The paper titled "The genome sequence and transcriptome of Potentilla micrantha shed light on the origins of strawberry fruit development" reports the new genome and transcriptome data of Potentilla micrantha, a species that belongs to the genus Potentilla that is closely related to that of Fragaria. The work is important for the researchers who are interested in the mechanism of fruit development in Fragaria. However, I feel that some of the conclusions and claims made in the manuscript, including the title, cannot be justified by the data. Below are two main examples. 1) Synteny analysis The scaffolds have not assembled into a larger chromosome, so the macrosynteny conservation could not be evaluated as stated in the methods section. In the results section, however, authors state that "Comparison of the two genomes revealed a remarkable degree of synteny with P. micrantha scaffolds spanning the entirety of the F. vesca genome sequence". The authors need to clarify that the level of synteny detected is micro-level throughout the manscript, not just in Methods section. The resolution of the Figure 3 (Figure 2?) is too low to see any letters but it looks like a couple of hundreds scaffolds were anchored to each F. vesca chromosome. There is no evidence that majority of these scaffolds aligned to one chromosome is in the same P. micrantha chromosome. 2) RNA-seq data The authors reported 1,556 differentially expressed genes between the four developmental stages in P. micrantha, and 816 in F. vesca. They did GO annotation on these genes but they didn't seem to have looked any further. Were there any difference in the profile of the differentially expressed genes in both species and that only in F. vesca?

In conclusion, a lot more work needs to be done (anchoring scaffolds to chromosomes to assess the level of macrosynteny and do a further analyses to develop at least some hypotheses on the genetic mechanism of the fruit development). On the other hand, I feel this work is worthwhile to be published as long as the title and text is appropriately edited to reflect the results accurately.

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

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

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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).