Transcriptomic Determination of the Core Genes Regulating the Growth and Physiological Traits of Quercus mongolica Fisch. ex Ledeb

Round 1

Reviewer 1 Report (Previous Reviewer 2)

The manuscript has been improved following the suggestions of the reviewer.

Minor English language editing required. There are some typos (L15) and repetitions (L56).

Author Response

Detailed Response to Reviewers

Dear reviewers or editors,

We would like to thank you for your careful reading, helpful comments, and constructive suggestions, which has significantly improved the presentation of our manuscript. We quite agree with your comments and revise our manuscript according to these suggestions as shown below. The manuscript has also been errors we found have been corrected. We hope our revised manuscript can be accepted for publication. If there are other problems with the manuscript, we are happy to revise it again.

1. Please submit the RNA sequencing data to NCBI-SRA and quote the accession number in paper.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have uploaded the RNA sequencing data and quoted the login number in the article.

2. WGCNA is generally used for trait and module (gene expression correlation) relationship. Using DEGs in WGCNA doesn’t scientifically sounds good. Authors thought?

The answer to this question: Thank you for your suggestion, which is very useful to us. WGCNA is generally used for trait and module (gene expression correlation) relationship.The purpose of this study is to explore the molecular mechanisms underlying the differential growth and development of Mongolian oak from different sources, and to use differentially expressed genes to better screen core genes that regulate the growth and physiological and biochemical indicators of Mongolian oak from different sources, in order to achieve our research objectives. Some of the literature I referenced also used differentially expressed gene sets as source data for WGCNA analysis. Such as Jiang, M.; Li, X. M.; Yuan, Y. C.; Zhang, G. W.; Pang, J. S.; Ren, J. J.; Wang, J. M.; Yang M.S. Integrated physiological and transcriptomic analyses reveal the molecular mechanism behind the response to cultivation in Quercus mongolica. Front. Plant Sci. 2022, 13 , 947696. Therefore, I believe that using differentially expressed gene sets as source data for WGCNA is not a problem.

3. Please provide the R code of WGCNA analysis as a supplementary file.

The answer to this question: Thank you for your suggestion, which is very useful to us. We apologize for any issues with this section of the content description. Our WGCNA analysis was conducted on the omicsmart (https://www.omicsmart.com/）platform, and we have made modifications in the article.

4. Did you obtain trait module relationship in WGCNA? authors need to explain/write those results also.

The answer to this question: Thank you for your suggestion, which is very useful to us. Previously, we added the correlation heatmap between traits and modules to the supplementary materials. Now, we have added this section to the results and analysis section and described it.

5. What is significance of current study? What is future implication? Add or explore this part.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have added this section to the discussion section.

6. Provide high quality figures.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have improved the pixel size of the image.

7. Line 448. What do you mean by core genes here? Where are the hub genes?

We sorted the genes of the selected specific modules according to the size of the Weight value, and selected the top 50 relationships with the highest Weight value to plot the regulatory network between genes, select several genes with high connectivity in the co expression network as core genes.

8. Line 470. What do you mean by core genes here? Where are the hub genes?

We sorted the genes of the selected specific modules according to the size of the Weight value, and selected the top 50 relationships with the highest Weight value to plot the regulatory network between genes, select several genes with high connectivity in the co expression network as core genes.

9. Line 583. What do you mean by “Transcription-level qRT-PCR”?

The answer to this question: Thank you for your suggestion, which is very useful to us. We selected 12 core genes with relatively high FPKM values for qRT-PCR validation, the main purpose of which is to verify whether the trend of FPKM values in the transcriptome data of Quercus mongolica of different provenances is consistent with the relative expression, and to verify whether the screened core genes and transcriptional data are reliable.

10. Extensive editing of English language required.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have read and corrected all English language errors in the article

11. Line 155. The sentence “WGCNA were ensured by filtering outDEGs with fragments per kilobase of exon per million mapped fragments (FPKM) values < 1,”The sentence seems to be wrong. How DEGs and FPKM related. I feel Authors needs to re-run the whole WGCNA analysis.

The answer to this question: Thank you for your suggestion, which is very useful to us. We filtered out differentially expressed genes with FPKM<1 for WGCNA analysis, mainly because the FPKM values of these genes were too low and had little or no effect in the plant body. Therefore, we filtered them out and conducted WGCNA analysis, So we have no problem selecting the differentially expressed gene set with FPKM>1 as the source data for WGCNA analysis.

12. Line 167. The sentence “Cytoscape_3.7.1 was used to draw the weighted gene co-expression network diagram” is wrong.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have made modifications in the article.

13. Comments on the Quality of English Language Minor English language editing required. There are some typos (L15) and repetitions (L56).

The answer to this question: Thank you for your suggestion, which is very useful to us. We have made modifications in the article.

Reviewer 2 Report (New Reviewer)

 

Suggestions,

 

I feel paper is poorly written. Lots of sentence need to be re-written/. Also, authors need to consider re-running WGCNA analysis. There is lot of confusion and information (WGCNA and Cytoscape) is misleading.

 

1)    Please submit the RNA sequencing data to NCBI-SRA and quote the accession number in paper.

2)    WGCNA is generally used for trait and module (gene expression correlation) relationship. Using DEGs in WGCNA doesn’t scientifically sounds good. Authors thought?

3)    Please provide the R code of WGCNA analysis as a supplementary file.

4)    Did you obtain trait module relationship in WGCNA? authors need to explain/write those results also.

5)    What is significance of current study? What is future implication? Add or explore this part.

6)    Provide high quality figures.

7)    Line 448. What do you mean by core genes here? Where are the hub genes?

8)    Line 470. What do you mean by core genes here? Where are the hub genes?

9)    Line 583. What do you mean by “Transcription-level qRT-PCR”?

10) Extensive editing of English language required.

11) Line 155. The sentence “WGCNA were ensured by filtering out DEGs with fragments per kilobase of exon per million mapped fragments (FPKM) values < 1,”

The sentence seems to be wrong. How DEGs and FPKM related.  I feel Authors needs to re-run the whole WGCNA analysis.

12) Line 167. The sentence “Cytoscape_3.7.1 was used to draw the weighted gene co-expression network diagram” is wrong.

Extensive editing of English language required

Author Response

Detailed Response to Reviewers

Dear reviewers or editors,

We would like to thank you for your careful reading, helpful comments, and constructive suggestions, which has significantly improved the presentation of our manuscript. We quite agree with your comments and revise our manuscript according to these suggestions as shown below. The manuscript has also been errors we found have been corrected. We hope our revised manuscript can be accepted for publication. If there are other problems with the manuscript, we are happy to revise it again.

1. Please submit the RNA sequencing data to NCBI-SRA and quote the accession number in paper.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have uploaded the RNA sequencing data and quoted the login number in the article.

2. WGCNA is generally used for trait and module (gene expression correlation) relationship. Using DEGs in WGCNA doesn’t scientifically sounds good. Authors thought?

The answer to this question: Thank you for your suggestion, which is very useful to us. WGCNA is generally used for trait and module (gene expression correlation) relationship.The purpose of this study is to explore the molecular mechanisms underlying the differential growth and development of Mongolian oak from different sources, and to use differentially expressed genes to better screen core genes that regulate the growth and physiological and biochemical indicators of Mongolian oak from different sources, in order to achieve our research objectives. Some of the literature I referenced also used differentially expressed gene sets as source data for WGCNA analysis. Such as Jiang, M.; Li, X. M.; Yuan, Y. C.; Zhang, G. W.; Pang, J. S.; Ren, J. J.; Wang, J. M.; Yang M.S. Integrated physiological and transcriptomic analyses reveal the molecular mechanism behind the response to cultivation in Quercus mongolica. Front. Plant Sci. 2022, 13 , 947696. Therefore, I believe that using differentially expressed gene sets as source data for WGCNA is not a problem.

3. Please provide the R code of WGCNA analysis as a supplementary file.

The answer to this question: Thank you for your suggestion, which is very useful to us. We apologize for any issues with this section of the content description. Our WGCNA analysis was conducted on the omicsmart (https://www.omicsmart.com/）platform, and we have made modifications in the article.

4. Did you obtain trait module relationship in WGCNA? authors need to explain/write those results also.

The answer to this question: Thank you for your suggestion, which is very useful to us. Previously, we added the correlation heatmap between traits and modules to the supplementary materials. Now, we have added this section to the results and analysis section and described it.

5. What is significance of current study? What is future implication? Add or explore this part.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have added this section to the discussion section.

6. Provide high quality figures.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have improved the pixel size of the image.

7. Line 448. What do you mean by core genes here? Where are the hub genes?

We sorted the genes of the selected specific modules according to the size of the Weight value, and selected the top 50 relationships with the highest Weight value to plot the regulatory network between genes, select several genes with high connectivity in the co expression network as core genes.

8. Line 470. What do you mean by core genes here? Where are the hub genes?

We sorted the genes of the selected specific modules according to the size of the Weight value, and selected the top 50 relationships with the highest Weight value to plot the regulatory network between genes, select several genes with high connectivity in the co expression network as core genes.

9. Line 583. What do you mean by “Transcription-level qRT-PCR”?

The answer to this question: Thank you for your suggestion, which is very useful to us. We selected 12 core genes with relatively high FPKM values for qRT-PCR validation, the main purpose of which is to verify whether the trend of FPKM values in the transcriptome data of Quercus mongolica of different provenances is consistent with the relative expression, and to verify whether the screened core genes and transcriptional data are reliable.

10. Extensive editing of English language required.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have read and corrected all English language errors in the article

11. Line 155. The sentence “WGCNA were ensured by filtering outDEGs with fragments per kilobase of exon per million mapped fragments (FPKM) values < 1,”The sentence seems to be wrong. How DEGs and FPKM related. I feel Authors needs to re-run the whole WGCNA analysis.

The answer to this question: Thank you for your suggestion, which is very useful to us. We filtered out differentially expressed genes with FPKM<1 for WGCNA analysis, mainly because the FPKM values of these genes were too low and had little or no effect in the plant body. Therefore, we filtered them out and conducted WGCNA analysis, So we have no problem selecting the differentially expressed gene set with FPKM>1 as the source data for WGCNA analysis.

12. Line 167. The sentence “Cytoscape_3.7.1 was used to draw the weighted gene co-expression network diagram” is wrong.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have made modifications in the article.

13. Comments on the Quality of English Language Minor English language editing required. There are some typos (L15) and repetitions (L56).

The answer to this question: Thank you for your suggestion, which is very useful to us. We have made modifications in the article.

Round 2

Reviewer 2 Report (New Reviewer)

I think authors need to take help of native English speaker to revise the paper. Still paper is not in a good shape. Lot of sentences needs revision. 

The extensive editing of English language is required. 

Author Response

Detailed Response to Reviewers

Dear reviewers or editors,

We would like to thank you for your careful reading, helpful comments, and constructive suggestions, which has significantly improved the presentation of our manuscript. We quite agree with your comments and revise our manuscript according to these suggestions as shown below. The manuscript has also been errors we found have been corrected. We hope our revised manuscript can be accepted for publication. If there are other problems with the manuscript, we are happy to revise it again.

1. I think authors need to take help of native English speaker to revise the paper. Still paper is not in a good shape. Lot of sentences needs revision.

   The answer to this question: Thank you for your suggestion, which is very useful to us. We have polished the manuscript in English and marked any modifications.

This manuscript is a resubmission of an earlier submission. The following is a list of the peer review reports and author responses from that submission.

Round 1

Reviewer 1 Report

Dear authors,

My following comments about your manuscript are:

Line 93: the seeds were sown...

Line 107-108 and 121. Physiological traits are only photosynthesis and P and N content. Protein, sugars, chlorophyll, hormone content etc are biochemical indicators. Please the authors should revise better these notions.

Line 209: I think that the sentences “…the geographical adaptation and evolution has occurred” is not sustained by the results presented. I think that the authors should only indicated the geographical adaptation and then they should explain as the physiological and biochemical changes did contribute adaptation to different climates in Quercus tress. Such comments should be included in discussion section and not in results.

The description of Figure 3 should be improved (222-228). The ion nutrients are P e N. Sugar and protein are not nutrients. The figure show that auxin only did correlate with Chla and N. Please verify.

Line 237: PC3 is not indicated on figure.

The figures have poor resolution. It is very difficult to make a analysis of it.

Line 262: common DEG refers to genes with similar expression? Genes with differential expression are too common genes to Quercus trees with different provenances.

Line 271-273. Please revise the data of upregulated and downregulated genes.

Line 282: I did not understand the phrase.

Figure 7d: Please the scale on figure should be corrected.

On 3.4, 3.5, 3.6 and 3.7: The authors only describe the modules (figure 7) that higher positive or negative correlation, being that the results shown other module has high correlation too? Why the authors choose to make it? I think that it should be explain.

Please improve the description of figure 12. The author should include better comments.

About the phrase: …”consistent with the gradual decrease …..from north to south” (line 387-389 and in other parts of the manuscript):  The authors attribute the adaptative responses among Quercus trees  for different environment to metabolic and physiological changes in relation to proteins, sugars, nutrient, Pn. In discussion section, the authors should indicate how these changes support the adaptation to different climates. I do not observe these comments. Please include what is physiological role of theses responses to Quercus adaptation to different climate.

414-416, 427. Please revise the phrase.

Other questions:

If the distribution to north (cool environment) represents a stressful environment for Quercus, what the authors explain there is an increase in Auxin content but not in ABA content. ABA is known as stress hormone.

Please indicate the name of SDH, APA1, UGT.

458: ROS?

In conclusion section: 

491 The author did not show the expression of genes involved in ion transport and absorption.

 

With kind regards

Author Response

Dear reviewers or editors,

We would like to thank you for your careful reading, helpful comments, and constructive suggestions, which has significantly improved the presentation of our manuscript. We quite agree with your comments and revise our manuscript according to these suggestions as shown below. The manuscript has also been errors we found have been corrected. We hope our revised manuscript can be accepted for publication. If there are other problems with the manuscript, we are happy to revise it again.

1.Line 93: the seeds were sown.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

2.Line 107-108 and 121. Physiological traits are only photosynthesis and P and N content. Protein, sugars, chlorophyll, hormone content etc are biochemical indicators. Please the authors should revise better these notions.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

3.Line 209: I think that the sentences “…the geographical adaptation and evolution has occurred” is not sustained by the results presented. I think that the authors should only indicated the geographical adaptation and then they should explain as the physiological and biochemical changes did contribute adaptation to different climates in Quercus tress. Such comments should be included in discussion section and not in results.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.We have removed such expressions from the results and will add this section to the discussion.

4.The description of Figure 3 should be improved (222-228). The ion nutrients are P e N. Sugar and protein are not nutrients. The figure show that auxin only did correlate with Chla and N. Please verify.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions. After careful consideration, we have decided to delete this part of the content as it affects the entire article.

5.Line 237: PC3 is not indicated on figure.

The figures have poor resolution. It is very difficult to make a analysis of it.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

6.Line 262: common DEG refers to genes with similar expression? Genes with differential expression are too common genes to Quercus trees with different provenances.

The answer to this question: Thank you for your suggestion, which is very useful to us. The common differentially expressed genes refer to the portion of genes that are shared among all differentially expressed genes among Quercus mongolica species of different provenance.

7.Line 271-273. Please revise the data of upregulated and downregulated genes.

The answer to this question: Thank you for your suggestion, which is very useful to us.After inspection, my data is not incorrect, and it is also possible that I did not understand your meaning.

8.Line 282: I did not understand the phrase.

The answer to this question: Thank you for your suggestion, which is very useful to us.The meaning of this sentence is that these differential genes are enriched in carbohydrate metabolism, biosynthesis of other secondary metabolites, signal transduction, and environmental adaptation et KEGG metabolic pathways.

9.Figure 7d: Please the scale on figure should be corrected.

The answer to this question: Thank you for your suggestion, which is very useful to us.We have modified the manuscript according to your suggestions.

10.On 3.4, 3.5, 3.6 and 3.7: The authors only describe the modules (figure 7) that higher positive or negative correlation, being that the results shown other module has high correlation too? Why the authors choose to make it? I think that it should be explain.

The answer to this question: Thank you for your suggestion, which is very useful to us.Due to the large number of significantly correlated modules, we only selected the module with the highest correlation for detailed discussion.We have modified the manuscript according to your suggestions(Line 421).

11.About the phrase: …”consistent with the gradual decrease …..from north to south” (line 387-389 and in other parts of the manuscript):  The authors attribute the adaptative responses among Quercus trees  for different environment to metabolic and physiological changes in relation to proteins, sugars, nutrient, Pn. In discussion section, the authors should indicate how these changes support the adaptation to different climates. I do not observe these comments. Please include what is physiological role of theses responses to Quercus adaptation to different climate.

The answer to this question: Thank you for your suggestion, which is very useful to us.We have modified the manuscript according to your suggestions.We have added this section to the discussion.

12.414-416, 427. Please revise the phrase.

The answer to this question: Thank you for your suggestion, which is very useful to us.We have modified the manuscript according to your suggestions.

13.If the distribution to north (cool environment) represents a stressful environment for Quercus, what the authors explain there is an increase in Auxin content but not in ABA content. ABA is known as stress hormone.

The answer to this question: Thank you for your suggestion, which is very useful to us.We are very sorry for the error in our description in the paper. As shown in Figure 2e, the ABA content gradually increases with the Mongolian oak and Mongolian oak source from south to north, while the IAA content gradually decreases with the Mongolian oak and Mongolian oak source from south to north. This also confirms your statement. Thank you for your reminder.We have made modifications in the manuscript.

14.Please indicate the name of SDH, APA1, UGT.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

15.458: ROS?

Thank you for your suggestion, which is very useful to us. We have modified the active oxygen to reactive oxygen species.

16.491 The author did not show the expression of genes involved in ion transport and absorption.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.We have removed it in the conclusion section.

Author Response File: Author Response.docx

Reviewer 2 Report

Manuscript ID: forests-2328430

 

In this ms, ID: forests-2328430 and entitled “Determination of the core genes regulating the growth and physiological traits of Quercus mongolica of different provenances based on transcriptomics”, the Authors characterized the molecular basis for the main differences in the growth and physiological traits by performing transcriptome analysis of Q. mongolica seedlings from different regions of Northern China.

Specific comments are following:

 

TITLE

Here and where it occurs, use the complete name: Quercus mongolica Fisch. ex Ledeb.

Can use a simpler title, for example “Transcriptomic Determination of the Core Genes Regulating the Growth and Physiological Traits of Quercus mongolica Fisch. ex Ledeb”

 

ABSTRACT

L15: check for typos in seedings -> seedlings

 

INTRO

L41: add pertinent reference(s)

L47: here, the first time, use the full name: Quercus mongolica Fisch. ex Ledeb.

L51: check for English language “tress” - > “trees”

L54: add pertinent reference(s)

L57: remove redundancy of “provenance”, and then explain better the concept

L79, please, add the place of study “from the Northern China”

L97: the samples are calculated by 6 places x 10 trees each = 60, fix or explain better why you indicated 70…

 

M&M

L108: there some typos, fix two commas and add a space before IAA

L113: add “content” after “soluble protein”

L123: add brand

 

RESULTS

For all Figures, Authors have to improve resolution.

L229: in Figure 3, check for typos in “seeding height” -> “seedling height”

L241: change semicolons to commas

L246: please, explain the concept more clearly

L275,279,286,299,404 : indicate Supplementary Figures as Supplementary Figures S1, S2 etc

L306: add Figure 7

L318: check for “limone”, did you mean “limonene”?

L330: fix typos in “contenr”

 

DISCUSSION

L427: use “auxins”

L431: check for “which”

 

CONCLUSIONS

L483: add “soluble protein content”

L495: add the main aim of these plant regulations, for example “for the adaptation to environment”

Author Response

Dear reviewers or editors,

We would like to thank you for your careful reading, helpful comments, and constructive suggestions, which has significantly improved the presentation of our manuscript. We quite agree with your comments and revise our manuscript according to these suggestions as shown below. The manuscript has also been errors we found have been corrected. We hope our revised manuscript can be accepted for publication. If there are other problems with the manuscript, we are happy to revise it again.

TITLE

1.Here and where it occurs, use the complete name: Quercus mongolica Fisch. ex Ledeb.

Can use a simpler title, for example “Transcriptomic Determination of the Core Genes Regulating the Growth and Physiological Traits of Quercus mongolica Fisch. ex Ledeb”

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

ABSTRACT

INTRO

2.L41: add pertinent reference(s)

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

3.L47: here, the first time, use the full name:Quercus mongolica Fisch. ex Ledeb.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

4.L51: check for English language “tress” - > “trees”

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

5.L54: add pertinent reference(s)

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

6.L57: remove redundancy of “provenance”, and then explain better the concept

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

7.L79: please, add the place of study “from the Northern China”

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

8.L97: the samples are calculated by 6 places x 10 trees each = 60, fix or explain better why you indicated 70…

The answer to this question: Thank you for your suggestion, which is very useful to us. We seeded 70 seeds per provenance for 3 replicates, and then selected 10 seedlings per replicate for the experiment (30 seedlings per provenance). 70 is not the number of seedlings tested.

M&M

9.L108: there some typos, fix two commas and add a space before IAA

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

10.L113: add “content” after “soluble protein”

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

11.L123: add brand

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

RESULTS

12.For all Figures, Authors have to improve resolution.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

13.L229: in Figure 3, check for typos in “seeding height” -> “seedling height”

The answer to this question: Thank you for your suggestion, which is very useful to us. After careful consideration, we have removed the part of Figure 3.

14.L241: change semicolons to commas

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

15.L246: please, explain the concept more clearly

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

16.L275,279,286,299,404 : indicate Supplementary Figures as Supplementary Figures S1, S2 etc

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

17.L306: add Figure 7

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

18.L318: check for “limone”, did you mean “limonene”?

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

19.L330: fix typos in “contenr”

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

DISCUSSION

20.L427: use “auxins”

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

21.L431: check for “which”

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

CONCLUSIONS

22.L483: add “soluble protein content”

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

23.L495: add the main aim of these plant regulations, for example “for the adaptation to environment”

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions

Author Response File: Author Response.docx

Round 2

Reviewer 1 Report

Dear author,

My comments about your manuscript are:

Soluble protein and sugar content are biochemical traits. Also, verify lanes 216-218.

Please, observe the Figure 2b.

Line 234-241 Please the authors should improve the description. Please be more explicit for describing the figure.

What means common DEG? Please explain. The common genes are found in all the Quercus trees of different provenance, but some genes are differentially expressed (the Quercus trees from North expressed different genes as compared with trees from south). Thus, I think that common DEG is a term incorrect and thus The authors must remove the term “common”.     

On 3.4, 3.5, 3.6 and 3.7: The authors only describe the modules (figure 7) that higher positive or negative correlation, being that the results shown other module has high correlation too? Why the authors choose to make it? I think that it should be explained.

Line 428-444 In discussion section, the authors should indicate how these changes support the adaptation to different climates. I do not observe these comments. Please include what is physiological role of these responses to Quercus adaptation to different climate. The statement indicated in discussion is a basic opinion and it does not explain the result found.

 

The author indicate: “… the four main indicators, ABA content, IAA content, soluble sugar content, and soluble protein content, have the strongest response to different environmental conditions.” How such changes can explain the Quercus tree adaptation to different envinroment”

With kind regards

 

Author Response

Detailed Response to Reviewers

Dear reviewers or editors,

We would like to thank you for your careful reading, helpful comments, and constructive suggestions, which has significantly improved the presentation of our manuscript. We quite agree with your comments and revise our manuscript according to these suggestions as shown below. The manuscript has also been errors we found have been corrected. We hope our revised manuscript can be accepted for publication. If there are other problems with the manuscript, we are happy to revise it again.

 

1. Soluble protein and sugar content are biochemical traits. Also, verify lanes 216-218.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

2. Please, observe the Figure 2b.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

3. Line 234-241 Please the authors should improve the description. Please be more explicit for describing the figure.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

4. What meanscommon DEG? Please explain. The common genes are found in all the Quercus trees of different provenance, but some genes are differentially expressed (the Quercus trees from North expressed different genes as compared with trees from south). Thus, I think that common DEG is a term incorrect and thus The authors must remove the term “common”.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.Figure 5b reflects the same number of differentially expressed genes in different comparison groups, therefore, we changed “common” to “same”，If this modification is not feasible, we can consider removing this part of the content.

5. On 3.4, 3.5, 3.6 and 3.7: The authors only describe the modules (figure 7) that higher positive or negative correlation, being that the results shown other module has high correlation too? Why the authors choose to make it? I think that it should be explained.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

6. Line 428-444 In discussion section, the authors should indicate how these changes support the adaptation to different climates. I do not observe these comments. Please include what is physiological role of these responses to Quercus adaptation to different climate. The statement indicated in discussion is a basic opinion and it does not explain the result found.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

7. Detailed Response to Reviewers

   Dear reviewers or editors,

   We would like to thank you for your careful reading, helpful comments, and constructive suggestions, which has significantly improved the presentation of our manuscript. We quite agree with your comments and revise our manuscript according to these suggestions as shown below. The manuscript has also been errors we found have been corrected. We hope our revised manuscript can be accepted for publication. If there are other problems with the manuscript, we are happy to revise it again.

    

   1. Soluble protein and sugar content are biochemical traits. Also, verify lanes 216-218.

   The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

   2. Please, observe the Figure 2b.

   The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

   3. Line 234-241 Please the authors should improve the description. Please be more explicit for describing the figure.

   The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

   4. What meanscommon DEG? Please explain. The common genes are found in all the Quercus trees of different provenance, but some genes are differentially expressed (the Quercus trees from North expressed different genes as compared with trees from south). Thus, I think that common DEG is a term incorrect and thus The authors must remove the term “common”.

   The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.Figure 5b reflects the same number of differentially expressed genes in different comparison groups, therefore, we changed “common” to “same”，If this modification is not feasible, we can consider removing this part of the content.

   5. On 3.4, 3.5, 3.6 and 3.7: The authors only describe the modules (figure 7) that higher positive or negative correlation, being that the results shown other module has high correlation too? Why the authors choose to make it? I think that it should be explained.

   The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

   6. Line 428-444 In discussion section, the authors should indicate how these changes support the adaptation to different climates. I do not observe these comments. Please include what is physiological role of these responses to Quercus adaptation to different climate. The statement indicated in discussion is a basic opinion and it does not explain the result found.

   The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

   7. The author indicate: “… the four main indicators, ABA content, IAA content, soluble sugar content, and soluble protein content, have the strongest response to different environmental conditions.” How such changes can explain the Quercus tree adaptation to different envinroment”.

   The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

   The author indicate: “… the four main indicators, ABA content, IAA content, soluble sugar content, and soluble protein content, have the strongest response to different environmental conditions.” How such changes can explain the Quercus tree adaptation to different envinroment”.

The answer to this question: Thank you for your suggestion, which is very useful to us. We have modified the manuscript according to your suggestions.

Author Response File: Author Response.docx