Molecular Cloning of QwMYB108 Gene and Its Response to Drought Stress in Quercus wutaishanica Mayr
Round 1
Reviewer 1 Report (Previous Reviewer 1)
Comments and Suggestions for AuthorsGenerally, the manuscript has been improved, and enriched with new chapters (2.6, 3.6) a reformulated Discussion, and a Conclusion.
Nevertheless, it still needs some correction, especially in writing e.g. citations [19 25 26 27 ] in line 64, or lack of "]" or dots at the end of phrases (revise new chapters with this in mind).
Names of all producers or companies, "Pressen" or "Thermo" normally should be accompanied by city and country details, e.g. "ThermoFisher Scientific (Waltham, MA, USA)"
While first time cited, the Latin name of the species should be written in the full botanic description, i.e. "Q. wutaishanica Mayr" in the title, or line 10. It was correctly presented for "Poncirus trifoliata L.", firstly cited in line 304
"Lablab purpureus" should be in italic font.
Line 156: the font in the Table title should be unified "qRT PCR" is not the same as "primers sequence."
I did not receive a letter, or note with answers from the Authors, but I hope they will adapt the manuscript's content to the Journal rules.
Author Response
Authors’ Response to the Review Comments
Title: Molecular cloning of QwMYB108 gene and its response to drought stress in Quercus wutaishanica
Authors: ZHAO Xue-Fei, SUN Ying, WANG Yong, Shao Di, CHEN Gang, JIANG Yi-Ren*, QIN Li
Manuscript ID: forests-3146786
Dear Editor and Reviewers:
Thank you for your letter and for the reviewers’ constructive comments concerning our manuscript entitled “Molecular cloning of QwMYB108 gene and its response to drought stress in Quercus wutaishanica”. We have studied the comments carefully and made necessary revisions following the suggestions. We hope that the revised manuscript now meets the publication standard of Forests.
The point-by-point response to the comments and suggestions are listed below.
Hopefully our answers are clear and with our best regards to you!
Yours sincerely,
All authors
August 18, 2024
Response to the reviewer’s comments:
Comment:1. Nevertheless, it still needs some correction, especially in writing e.g. citations [19 25 26 27 ] in line 64, or lack of "]" or dots at the end of phrases (revise new chapters with this in mind).
Response: Thank you for your suggestion. This was an oversight on our part and we have corrected it here. Once again, thank you very much for your comments and suggestions.
Comment:2. Names of all producers or companies, "Pressen" or "Thermo" normally should be accompanied by city and country details, e.g. "ThermoFisher Scientific (Waltham, MA, USA)".
Response: We sincerely appreciate the valuable comments. We have reviewed the article carefully and added the details of the manufacturer or company in the corresponding place.
Comment:3. While first time cited, the Latin name of the species should be written in the full botanic description, i.e. "Q. wutaishanica Mayr" in the title, or line 10. It was correctly presented for "Poncirus trifoliata L.", firstly cited in line 304.
Response: We totally understand the reviewer’s concern. Thank you for pointing out this problem in manuscript. We have added a note after the Latin name of the plant that first appears.
Comment:4. "Lablab purpureus" should be in italic font.
Response: We sincerely appreciate the valuable comments. Thank you for finding this problem, it was our negligence that led to this error, which has been revised in the manuscript
Comment:5. Line 156: the font in the Table title should be unified "qRT PCR" is not the same as "primers sequence."
Response: Thank you for your suggestion. We have modified here. Thanks again for your suggestion.
Comment:6. I did not receive a letter, or note with answers from the Authors, but I hope they will adapt the manuscript's content to the Journal rules.
Response: We are very sorry that it is our mistake that we did not attach the letter when we submitted it. Thank you for your good wishes to us, we will comply with the requirements of the journal to revise the manuscript. Thank you again for your valuable suggestion to us.
Reviewer 2 Report (Previous Reviewer 2)
Comments and Suggestions for AuthorsSecond review of Zhao et al., “Molecular cloning…Quercus wutaishanica”
The present comments represent my second look at this manuscript. Although I am not aware of problems with the core science, the manuscript is not ready for publication. Throughout the paper are typos, inconsistencies. As a reviewer, it is not my place to seek out every minor issue, but to give a sampler of 10 examples:
Line 23: sentence incomplete
Line 33: error still needs correction
Line 72. Quercus is not a species group. It is a genus.
Line 72. Fagaceae should be capitalized
Line 102: Sentence need rewriting
Line 175: pollution-free should be contamination-free
Line 292. The genus names should be given, not abbreviated with no prior indication of what O and A stand for
Line 305. The use of authorships connected to species names is inconsistent.
Line 306: “The results of this study are consistent with the results” needs rewriting.
Line 316. Use of italics for species names is inconsistent.
and more….
The end of the perp still does not read well. The discussion is not really an analysis of the results and their implications. It is largely a confusing recount of prior research on MYB-related genes, which may fit better in the Intro. Or if these genes in other species are directly relevant to understanding the present results, this should be explained with more clarity (and brevity).
The basic science in this manuscript no doubt merits publication, but there is a disconnect between the basic science and careless manuscript preparation, especially being a 2nd submission. This needs correction before publication.
Comments on the Quality of English LanguageEnglish mostly ok, needs minor copy editing.
Author Response
Authors’ Response to the Review Comments
Title: Molecular cloning of QwMYB108 gene and its response to drought stress in Quercus wutaishanica
Authors: ZHAO Xue-Fei, SUN Ying, WANG Yong, Shao Di, CHEN Gang, JIANG Yi-Ren*, QIN Li
Manuscript ID: forests-3146786
Dear Editor and Reviewers:
Thank you for your letter and for the reviewers’ constructive comments concerning our manuscript entitled “Molecular cloning of QwMYB108 gene and its response to drought stress in Quercus wutaishanica”. We have studied the comments carefully and made necessary revisions following the suggestions. We hope that the revised manuscript now meets the publication standard of Forests.
The point-by-point response to the comments and suggestions are listed below.
Hopefully our answers are clear and with our best regards to you!
Yours sincerely,
All authors
August 18, 2024
Response to the reviewer’s comments:
Comment:1. The present comments represent my second look at this manuscript. Although I am not aware of problems with the core science, the manuscript is not ready for publication. Throughout the paper are typos, inconsistencies. As a reviewer, it is not my place to seek out every minor issue, but to give a sampler of 10 examples:
Line 23: sentence incomplete
Line 33: error still needs correction
Line 72. Quercus is not a species group. It is a genus.
Line 72. Fagaceae should be capitalized
Line 102: Sentence need rewriting
Line 175: pollution-free should be contamination-free
Line 292. The genus names should be given, not abbreviated with no prior indication of what O and A stand for
Line 305. The use of authorships connected to species names is inconsistent.
Line 306: “The results of this study are consistent with the results” needs rewriting.
Line 316. Use of italics for species names is inconsistent.
and more….
Response: We sincerely appreciate the valuable comments. Your suggestions are very important to us, we have corrected the problems you raised one by one, and carefully examined the manuscript to correct the existing problems. Thank you again for your warm work earnestly.
Comment:2. The end of the perp still does not read well. The discussion is not really an analysis of the results and their implications. It is largely a confusing recount of prior research on MYB-related genes, which may fit better in the Intro. Or if these genes in other species are directly relevant to understanding the present results, this should be explained with more clarity (and brevity).
Response: Thank you for your suggestion. We tried our best to improve the manuscript. We appreciate for the reviewer’s warm work earnestly, and hope the correction will meet with approval. Once again, thank you very much for your comments and suggestions.
Reviewer 3 Report (Previous Reviewer 3)
Comments and Suggestions for AuthorsI have no comments.
Author Response
Authors’ Response to the Review Comments
Title: Molecular cloning of QwMYB108 gene and its response to drought stress in Quercus wutaishanica
Authors: ZHAO Xue-Fei, SUN Ying, WANG Yong, Shao Di, CHEN Gang, JIANG Yi-Ren*, QIN Li
Manuscript ID: forests-3146786
Dear Editor and Reviewers:
Thank you very much for your careful review of our manuscript entitled “Molecular cloning of QwMYB108 gene and its response to drought stress in Quercus wutaishanica”. Your reply gives us great encouragement in our work. Thank you again for your review. Best wishes to you!
Yours sincerely,
All authors
August 18, 2024
Reviewer 4 Report (New Reviewer)
Comments and Suggestions for AuthorsThe authors obtained the full-length sequence of the QwMYB108 gene by gene cloning and performed bioinformatics analysis. They examined the expression of QwMYB108 in various tissues and its response to drought stress using real-time fluorescence qRT PCR. However, the manuscript has the following minor and major concerns before acceptance of the article for publication.
Abstract: Presenting the results quantitatively in the abstract is preferable, rather than merely descriptive. Additionally, it is recommended to base the presentation of results on statistical tests.
Keywords: Keywords should be in alphabetical order and different from title words.
Line 33: Please resolve the problem.
Line 64: Please correct citations.
Lines 87-93: At the end of the introduction section, first, briefly mention what the scientific gap is in this field. Why did you have this goal?
The authors mentioned what they did. These items are mentioned in Materials and Methods. What were your goals?
Line 97: Please add, city and country names.
Line 107-116: Did you have biological replications? How many replications were there? In the Results section, you mentioned using the Duncan mean comparison test, which implies it was based on an experimental design. You should specify the type of experimental design in the Materials and Methods section. In addition, the software that you used.
Line 151-154: Statistical analysis of gene expression was not performed??
The statistical analysis part is missing.
Line 254: Please mention the method of phylogenetic analysis and the software used in the Materials and Methods section.
Line 265: The description of these analyses and the software used must be included in the Materials and Methods section.
Comments for author File: 
Comments.pdf
Minor editing of English language required.
Author Response
Authors’ Response to the Review Comments
Title: Molecular cloning of QwMYB108 gene and its response to drought stress in Quercus wutaishanica
Authors: ZHAO Xue-Fei, SUN Ying, WANG Yong, Shao Di, CHEN Gang, JIANG Yi-Ren*, QIN Li
Manuscript ID: forests-3146786
Dear Editor and Reviewers:
Thank you for your letter and for the reviewers’ constructive comments concerning our manuscript entitled “Molecular cloning of QwMYB108 gene and its response to drought stress in Quercus wutaishanica”. We have studied the comments carefully and made necessary revisions following the suggestions. We hope that the revised manuscript now meets the publication standard of Forests.
The point-by-point response to the comments and suggestions are listed below.
Hopefully our answers are clear and with our best regards to you!
Yours sincerely,
All authors
August 18, 2024
Response to the reviewer’s comments:
Comment:1. Abstract: Presenting the results quantitatively in the abstract is preferable, rather than merely descriptive. Additionally, it is recommended to base the presentation of results on statistical tests.
Response: Thank you for your suggestion. Your opinion is very important to us. We have revised this section to add statistical analysis here.
Comment:2. Keywords: Keywords should be in alphabetical order and different from title words.
Response: We sincerely appreciate the valuable comments. Your advice is very valuable. We have reordered the keywords. Thank you again for your warm work.
Comment:3. Line 33: Please resolve the problem.
Response: We totally understand the reviewer’s concern. We are very sorry for the mistake caused by our negligence. This has been modified. Thank you for your careful review.
Comment:4. Line 64: Please correct citations.
Response: We sincerely appreciate the valuable comments. We are very sorry for the mistake caused by our negligence. This has been modified. Thank you for your careful review.
Comment:5. Lines 87-93: At the end of the introduction section, first, briefly mention what the scientific gap is in this field. Why did you have this goal?
The authors mentioned what they did. These items are mentioned in Materials and Methods. What were your goals?
Response: Thank you for your suggestion. We do our best to revise this section. At present, it is well known that Quercus wutaishanica has drought tolerance, but its regulation mechanism to drought stress is not clear. We want to explore his molecular mechanism. The seedlings of Quercus liaodongensis are highly susceptible to drought stress. We wanted to explore its molecular mechanism to lay a foundation for future germplasm innovation.
Comment:6. Line 97: Please add, city and country names.
Response: We sincerely appreciate the valuable comments.We have reviewed the article carefully and added the details of the manufacturer or company in the corresponding place.
Comment:7. Line 107-116: Did you have biological replications? How many replications were there? In the Results section, you mentioned using the Duncan mean comparison test, which implies it was based on an experimental design. You should specify the type of experimental design in the Materials and Methods section. In addition, the software that you used.
Response: We sincerely appreciate the valuable comments. We did biological replication. We set up a total of four gradients of the experiment, each gradient using four POTS of seedlings as replicates. We have added the software used later. Thank you again for your valuable advice.
Comment:8. Line 151-154: Statistical analysis of gene expression was not performed??
The statistical analysis part is missing.
Response: Thank you for your suggestion. We did a statistical analysis. Here we have added software for statistical analysis and software for drawing images. Thank you again for your warm work.
Comment:9. Please mention the method of phylogenetic analysis and the software used in the Materials and Methods section.
Response: We sincerely appreciate the valuable comments.Your suggestion is very important to us. We have added the analysis method and the software used in this section.
Comment:10. Line 265: The description of these analyses and the software used must be included in the Materials and Methods section.
Response: We totally understand the reviewer’s concern. We have made changes to this place. Your suggestion is very important to us. Thank you again for your valuable suggestion.
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
Comments and Suggestions for AuthorsDrought stress is among the most threatening factor to many forest trees, including Quercus sp. in Asia and other continents. As proven by the current study presented by the Authors, one of the key factors in plant growth and development, and in a complex way of homeostasis regulation in the presence of abiotic stress is the transcription factor QwMYB108 in Q. wutaishanica, which shows high similarity in amino-acid sequences to Q. robur.
The article is original and has high scientific interest but needs improvement, especially in wording and English style. The title, abstract, and keywords reflect the paper's content. The introduction explicitly presents the problem. Experimental methods are correct but need small clarifications. To be precise, it is better to mention how many plants per variant CK, LD, MD, and SD were examined, but not “pots” because sometimes two or more seedlings may be grown in one pot.
Results are justified by figures and tables in the main text and supplementary materials. My only doubt is about “gene cloning” (lines 115 in Methods and 144 in Results) because you amplified the fragments and did not clone them in plasmids. Please give more explanation.
The discussion is concise. References are complete, but the position [49] was omitted in the main text.
In general, the content of the manuscript needs some improvements:
Line 25: please check if the citation of the references should look in the whole text like “1,2” or rather [1,2]
Line 29: to cope, not “to copy” with abiotic …
Line 69, 284: Latin names, like “O. sativa”, “Q. wutaishanica“ should be in Italic font
Line 70: Reformulate “Q. wutaishanica is a strong resistance to reverse tree species” because the sens is not clear
Line 90: Q. wutaishanica “was used” and I recommend to check the whole text by a native speaker
Line 95: Please mention which apparatus (name, producer) have you used to measure the soil moisture
Line 113: the same as above for “ultramicrospectrophotometer”
Line 161-162: please reformulate, because “Band size of this target sequence is between 750 and 161 1 000 bp. Consistent with the length of the candidate genes” is unclear
Lines 158 and 159: there is redundant numbering for the Figure 1. Please use only once “Figure 1. with its description” – and the same remarks should be applied to all the figures
Line 305: what means “wabundantly”?
Line 320: According to the research, you cannot extrapolate the results to all “plants” The experiment concerned only Quercus wutaishanica. So it would be safer to conclude “in Quercus sp.”
Comments on the Quality of English LanguageSome details in the research content, the English wording, and the quality of figures need correction in their descriptions to avoid confusion.
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsMay 25 2024
Review of Zhao et al., “Molecular cloning of QwMYB108…”
General comments:
The manuscript seems almost ready for publication, although it does need a round of copy-editing to sandpaper the English, and to fix additional minor editorial issues, some of these listed below. The work is thorough and detailed, revealing great skill and ability. The value of delving deeply into the genetics of tree stress responses is obvious and welcome. It would be interesting as the authors advance their future research to see the effects of additional types of non-drought stresses on the expression of QwMYB108 and related genes, and related cell signalling. Thus this paper appears to be a promising step along a path to treasure.
The article might benefit from more context on Quercus wutaishanica, including its authorship (https://powo.science.kew.org/results?q=quercus%20wutaishanica), and reference to source of more info on it. Please give at least its distribution and taxonomic position within Quercus (see comments on phylogeny below). What is its commercial significance? Is it propagated commercially or for habitat restoration? Because the article deals with the stress biology of Q. wutaishanca, what are its geo-ecological limits and preferences? Does it grow where drought stress is constant? frequent? rare? seasonal? Temperature stress? Disease? Can you include a photo of the species? Oaks can be difficult to ID, or undergo taxonomic adjustment, or worse, may be hybridized. For such reasons it is useful to cite a permanent voucher specimen of the study material in a herbarium. As the study material came from cultivated material (line 91), a voucher from the same material is still possible? Or maybe the nursery has already preserved herbarium vouchers?
Typos and similar minor fixes:
Line 14 “close to”
22/23: fix wording without repeating “increase[d]
26: acknowledged
27: players
34: six families mention, list all of them?
35: family
55: adapt? or adjust? or acclimate? “Adapt” implies evolutionary change.
56-67: remove this long complex paragraph and condense info into table?
68: Quercus is not the angiosperm genus with the most species.
69: replace “has” with “have”
76 and 80: these sentences do not read well
97: how was soil moisture measured? Were the data logged?
135. Might help to make it clear that “phylogenetic relationships” refers to genes, not to species as such. In that connection, it might be worthwhile to compare Fig. 8 (and lines 231-235) for MYB with species-level molecular phylogeny (e.g., see Yang et al. 2021. Genomics 113:1438-1447). That would help with context on Q. wutaishanica.
200: citation for PLN03091 superfamily?
237-241, 248-251, and additional captions: inconsistencies with spacing, especially with respect to semicolons
243 and elsewhere: give citations for software used? Maybe all in one list?
Figure 10. I may be confused by something obvious I’m overlooking. Even so, I’ll point out my confusion in case it has substance, or in case other readers have same confusion:
As stated on lines 268 and 269 (and 277,278, 319,320), QwMYB108 expression, “increased with the stress degree and was highest during severe dry stress.” But in Fig. 10 the bar showing high relative expression is “SD.” But SD according to the caption (273) represents “SD, mild drought stress,” and the bar showing severe drought stress (“LD, severe drought stress” 273) shows the lowest non-control relative expression. Are the bars mislabeled? Was LD meant to mean “low drought,” and was SD meant to mean “severe drought”?
284: put species name in italics
284 285: use of italics for gene name inconsistent
298: is oxidative stress relevant here? From closed stomates? Seems mildly abruptly introduced or out of place.
305: typo
305-317: belongs here, or in intro?
All of my observations seem to have ready fixes, to the extent the authors/editors wish to adjust the MS. Thank you for the opportunity to learn about the gene QwMYB108, a pleasure to read.
Comments on the Quality of English Language
English mostly excellent but there is need for copy edit to remove some rough spots.
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
Reviewer 3 Report
Comments and Suggestions for AuthorsThis study examined the function of QwMYB108 in response to drought stress. Some comments.
It is advisable to provide a photo of the material being studied (Quercus wutaishanica)
In the Materials and Methods section it is necessary to provide a separate statistical analysis.
Justify the fact that the highest expression is found in leaves.
It is advisable to carry out intravital determination of ROS as a reaction to stress.
It is advisable to demonstrate the predicted localization of the protein using microscopy.
It is necessary to provide a separate Conclusion section with extended conclusions.
It is necessary to edit the text and list of references in accordance with the requirements of the journal.
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
Reviewer 4 Report
Comments and Suggestions for AuthorsComments and Suggestions for Authors
The manuscript titled " Molecular Cloning of QwMYB108 Gene and Its Response to Drought Stress in Quercus wutaishanica" by Xue-Fei et al., while the study successfully isolated and characterized the QwMYB108 gene and explored their expression patterns in different tissues, it does not delve deeply into the functional roles of this gene in Quercus wutaishanica.
1. Incomplete Storyline: While the manuscript covers various aspects related to the isolation and characterization of QwMYB108 gene in Quercus wutaishanica, it lacks depth in certain areas. For example, the discussion of the results could be expanded to provide deeper insights into the significance of the findings and their implications for the field. One area that appears to be missing from the manuscript is a comprehensive analysis of the functional significance of the identified QwMYB108 gene.
2. The manuscript provides minimal contextualization of the research within the broader scientific literature. The manuscript could benefit from providing a more comprehensive review of existing literature related to the topic.
3. Results: Information on the subcellular localization of QwMYB108 proteins is essential for understanding their cellular functions. Including predictions or experimental data on the subcellular localization of QwMYB108 proteins would enhance the interpretation of their roles in different cellular processes.
4. The discussion section is very brief. In this section, the key results should be interpreted, but unfortunately, the authors have addressed them superficially.
55. It is suggested to add a conclusion section to the manuscript
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
Round 2
Reviewer 1 Report
Comments and Suggestions for AuthorsIn general, the Authors have answered the majority of my questions. Still, the layout must be adapted to the journal rules (especially, the citations as numbers should be in brackets like [51] in line 288).
About "cloning" - I would reserve this terminology to the amplification of the DNA fragments in plasmids. Here was the simple PCR amplification, i.e. replication DNA-DNA.
Only one reference gene was used in the qPCR analysis, but it is acceptable.
In methods, I do not see the producer's name (neither Preissen nor Thermo) in the text.
In Discussion, line 272 and next lines: please correct "4141", "4344", etc.
Author Response
Comments 1: In general, the Authors have answered the majority of my questions. Still, the layout must be adapted to the journal rules (especially, the citations as numbers should be in brackets like [51] in line 288).
Response 1: We sincerely appreciate the valuable comments. We have revised the relevant part. We are very sorry that we did not notice the difference between different working software before, which is our negligence. Thank you again for your valuable advice.
Comments 2: About "cloning" - I would reserve this terminology to the amplification of the DNA fragments in plasmids. Here was the simple PCR amplification, i.e. replication DNA-DNA.
Response 2: We sincerely thank you for your valuable comments, which provide important ideas for our future experiments. We will improve this point in future experiments
Comments 3: Only one reference gene was used in the qPCR analysis, but it is acceptable.
Response 3: We sincerely thank you for your valuable comments, which provide important ideas for our future experiments, and we will improve this point in future experiments.
Comments 4: In methods, I do not see the producer's name (neither Preissen nor Thermo) in the text.
Response 4: Thank you for your suggestion. This is our negligence, we did not add the corresponding part. Now we have completed the modification of the corresponding part.
Comments 5: In Discussion, line 272 and next lines: please correct "4141", "4344", etc.
Response 5: Thank you for your suggestion. We checked. And modified the corresponding part.
Reviewer 4 Report
Comments and Suggestions for AuthorsUnfortunately, the authors have not been able to improve the quality of the article and this manuscript cannot be accepted as a complete article. Still, the topic of the work has not been well highlighted and the results have not been properly interpreted.
Author Response
Comments : Unfortunately, the authors have not been able to improve the quality of the article and this manuscript cannot be accepted as a complete article. Still, the topic of the work has not been well highlighted and the results have not been properly interpreted.
Response: Thank you for your suggestion. We tried our best to improve the manuscript. We appreciate for the reviewer’s warm work earnestly, and hope the correction will meet with approval. Once again, thank you very much for your comments and suggestions.
