In this manuscript the authors report the genome sequencing, annotation and analysis of P. micrantha and compare transcriptome&genome data to the related Fragaria clade to investigate fleshy fruit development. I agree with the authors that this new resource represents a valuable tool to further and in-depth study fruit development and evolution in this clade and beyond. The analysis of exactly this, however, remains superficial in this study albeit the title promises more…this is my main point of criticism. The identification of the three differentially expressed orthologous clades seems sound from the methodology point of view but lacks any further evaluation or analysis. What about the promotor regions of these orthologs? Any explanation for the different expression profiles? I understand this is a genome and comparative genomics study but it would be nice to see some additional (e.g. experimental) evidence for the functional role of those genes except of their sequence homology to Arabidopsis. Also, do you find any additional (differentially expressed or not) genes potentially related to fruit development (e.g. known genes from Fragaria)? Until this is not included, you should at least tone down the titel's promises… Additional points to consider: a.) Figure numbering is incorrect between legends and actual figures. b.) Figure 3 (anchoring…fig 2 in the legend): I understand that this figure represents the anchoring of the scaffolds on the pseudochromosomes of Fragaria but I also feel that this figure is somewhat suggestive of an aspect that the authors cannot really assess. As the scaffolds are not ordered or oriented along a map (see pg. 18…and no attempts were made either according to authors) the authors can assess the micro-synteny but not the macro-synteny (this is also clearly mentioned in the methods). The ordering along the Fragaria pseudochromosomes in Figure 3 together with too general conclusions about syntenic conservation (see chapter "Scaffold anchoring and synteny…" and conclusions pg.12, ln 22) between P. micrantha and Fragaria give the impression about high conservation on the macro-synteny level, too (though possible, but not shown). c.) Annotation: there is no real evaluation of the gene prediction quality other than BLAST searches and BLAST2GO annotations. It would be nice to see a BUSCO evaluation or even a gene family clustering with related species…this would give a good proxy on gene prediction completeness and also quality. What about the ~9,000 P. micrantha genes not identified on the F. vesca pseudomolecules? Are they all true species-specific genes? Is there expression evidence for them in your data? d.) Gene expression during fruit development: with 1,556 DEGs in P. micrantha and 816 DEGs in F. vesca I was wondering about the overlap and differences between these two genes sets? This would be much more informative than the GO annotation statistics for these…in that context, I do not understand Fig. S1. How are the different categories exactly defined and what should be the conclusion of it? I was also wondering about the comparability of the expression data generated in this study and the one by Kang et al. Although they should represent identical tissues etc., is there any statistical and/or technical evaluation available (e.g. PCA etc.)? e.) Parts of the transposon analysis read extremely descriptive without major conclusions…this could be substantially shortened in my view. f.) Hormonal treatment: this chapter seems very much isolated…what is the conclusion here and how does it relate to the rest of the analyses? g.) Is there a reason for not showing the miR1511 data and analysis? This appears to be potentially interesting but cannot be assessed if just mentioned in the discussions…

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. 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 author
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.)
There are no statistics in the manuscript.

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

Authors' response to reviews: Reviewer 1 We have tones down the whole of the manuscript to reflect the descriptive nature of our data and have likewise changed the title of the paper to: The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry). The figure legends have been checked and corrected where necessary. The figure relating to anchoring of scaffolds has been moved to the supplementary material and replaced with figures relating to synteny of specific scaffolds rather than the genome as a whole. Additionally, we have ensured throughout the text that it is clear that only micro-synteny was evaluated. A BUSCO analysis has been performed and presented. An analysis showing the overlap between the DEGs in each species was performed, as well as a visualisation of the genes from each species and the GO class they fall into. The Transposon analysis section has been reduced. The hormonal treatment analysis has been removed from the paper. The miR1511 data has been removed from the paper as further work would have been required to strengthen this section sufficiently for publication which was not possible since almost all authors now no longer work at FEM where this work was initiated.

Reviewer 2 We appreciate the comments regarding the mechanisms of differentiation, and indeed at the inception of the project this was to be a major focus of the work; however, we were not able to progress in this area sufficiently to make this a major part of the manuscript. We hope that other groups will be able to study this area, building on the work we present here. We have added a space between x and ananassa. We have removed the redundancy and made clearer the objectives of the study. Figure numbering has been corrected. The ML study is presented the others have been referred to as data not shown. Plants were selected from Serbia as we had a collaborator there who guided us to a large population from which we could sample plant material easily. Redundancy has been removed from the HiSeq2000 methods section. We have adjusted the text relating to FPKM to clarify that highly expressed genes were those with FPKM >1000 and on/off genes were those where no expression data were observed. A space was added to sqrt (MSR). Abbreviations have been added for ML, MP and NJ in the text. Resolution of the figures has been improved and font size increased to improve clarity. Figure legends for the phylogenetic analysis have been improved. The text resolution on the submitted figures is much better than in the reviewer copy. We hope that in the revised version, the reviewers have access to higher resolution images where text is hopefully clear and legible.

Reviewer 3 The text has been modified throughout to make clearer that only micro-synteny was evaluated. Likewise, the figures relating to this section have been changed to reflect and emphasise the micro-synteny. The abundance of GO terms for the DEGs in each species has been highlighted through an additional figure, and those classes that were in greater abundance are identified. Likewise, a heatmap of the expression levels of genes shared between the two species has been produced and those that differ in their expression patterns have been identified. The title and text have been toned down to reflect the results presented more accurately.

We look forward to hearing from you in due course regarding this resubmission, Best regards, Dan Sargent (on behalf of all authors).

The authors addressed some of the main issues appropriately (synteny, figures etc.). However, for other issues like the transposon section, the hormonal treatment analysis and the miR1511 analysis the main action was just to shorten or completely drop the part. This is Ok and/or was suggested but on the other hand, no real efforts were made to strengthen the comparison/fleshy fruit analyses (or any other analytical part) and most of my suggestions/questions for this and also the annotation and gene expression part were simply ignored. As a result, this study as it stands now mostly provides an "extended description" of the resources generated (although potentially valuable) with clear shortcomings in the analysis and interpretation of the data. Along that lines, I appreciate that the authors in the new version resign from claiming analytical results not there or possible. Additional comments: a.) Your BUSCO analysis shows that you are missing ~6% of the BUSCO genes from the genome sequence (present) to the final gene prediction (absent). Are they completely missing in the gene prediction or fragmented etc.? b.) I still wonder about the ~9,000 gene predictions not showing a hit on the F. vesca pseudomolecules…do those genes have functional annotation and expression support? c.) I cannot make much sense out of figure 2B. In the figure resolution I have, individual lines look like they correspond to a single (or very few) gene(s), although I suspect it has to be more genes. It would be good to define the sizes of the blocks somewhere. d.) I'd move figure 9 to the supplementary material and drop sup Figure S1. It still has the same problem as when it was a main figure.

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 author
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.)
There are no statistics in the manuscript.

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

Authors' response to reviews: Q1. Overall, I am pleased that the reviewers agree that the latest, revised version of your manuscript presents useful and valuable data. However, I also agree with reviewer 1 that, in the absence of more in-depth analyses, the main value of the paper is now indeed the presentation of a high-quality resource, rather than new biological insights.

R1. Many thanks for the useful comments. We agree with your feeling that the paper describes more of a technical advance than a description of new biological insights at this stage, but hope we have provided a valuable dataset that can be used for future biological investigations.

Q2. I therefore feel that your revised manuscript may be more suitable for the format of a "Data Note". Data notes are indexed in the same way as research articles, but the emphasis is on presenting an exceptional resource, together with description and validation of the dataset. If you agree that we consider your next revised version as a data note, please adjust the format (see: https://academic.oup.com/gigascience/pages/data_note). I feel that this would require only minor adjustments to the text itself (e.g. the discussion part could be revised to demonstrate validation and re-use cases of the data). You can keep the Background section for the Data Note format (this is not quite clear from our Instructions).

Please let me know if you agree to this suggestion, and I'm happy to answer any questions regarding the Data Note format.

R2. We are happy for our paper to be published as a data note and have revised the manuscript accordingly (following the guidelines and taking recently published data note articles as examples).

Reviewer reports: Q3. Reviewer #1: The authors addressed some of the main issues appropriately (synteny, figures etc.). However, for other issues like the transposon section, the hormonal treatment analysis and the miR1511 analysis the main action was just to shorten or completely drop the part. This is Ok and/or was suggested but on the other hand, no real efforts were made to strengthen the comparison/fleshy fruit analyses (or any other analytical part) and most of my suggestions/questions for this and also the annotation and gene expression part were simply ignored. As a result, this study as it stands now mostly provides an "extended description" of the resources generated (although potentially valuable) with clear shortcomings in the analysis and interpretation of the data. Along that lines, I appreciate that the authors in the new version resign from claiming analytical results not there or possible.

R3. We appreciate the reviewer’s useful and constructive criticisms on the previous version of our paper and whilst we tried to incorporate as many of the suggested changes as was possible, the lead authors did not have the resources available to make all the suggested improvements, and as such we opted to remove the unsupported claims and refocus the paper as a technical report.

Additional comments: Q4. a.) Your BUSCO analysis shows that you are missing ~6% of the BUSCO genes from the genome sequence (present) to the final gene prediction (absent). Are they completely missing in the gene prediction or fragmented etc.?

R4. We have provided more detail in the manuscript, detailing the complete and fragmented BUSCO sequences retrieved. We have also performed a BUSCO analysis on the F. vesca gene predictions and provided a comparison of the two to demonstrate that the P. micrantha set is virtually as complete as the F. vesca set.

Q5. b.) I still wonder about the ~9,000 gene predictions not showing a hit on the F. vesca pseudomolecules…do those genes have functional annotation and expression support?

R5. Our sincere apologies for not making this section clearer (it was not explained carefully enough what analyses we are performing and the results were not reported in detail). The Inparanoid analysis attempted to identify orthologous genes between the P. micrantha and F. vesca datasets using protein sequences. This analysis revealed 33,127 P. micrantha genes that had a putative match in the F. vesca gene set (98.6%). However, for the analysis of synteny, we chose only those genes where there was a clear and unambiguous orthologous relationship between the two genomes. This is the reason only 24,555 genes were considered for the synteny analysis. We have amended the text to clarify these points.

Q6. c.) I cannot make much sense out of figure 2B. In the figure resolution I have, individual lines look like they correspond to a single (or very few) gene(s), although I suspect it has to be more genes. It would be good to define the sizes of the blocks somewhere.

R6. We have added the number of genes in each conserved region which are split between pseudomolecules on the F. vesca genome. We have also made it clearer that these are only scaffolds that are split between pseudomolecules (i.e. evidence of major rearrangements). There were many instances of individual genes that did not fall into syntenic blocks.

Q7. d.) I'd move figure 9 to the supplementary material and drop sup Figure S1. It still has the same problem as when it was a main figure.

R7. Done as suggested

Reviewer #3: The authors have addressed all my comments and concerns. Q8. I have one minor comment -I found 'CDs' in multiple places. Could you spell it out when it first appears? If it stands for coding DNA sequence, I think 'CDS' is a more common abbreviation.

R8. Done as suggested.