David Neale reviewed the original version of this manuscript, this is their report from 27 July, 2016:

This paper reports a high quality sequence, assembly and annotation of an important plant species, Ginkgo biloba, a gymnosperm. It merits publication. However, the paper fails to cite and compare the work presented here with other published conifer genome sequences. It is if this paper was written in 2013. See a recent paper in Plant Journal on the white spruce genome and four papers on the loblolly pine genome in Genome Biology, 2 in Genetics and PLoS ONE. All of these papers have detailed discussion of the large genomes of gymnosperms and the nature of the repetitive elements. This paper need to be rewritten and all the current literature on this topic discussed relative to this new gymnosperm sequence. 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 minimum standards of reporting? If not, please specify what is required in your comments to the authors. No.

Are you able to assess all statistics in the manuscript, including the appropriateness of statistical tests used? Yes, and I have assessed the statistics in my report.

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

Declaration of competing interests Please complete a declaration of competing interests, consider the following questions: Have you in the past five years received reimbursements, fees, funding, or salary from an organization that may in any way gain or lose financially from the publication of this manuscript, either now or in the future? Do you hold any stocks or shares in an organization that may in any way gain or lose financially from the publication of this manuscript, either now or in the future? Do you hold or are you currently applying for any patents relating to the content of the manuscript? Have you received reimbursements, fees, funding, or salary from an organization that holds or has applied for patents relating to the content of the manuscript? Do you have any other financial competing interests? Do you have any non-financial competing interests in relation to this manuscript? If you can answer no to all of the above, write ‘I declare that I have no competing interests’ below. If your reply is yes to any, please give details below. I declare that I have no competing interests.

I agree to the open peer review policy of the journal. I understand that my name will be included on my report to the authors and, if the manuscript is accepted for publication, my named report including any attachments I upload will be posted on the website along with the authors' responses. I agree for my report to be made available under an Open Access Creative Commons CC-BY license (http://creativecommons.org/licenses/by/4.0/). I understand that any comments which I do not wish to be included in my named report can be included as confidential comments to the editors, which will not be published. I agree to the open peer review policy of the journal.

REVIEW 1, REVIEWED ON AUGUST 20, 2016

Reviewer's report: The authors have now written a paper that includes comparison to other gymnosperms genomes sequenced to date. It remains quite surprising this was not done in the first place.

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 minimum standards of reporting?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 EnglishPlease indicate the quality of language in the manuscript:
Acceptable

Declaration of competing interestsPlease complete a declaration of competing interests, consider
the following questions:

1. Have you in the past five years received reimbursements, fees, funding, or salary from an
organization that may in any way gain or lose financially from the publication of this
manuscript, either now or in the future?
2. Do you hold any stocks or shares in an organization that may in any way gain or lose
financially from the publication of this manuscript, either now or in the future?
3. Do you hold or are you currently applying for any patents relating to the content of the
manuscript?
4. Have you received reimbursements, fees, funding, or salary from an organization that holds
or has applied for patents relating to the content of the manuscript?
5. Do you have any other financial competing interests?
6. Do you have any non-financial competing interests in relation to this manuscript?
If you can answer no to all of the above, write ‘I declare that I have no competing interests’ below.
If your reply is yes to any, please give details below.

‘I declare that I have no competing interests.

I agree to the open peer review policy of the journal. I understand that my name will be included
on my report to the authors and, if the manuscript is accepted for publication, my named report
including any attachments I upload will be posted on the website along with the authors'
responses. I agree for my report to be made available under an Open Access Creative Commons
CC-BY license (http://creativecommons.org/licenses/by/4.0/). I understand that any comments
which I do not wish to be included in my named report can be included as confidential comments
to the editors, which will not be published.

I agree to the open peer review policy of the journal.

Authors' response to reviews: (https://static-content.springer.com/openpeerreview/art%3A10.1186%2Fs13742-016-0154-1/13742_2016_154_AuthorComment_V1.pdf)