Expression Profiling of Salt-Responsive Genes and Transcription Factors in Leaf Transcriptome of Arabidopsis thaliana
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsDear Authors
The manuscript entitled “Expression profiling of salt-responsive genes and transcription factors in leaf transcriptome of Arabidopsis thaliana” encompasses information pertaining to upregulated genes belonging to diverse pathways in response to salt stress in A. thaliana. The work conducted does not hold novelty as extensive research has been conducted both at in silico and laboratory levels. There are certain comments which could improve your manuscript:
1. Why the work was conducted only at 200mM NaCl concentration? If the preliminary work was conducted at other NaCL concentrations, the data should be given in the supplementary file.
2. A total of 139 references were cited in the manuscript. While reviewing, it felt like reading a review paper not research paper. Please cite the most relevant references only. Instead of citing many references for supporting your study, the authors should have discussed their own predicted reasons for the results obtained. This is lacking in the discussion section. Please give relevant predicted reasons pertaining to mechanism of resistance in Arabidopsis against salt stress.
3. Following concern was related to English, the manuscript was written with very difficult English words. It does not connect with the research problem origin and its outputs. The manuscript should be written in a way to transcend the information gathered from one to another. If possible, make it simple.
4. Materials and Methods:
Line 83- Replace Arabidopsis with A. thaliana
Line 84: Please del Arabidopsis and rewrite as A. thaliana
Line 93: Del the word “meticulously prepared”
Line 95,113,142,152: Del the word “meticulous/meticulously”.
Line 115: Make A. thaliana in italics
Line 117: Del ‘the judicious deployment of”
Line 121: Please check the font size
Line 125: Replace Arabidopsis thaliana with A. thaliana and make it in italics.
Line 136: Del “Virus Induced Gene Silencing”. Keep it as VIGS only.
5. Results
Line 165: Del 200mM NaCl mentioned in bracjets. The concentration is already mentioned in the materials and methods section.
Line 167: Del “Principal Component Analysis”. Keep it as PCA only.
Line 188: Clusters associated with downregulated genes should be given in the supplementary file. Please add.
Line 239: Table 1 include information on clusters with upregulated genes under salt stress. A column should be added in the table which indicates which colour denote which family does it belong to. Is it an auxin metabolic pathway or aromatic amino acid biosynthetic pathways. This comprehensive information should also be given in the table.
6. Conclusions: While summarizing the results, a predicted model needs to be prepared which would include major responsive genes belonging to ndiverse KEGG pathway in the form of figure.
Comments on the Quality of English Language
Dear Authors
The manuscript was written with difficult english which obstructs the connectivity of research work conducted, written and transcend knowledge to the readers. The manuscript is not prepared with the aim of sharing information to the scientists rather prepared for using high vocabulary english.
Author Response
Reviewer 1
Dear Authors
The manuscript entitled “Expression profiling of salt-responsive genes and transcription factors in leaf transcriptome of Arabidopsis thaliana” encompasses information pertaining to upregulated genes belonging to diverse pathways in response to salt stress in A. thaliana. The work conducted does not hold novelty as extensive research has been conducted both at in silico and laboratory levels. There are certain comments which could improve your manuscript:
- Why the work was conducted only at 200mM NaCl concentration? If the preliminary work was conducted at other NaCl concentrations, the data should be given in the supplementary file.
Response: Arabidopsis is glycophytic or less resistant to salt stress and is unable to withstand higher salt concentrations. Previous reports advised using 200 mM NaCl concentration primarily in incremental increases, as shown by the examples below:
- Fan, Y., Yin, X., Xie, Q., Xia, Y., Wang, Z., Song, J., ... & Jiang, X. (2019). Co-expression of SpSOS1 and SpAHA1 in transgenic Arabidopsis plants improves salinity tolerance. BMC plant biology, 19(1), 1-13.
- Bahieldin, A., Atef, A., Edris, S., Gadalla, N. O., Ramadan, A. M., Hassan, S. M., ... & El-Domyati, F. M. (2018). Multifunctional activities of ERF109 as affected by salt stress in Arabidopsis. Scientific reports, 8(1), 6403.
- Hamaji, K., Nagira, M., Yoshida, K., Ohnishi, M., Oda, Y., Uemura, T., ... & Mimura, T. (2009). Dynamic aspects of ion accumulation by vesicle traffic under salt stress in Arabidopsis. Plant and Cell Physiology, 50(12), 2023-2033.
- Ndimba, B. K., Chivasa, S., Simon, W. J., & Slabas, A. R. (2005). Identification of Arabidopsis salt and osmotic stress responsive proteins using two‐dimensional difference gel electrophoresis and mass spectrometry. Proteomics, 5(16), 4185-4196.
- A total of 139 references were cited in the manuscript. While reviewing, it felt like reading a review paper not research paper. Please cite the most relevant references only. Instead of citing many references for supporting your study, the authors should have discussed their own predicted reasons for the results obtained. This is lacking in the discussion section.
Response: As requested, the number of references is lowered to 89.
- Please give relevant predicted reasons pertaining to mechanism of resistance in Arabidopsis against salt stress.
Response: The Discussion section covered the mechanism of Arabidopsis resistance to salt stress. It alludes to indole acetic acid, which coordinates a complex series of regulatory processes that improve a plant's resistance to salt stress. To provide a clearer picture of the role that indole acetic acid plays in coordinating certain crosstalking pathways and in the development of salt-stress tolerance, a new figure (Figure 6) was inserted in the Discussion section.
- Following concern was related to English, the manuscript was written with very difficult English words. It does not connect with the research problem origin and its outputs. The manuscript should be written in a way to transcend the information gathered from one to another. If possible, make it simple.
Response: Difficult words were made simpler as possible.
- Materials and Methods:
Line 83- Replace Arabidopsis with A. thaliana
Response: Done as requested
Line 84: Please del Arabidopsis and rewrite as A. thaliana
Response: Done as requested
Line 93: Del the word “meticulously prepared”
Response: Done as requested
Line 95,113,142,152: Del the word “meticulous/meticulously”.
Response: Done as requested
Line 115: Make A. thaliana in italics
Response: Done as requested
Line 117: Del ‘the judicious deployment of”
Response: Done as requested
Line 121: Please check the font size
Response: Done as requested
Line 125: Replace Arabidopsis thaliana with A. thaliana and make it in italics.
Response: Done as requested
Line 136: Del “Virus Induced Gene Silencing”. Keep it as VIGS only.
Response: Done as requested
- Results
Line 165: Del 200mM NaCl mentioned in brackets. The concentration is already mentioned in the materials and methods section.
Response: Done as requested
Line 167: Del “Principal Component Analysis”. Keep it as PCA only.
Response: Done as requested
Line 188: Clusters associated with downregulated genes should be given in the supplementary file. Please add.
Response: Clusters with upregulated and downregulated genes are shown in the supplementary Figure S1 and Table S2.
Line 239: Table 1 include information on clusters with upregulated genes under salt stress. A column should be added in the table which indicates which colour denote which family does it belong to. Is it an auxin metabolic pathway or aromatic amino acid biosynthetic pathways. This comprehensive information should also be given in the table.
Response: Thank you for the insightful feedback. As requested, data on the stress-related gene families and TF gene families were added to Table 1.
- Conclusions: While summarizing the results, a predicted model needs to be prepared which would include major responsive genes belonging to diverse KEGG pathway in the form of figure.
Response: We appreciate the reviewer's insightful feedback. To provide a brief overview of the pathway that auxin-related genes take to improve resistance to salt stress in A. thaliana, a new Figure 6 was added to the text in the Discussion section where appropriate.
Comments on the Quality of English Language
Dear Authors
The manuscript was written with difficult English which obstructs the connectivity of research work conducted, written and transcend knowledge to the readers. The manuscript is not prepared with the aim of sharing information to the scientists rather prepared for using high vocabulary English.
Response: English vocabulary was simplified as possible.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsI have reviewed your manuscript titled "Expression profiling of salt-responsive genes and transcription factors in leaf transcriptome of Arabidopsis thaliana" submitted to the journal Diversity. I appreciate your research effort and would like to provide constructive feedback to help improve the quality and clarity of your manuscript.
General Comments:
Your study, which investigates the expression profiles of genes in Arabidopsis thaliana under salt stress conditions, is promising and relevant. It adds valuable insights into salt stress responses and their regulatory mechanisms. However, there are areas that require attention to enhance the manuscript's overall quality.
Specific Comments:
Salt Concentration Rationale: You mentioned using "200 mM NaCl" for salt stress, but the rationale behind choosing this specific concentration is not provided. Explaining why this concentration was selected or referencing relevant studies would add context.
RNA Isolation: It would be beneficial to clarify how you determined the sampling time for RNA isolation.
Conclusion Section: While the conclusion section is well-written, it could be expanded. Discuss the broader implications of your findings and how they could be applied in the context of molecular breeding programs. Providing a more comprehensive conclusion will enhance the manuscript's impact.
Language Clarity: Ensure that the language throughout the manuscript is clear and concise. There are a few sentences that could be rewritten for better readability.
Overall Impression:
Your study has the potential to make a significant contribution to the field of salt stress responses in plants. With the necessary revisions and additional information, your manuscript can be improved for publication. Please address the specific comments and revise your manuscript accordingly. Thank you for your contribution to the scientific community, and I look forward to seeing an improved version of your work.
Author Response
Reviewer 2
Comments and Suggestions for Authors
I have reviewed your manuscript titled "Expression profiling of salt-responsive genes and transcription factors in leaf transcriptome of Arabidopsis thaliana" submitted to the journal Diversity. I appreciate your research effort and would like to provide constructive feedback to help improve the quality and clarity of your manuscript.
General Comments:
Your study, which investigates the expression profiles of genes in Arabidopsis thaliana under salt stress conditions, is promising and relevant. It adds valuable insights into salt stress responses and their regulatory mechanisms. However, there are areas that require attention to enhance the manuscript's overall quality.
Specific Comments:
Comment: Salt Concentration Rationale: You mentioned using "200 mM NaCl" for salt stress, but the rationale behind choosing this specific concentration is not provided. Explaining why this concentration was selected or referencing relevant studies would add context.
Response: Arabidopsis is glycophytic or less resistant to salt stress and is unable to withstand higher salt concentrations. Previous reports advised using 200 mM NaCl concentration primarily in incremental increases, as shown by the examples below:
- Fan, Y., Yin, X., Xie, Q., Xia, Y., Wang, Z., Song, J., ... & Jiang, X. (2019). Co-expression of SpSOS1 and SpAHA1 in transgenic Arabidopsis plants improves salinity tolerance. BMC plant biology, 19(1), 1-13.
- Bahieldin, A., Atef, A., Edris, S., Gadalla, N. O., Ramadan, A. M., Hassan, S. M., ... & El-Domyati, F. M. (2018). Multifunctional activities of ERF109 as affected by salt stress in Arabidopsis. Scientific reports, 8(1), 6403.
- Hamaji, K., Nagira, M., Yoshida, K., Ohnishi, M., Oda, Y., Uemura, T., ... & Mimura, T. (2009). Dynamic aspects of ion accumulation by vesicle traffic under salt stress in Arabidopsis. Plant and Cell Physiology, 50(12), 2023-2033.
- Ndimba, B. K., Chivasa, S., Simon, W. J., & Slabas, A. R. (2005). Identification of Arabidopsis salt and osmotic stress responsive proteins using two‐dimensional difference gel electrophoresis and mass spectrometry. Proteomics, 5(16), 4185-4196.
Comment: RNA Isolation: It would be beneficial to clarify how you determined the sampling time for RNA isolation.
Response: According to previous researches (ex., Bahieldin et al. 2018, cited above) and our experience using RNA-Seq approach to explore genes associated to salt stress, these stress-regulated genes restore their normal expression level after 24 hours of exposure to salt stress. We concluded that stress durations longer than 12 hours do not contribute to our comprehension of the processes and patterns of stress tolerance expression.
Comment: Conclusion Section: While the conclusion section is well-written, it could be expanded. Discuss the broader implications of your findings and how they could be applied in the context of molecular breeding programs. Providing a more comprehensive conclusion will enhance the manuscript's impact.
Response: Conclusion section was expanded a bit as requested.
Comment: Language Clarity: Ensure that the language throughout the manuscript is clear and concise.
Response: Thank you
Comment: There are a few sentences that could be rewritten for better readability.
Response: Feedback to Reviewer 1 comments has led to revisions to the text and simplification of some vocabulary.
Overall Impression:
Response: Thank you
Your study has the potential to make a significant contribution to the field of salt stress responses in plants. With the necessary revisions and additional information, your manuscript can be improved for publication. Please address the specific comments and revise your manuscript accordingly. Thank you for your contribution to the scientific community, and I look forward to seeing an improved version of your work.
Response: Thank you
Author Response File: Author Response.pdf
Round 2
Reviewer 1 Report
Comments and Suggestions for AuthorsDear Authors
The manuscript has been revised as per the suggestions. kindly include the reason of utilizing 200mM NaCl in the manuscript as well.
Thanking you both for revising the draft properly.
Regards
