This manuscript characterizes the genomic property of the ocean sunfish and provides insights into its phenotypic specialization. The primary product of the study, the genome assembly, is well prepared and exhibits very high completeness and continuity, largely thanks to the relatively small genome size and the relatively low frequency of repetitive elements in the genome. Overall, this study, supported by the high-quality genome assembly, should contribute to an advancement of the research field for actinopterygian fish genomics, and I recommend publication of this manuscript in GigaScience, provided that the points below are reconsidered for improving the manuscript.

1. Some morphological characteristics including the loss of caudal fin are mentioned, in search of possible genomic causes. But, little information in included in the manuscript, regarding the developmental process of the unique body plan. Is this because of the lack of records of embryological development?

2. Page 6 / line 101, 'show similarity to sequences in public databases' : similarity to nucleotide or protein sequences?

3. Some parts of the description in 'Analyses' include highly speculative expressions such as 'may have led to the extremely fast growth rate .' in page 9 line 169. It is recommended to move such speculative expressions to 'Discussion'

4. Page 11 / line 207, 'complete loss fa93e10 and scpp7': insert 'of' between 'loss' and 'fa93e10', if I understand correctly

5. Page 11 / line 211, 'an exact orthology' : Is 'exact' ortholog opposed to 'non-exact' orthology? It can't be. Thus, remove 'exact' from this sentence.

6. Has any phenotypic evolution been clearly shown to be attributed to a Hox gene loss? If that has not been shown before, it may not be justified to analyze Hox gene repertoire for identifying causes of the sunfish's unique morphology.

7. Page 15 / line 280, 'identified 98.4% of CEGs': I wonder if this is a figure for 'Complete' or 'Partial' gene detection in the CEGMA result?

Table S1: For mate pair libraries, the figures for the column 'insert size' should not be 'insert size' but something like 'mate distance'.

Are the methods appropriate to the aims of the study, are they well described, and are
necessary controls included?
If not, please specify what is required in your comments to the authors.

Yes

Are the conclusions adequately supported by the data shown?
If not, please explain in your comments to the authors.

Yes

Does the manuscript adhere to the journal’s guidelines on <a href=’http://resourcecms.springer.com/springercms/rest/v1/content/7117202/data/v1/Minimum+standards+of+reporting+checklist’target='
new'>minimum standards of reporting?</a>
If not, please specify what is required in your comments to the authors.

Yes

Are you able to assess all statistics in the manuscript, including the appropriateness of
statistical tests used?
(If an additional statistical review is recommended, please specify what aspects require further
assessment in your comments to the editors.)

Yes, and I have assessed the statistics in my report.

Quality of written English
Please indicate the quality of language in the manuscript:
Acceptable

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I declare that I have no competing interests.

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Authors' response to reviews: (https://static-content.springer.com/openpeerreview/art%3A10.1186%2Fs13742-016-0144-3/13742_2016_144_AuthorComment_V1.pdf)