraction process of stony corals is affected by calcium carbonate skeletons. How did you deal with this problem during the DNA extraction process? References: Please double-check the references for errors. Italics for species names, capitalization of journal titles, and so on.
Recommendation	Minor Revision