Response and Regulatory Network Analysis of Roots and Stems to Abiotic Stress in Populus trichocarpa
Round 1
Reviewer 1 Report
The authors responded to all my comments. Unfortunately, I am not able to verify whether the latest literature has been added because nothing has been changed in the list of cited publications (References).
Author Response
Dear Reviewer,
Thanks very much for taking your time to re-review this manuscript. We really thank you for the time and effort that you have put into reviewing the two previous version of the manuscripts. Based on the instructions provided in your letter, we have uploaded the revised manuscript with all the changes highlighted in red by using the track changes mode in MS Word. Please find my itemized responses below which are given directly afterward in a different color (blue) and my revisions/corrections in the re-submitted files.
Here are the general comment and our response :
Unfortunately, I am not able to verify whether the latest literature has been added because nothing has been changed in the list of cited publications (References).
We apologize that the change of the list of cited publications is not highlighted. In the previous modification，we only modified them in main body. Therefore, we highlight the references which was previously added in the new version. Thank you for pointing this out.
We hope that the revised manuscript is accepted for publication in the Journal of Forests.
Sincerely,
Ran Tao
Reviewer 2 Report
The paper entitled "Response and regulatory network analysis of roots and stems to abiotic stress in Populus trichocarpa" assessed the whole transcription spectrum and potential differentially expressed genes of 54 groups of roots and stem-xylem sequencing sample data under cold, drought, heat and salt stress in different duration. Paper prepared good, however, some general comments will improve the manuscript:
1. Title--> The scientific names of the species must be in Italic.
2. Figure 1--> the resolution is low that numbers and texts are unreadable. replace it with high resolution.
3. Figure 2 and other figures--> same as above comment. low resolution and some fonts with colors are not readable.
4. The discussion section prepared without any references and comparing with other studies. Specially, section 4.1 and 4.2.
You must work on discussion and discuss well about the results.
5. What is the scope for the future? How this study will help the readers?
Author Response
Dear Reviewer,
Thanks very much for taking your time to review this manuscript. I really appreciate all your comments and suggestions! Please find my itemized responses in below and my revisions/corrections in the re-submitted files. We thank you for the time and effort that you have put into reviewing the previous version of the manuscript. Your suggestions have enabled us to improve our work. Based on the instructions provided in your letter, we have uploaded a copy of the original manuscript with all the changes highlighted by using the track changes mode in MS Word. Appended to this letter is our point-by-point response to the comments raised by the reviewers. The comments are reproduced and our responses are given directly afterward in a different color (blue). We would like also to thank you for allowing us to resubmit a revised copy of the manuscript.
Here are the general comments and our responses :
1. Title--> The scientific names of the species must be in Italic.
Thank you for the title suggested. We have changed “Populus trichocarpa” into “Populus trichocarpa”.
2. Figure 1--> the resolution is low that numbers and texts are unreadable. replace it with high resolution.
Thank you for pointing this out. Figure 1 has been replaced by vector images with higher resolution.
3. Figure 2 and other figures--> same as above comment. low resolution and some fonts with colors are not readable.
We are grateful for the suggestion. Figure 2 has been replaced by vector images with higher resolution as well.
4. The discussion section prepared without any references and comparing with other studies. Specially, section 4.1 and 4.2.
You must work on discussion and discuss well about the results..
We agree with the reviewer that further elaborating on this point. However, we believe it is more meaningful to discuss 4.1-4.2 and 4.3 together to relate to others. Therefore, no citation is in these two parts. Besides, we also believe that it is necessary to summarize and briefly analyze the results of 3.1 and 3.2 first and then analyze them together with the following text. Therefore, we didn’t remove 4.1 and 4.2.
5. What is the scope for the future? How this study will help the readers?
Thank you for the impressive comment. In future studies, the research on the expression and function of homologous genes in multiple species is conducive to our understanding of the adaptive evolution process of species. The research on the molecular response mechanism of other plants under abiotic stress is worth deepening.The subsequent genetic improvement will be more targeted in the case of single or several abiotic stresses and preventing the situation that weakening the resistance to other stresses passively when improving the resistance of woods to the certain one.
We hope that the revised manuscript is accepted for publication in the Journal of Forests.
Sincerely,
Ran Tao
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
In the article entitled "Response and regulatory network analysis of roots and stems to abiotic stress in Populus trichocarpa", authors have doe a good piece of study. However, The main question is though several reports are already been available in Populus trichocarpa RNA se analysis under abiotic stress, what is novel in this study, i.e., what the new data reported in this manuscript?
Author Response
Dear Reviewer,
Thanks very much for taking your time to review this manuscript. I really appreciate all your comments and suggestions! Please find my responses in below and my revisions/corrections in the re-submitted files. We thank you for the time and effort that you have put into reviewing the previous version of the manuscript. Your suggestions have enabled us to improve our work. Based on the instructions provided in your letter, we uploaded the file of the revised manuscript. Accordingly, we have uploaded a copy of the original manuscript with all the changes highlighted by using the track changes mode in MS Word. Appended to this letter is our point-by-point response to the comments raised by the reviewers. The comments are reproduced and our responses are given directly afterward in a different color (blue).
Here is the general comments: The main question is though several reports are already been available in Populus trichocarpa RNA se analysis under abiotic stress, what is novel in this study, i.e., what the new data reported in this manuscript?
We apologize if our novelty is not clear enough. In fact, we are having a comprehensive and macroscopic study on the response to abiotic stresses while most of studies are aimed at one or two certain stress environments. We analyzed the same set of RNA-seq data in roots and stems for four abiotic stresses within different duration and compared the gene regulatory networks of P. trichocarpa that grow at the same duration under four abiotic stresses or at different duration under the same stress horizontally and vertically. The results from this study provide the common and specific characteristics of transcriptome in responding to four abiotic stresses. The subsequent genetic improvement will be more targeted in the case of single or several abiotic stresses and preventing the situation that weakening the resistance to other stresses passively when strengthening the resistance to the certain one.
This part has been added to the conclusion and abstract(page 1 and 13). We would like also to thank you for allowing us to resubmit a revised copy of the manuscript.
We hope that the revised manuscript is accepted for publication in the Journal of Forests.
Sincerely,
Ran Tao
Reviewer 2 Report
Dear Editors and Authors,
I have carefully read your manuscript entitled "Response and regulatory network analysis of roots and stems to abiotic stress in Populus trichocarpa". In my opinion, it is a very interesting paper, suitable for journal aims and scope. The text, however, requires adding some issues. Below my comments:
- use different keywords than words in the title;
- introduction requires further development, it would be worth describing the current knowledge on the impact of individual abiotic stress factors on plants, if possible mainly woody;
- in materials and methods, there is no description of the experiments in which the material for the tests described in points 2.1-2.4 was obtained; a detailed description of the experiments in which plants were exposed to particular stresses is necessary (cold, heat, drought and salt stress);
- the vast majority of discussion sections do not refer to any citations - after all, this is the purpose of the discussion, relating the obtained results to the results of other authors;
- the manuscript requires the addition of citations of the latest literature (from the last 3 years).
Best regards,
Reviewer
Author Response
Dear Reviewer,
Thanks very much for taking your time to review this manuscript. I really appreciate all your comments and suggestions! Please find my itemized responses in below and my revisions/corrections in the re-submitted files. We thank you for the time and effort that you have put into reviewing the previous version of the manuscript. Your suggestions have enabled us to improve our work. Based on the instructions provided in your letter, we uploaded the file of the revised manuscript. Accordingly, we have uploaded a copy of the original manuscript with all the changes highlighted by using the track changes mode in MS Word. Appended to this letter is our point-by-point response to the comments raised by the reviewers. The comments are reproduced and our responses are given directly afterward in a different color (blue). We would like also to thank you for allowing us to resubmit a revised copy of the manuscript.
Here are the general comments and our responses :
1.use different keywords than words in the title;
We are grateful for the suggestion. We have changed the keywords into “ poplar; cold stress; drought stress; heat stress; RNA-seq”.
2.introduction requires further development, it would be worth describing the current knowledge on the impact of individual abiotic stress factors on plants, if possible mainly woody;
Thank you for the pertinent comment. We have added more knowledge from the last 3 years on the impact of individual abiotic stress factors on woods.
3.in materials and methods, there is no description of the experiments in which the material for the tests described in points 2.1-2.4 was obtained; a detailed description of the experiments in which plants were exposed to particular stresses is necessary (cold, heat, drought and salt stress);
Your suggestion is greatly appreciated. To be more clear, we have added a description in 2.1.
4.the vast majority of discussion sections do not refer to any citations - after all, this is the purpose of the discussion, relating the obtained results to the results of other authors;
Thank you for pointing this out. We added more discussion on the comparison with the results of other authors in 4.3 and 4.4. However, 4.1 and 4.2 only discussed the results of the experiment. We think it is more meaningful to discuss 4.1-4.2 and 4.3 together to relate to others. Therefore, no citation is in these two parts.
5.the manuscript requires the addition of citations of the latest literature (from the last 3 years).
We appreciate your insightful suggestion. We have cited more articles in recent three years in Introduction and Discussion.
We hope that the revised manuscript is accepted for publication in the Journal of Forests.
Sincerely,
Ran Tao
Reviewer 3 Report
Authors need to improve the introduction and materials and methods sections, results section is a bit longer and needs to shortened. The discussion section needs some revisions to bring it in coherence with the results.
Author Response
Dear Reviewer,
Thanks very much for taking your time to review this manuscript. I really appreciate all your comments and suggestions! Please find my itemized responses in below and my revisions/corrections in the re-submitted files. We thank you for the time and effort that you have put into reviewing the previous version of the manuscript. Your suggestions have enabled us to improve our work. Based on the instructions provided in your letter, we uploaded the file of the revised manuscript. Accordingly, we have uploaded a copy of the original manuscript with all the changes highlighted by using the track changes mode in MS Word. Appended to this letter is our point-by-point response to the comments raised by the reviewers. The comments are reproduced and our responses are given directly afterward in a different color (blue). We would like also to thank you for allowing us to resubmit a revised copy of the manuscript.
Here is the comment and our response :
Authors need to improve the introduction and materials and methods sections, results section is a bit longer and needs to shortened. The discussion section needs some revisions to bring it in coherence with the results.
We appreciate your insightful suggestion. For introduction, we have added more knowledge from the last 3 years on the impact of individual abiotic stress factors on woods. For materials and methods, we have put a description of the experiments in which the material for the tests in 2.1. For results, some result descriptions which are less important and several statements describing charts were adjusted and shortened in 3.2. For discussion, We discussed the results in more detail and relating more obtained results to others in 4.4.
We hope that the revised manuscript is accepted for publication in the Journal of Forests.
Sincerely,
Ran Tao
