Reviewer name and names of any other individual's who aided in reviewer	Claudius Kratochwil
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?	No
Please add additional comments on language quality to clarify if needed	The text is understandable, but has many grammatical errors. The manuscript would greatly improve through language editing.
Are all data available and do they match the descriptions in the paper?	Yes
Additional Comments	I did not check every single file, but all data I looked for I found to be publicly available. It would help if the "Availability of supporting data and materials" statement would be a bit more comprehensive. Data A is deposited under X, Data B is deposited under Y-Z instead of just providing the project ID.
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	To the best of my knowledge. Not my area of expertise.
Is the data acquisition clear, complete and methodologically sound?	No
Additional Comments	I was lacking information about the transcriptomic data (it says in line 44 that RNA was extracted) that was used for the annotation? Was RNA only extracted from the muscle? Maybe the caveats that go along with that should be discussed. How was the data processed? How many reads etc. I think the manuscript lacks information about this unless I misunderstood where the data for the "transcript-based prediction" came from. Then this should be indicated more clearly.
Is there sufficient detail in the methods and data-processing steps to allow reproduction?	Yes
Additional Comments	To the best of my knowledge. I am not an expert on this. Minor comments: l 46: Which protocol?
Is there sufficient data validation and statistical analyses of data quality?	Not my area of expertise
Additional Comments	One thing that could be probably additionally done is to provide dot plots with the 1-2 more closely related species with chromosome level assemblies (probably Tilapia or Medaka).
Is the validation suitable for this type of data?	Yes
Additional Comments	As far as I can judge the analysis is fine.
Is there sufficient information for others to reuse this dataset or integrate it with other data?	Yes
Additional Comments	Genome and annotation are available, which is the most important for reuse and integration with other data sets. So as far as I can judge there is sufficient information for others.
Any Additional Overall Comments to the Author	From my viewpoint, this is a useful chromosome-level genome, so I support its publication. Beyond being a useful resource, I was however a bit disappointed by the 'scientific part' regarding the bi-color body formation. While the pigmentation of the bicolor angelfish is certainly a very exciting phenotype, the analysis performed is far too superficial to give any solid insights into the phenotype. I would suggest the authors toning this down in title, abstract and main text. It is fine to mention this as a future research direction and to state that the performed initial analysis (fig. 6 and 7) might aid these investigations, but the data does not permit further conclusions. Especially as GigaByte does not focus on analyses for biological findings, this should be completely sufficient.
Recommendation	Major Revision