This study presented the genome of Potentilla micrantha, a closely related species with Fragaria vesca, which is the model species of the cultivated strawberry, F. x ananassa and Rosaceae family, and the authors compared them. It is really interesting about the homology in the genome and morphological characteristics between the two species, and in the suggestion based on the results in comparison in MADs-box conserved domain-containing genes and transposable elements. Therefore, I consider that it is worthwhile to accept this paper in GigaScience. In globaly, Potentilla and Fragaria both "grow within the same ecological niches, and where their ranges of distribution overlap" as the authors presented in the introduction. In relation to the evolutionary context, why the two genus have been able to be separated? Because it is possible that gene flow could suppress adaptive differentiation at the beginning of the speciation if a non-mutated and a mutated individual have existed in the common habitat. And also, Potentilla or Fragaria, which genus is the closest genus that is remaining the characteristics of the common ancestor? If the authors discuss about the mechanisms affected on the differentiation, this study would attract attention from various researcher related with plant sciences. Anyway, the manuscript has been well constructed with detailed discription in Introduction, Results, Discussion, and Materials and Methods, although the authors have to make sure about the order of the numbering of the Figures and to improve the Figures. For the latter, high-resolution Figures and detailed descriptions as Figure legends have to be presented, because it is difficult to recognize about the contents and construction with viewing the figures.

Page Line Comments Page 1 Line 7 On the description for "F. × ananassa", a space have to be included between "×" and "ananassa". Page 4 Line 25 Here it can be seen that some redundant descriptions between the current paragraph and the last paragraph. Please present about clear objective in this study.

Page 7 Line 18 Number of the Figures are not matched with the actually presented. The number of the Fig. 2 and Fig. 3 should be converted because Fig.2 is a set of photographs about the flower/fruit developmental stages but not synteny with P. micrantha and the F. vesca genome sequence. Page 8 Line 20 The authors did not present the results of the two method, ML and MP, although they presented the results NJ in Fig.5, right? If so, please mention about the actual situation with the word "data not shown for ML and MP" for better understanding.

Page 15 Line 6 Why the authors have selected the plants from Serbia? Page 16 Line 20 The descriptions are redundant in the part of sequencing with HiSeq2000. please correct. Page 19 Line 15-16 How have the authors discriminated for the two sentences; "FPKM was used to distinguish expressed genes from inactive genes during the flower development in each species." and "FPKM was used to define a set of highly expressed genes." Page 19 Line 25 It is necessarily to insert a space into sqrt(MSR). Page 20 Line 12 Its better to include abbreviations for the three methods, Maximum Likelihood (ML), Maximum Parsimony (MP) and Neighbour-joining (NJ)

Resolution of the most of the figures should be improved because it is difficult to recognize about the contents details in the figures with low quality. Fig. 3 Text size is too small. improve the resolution of the figure Fig. 4 Text size is too small. improve the resolution of the figure Fig. 5 The authors have to present explanations about the circular heatmap, gene, the meaning of the A, B, C, and D in the Fig. 5 and Fig 6. Please also present the meaning of the black circle on the dendrogram. I could not recognize about the text in the Fig. 5 because the size is too small.

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.)
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 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).