Richard Buggs reviewed the original version of this manuscript, this is their report from 25 July, 2016:

This paper presents a Ginkgo genome assembly from 190x coverage with Illumina reads. It is assembled into 10.61GB of sequence, with a scaffold N50 of 1.36 Mp. No assembly is perfect, of course, but this seems to be a respectable, useful genome assembly and worthy of publication. However, the transcriptomic experiment and the sections on sex determination are not worthy of publication.

It is good that all PE libraries and one MP library were made from a single haploid endosperm. However, some heterozygosity is introduced by the other MP libraries that were made from other seeds from the same plant. Was this heterozygosity taken into account when assembling the genome? Could some of the apparently tandemly duplicated genes in fact be under-assembly of heterozygous alleles?

I am concerned about the claims in this paper about repeats in the Ginkgo genome (which form a significant part of this paper). Repeats are notoriously hard to assemble, and one cannot realistically expect them all to be correctly assembled in a de novo genome assembly. Therefore, caution is needed when making claims like "76.5% of the genome is made up of repeats". It may be that 76.5% of the assembly is made up of repeats, but the true repeat content of the actual genome cannot be measured so easily. It would be nice to see a measure of repeat content that is based on frequency analysis of the raw reads, in addition to one based on the genome assembly, for comparative purposes.

The authors devote a large part of the MS to differential expression between the sexes, based on two pools of RNA from (1) female organs from three trees and (2) male organs from four trees. Because the RNA from trees has been pooled into one female sample and one male sample, the study has n=2 and does not have statistical power to test for differences in gene expression between male and female. The conclusions that can be drawn from this study are therefore very few. Supplementary table 11 seems to me to be particularly weak, looking at differential expression of defence genes among male and female. Given the statistical concerns, and the fact that RNA was only collected from floral tissues, and defence responses must occur in all tissues, this seems a particularly poorly supported set of conclusions. I suggest that these analyses, and associated text, are removed from the MS.

The interaction network in Figure 3a is also questionable. It is not based on co-expression date from Ginkgo, but upon the gene interaction network of Arabidopsis, simply overlaid with BLAST hits from Ginkgo. It seems to assume that BLAST hits in the two species have similar functions, and share the same interaction networks, both of which assumptions are controversial. I suggest that this is removed from the MS.

The section on "candidate sex genes" in the discussion and in the results is not worthy of publication. It is mainly based on the n=2 transcriptomic study, and questionable and rather vague comparisons with angiosperms whose sex determination systems have been characterised. I have no idea why sex chromosomes are in the discussion as I can see no evidence from the data presented here that Ginkgo have sex chromosomes. Much of the "Results" section on sex determining genes is actually discussion, and makes lots of reference to the literature for various genes, outlining what they do in other species. This all needs to be removed from the results section, and probably from the manuscript, given that the transcriptomic experiment drawing our attention to these genes in Ginkgo is itself so weak.

The 10GB genome size of Ginkgo is smaller than the genome size of many conifers, so I would recommend dropping the use of "giga-" and "enormous" in the paper in reference to the Ginkgo genome.

Abstract: "unusual resistance/tolerance" to what? This needs to be specificed.

What do the authors mean by "high-resolution genome" in the abstract? All genome sequences are at the same level of resolution: the base-pair level. Genomes differ in their quality according to there contiguity and accuracy - they do not differ in their resolution.

The paper often uses comparative terms without specifiying what the comparison is with: "the longest introns" of what? All life? All plants? "Most insertions" compared to what?

There are several language errors throughout the MS that need correcting, including the use of "at last". 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. No.

Are the conclusions adequately supported by the data shown? If not, please explain in your comments to the authors. No.

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

Quality of written English Please indicate the quality of language in the manuscript: Not suitable for publication unless extensively edited

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 SEPTEMBER 30, 2016

I am content with the authors' responses to my reviews.

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.)

No, I do not feel adequately qualified to assess the statistics.

Quality of written EnglishPlease indicate the quality of language in the manuscript:
Needs some language corrections before being published.

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)