Study on Revealing Peanut-Related Disease Prevention Gene Clusters via Whole Transcriptome Sequencing
Round 1
Reviewer 1 Report (New Reviewer)
Comments and Suggestions for Authors
In this manuscript, authors have done excellent research entitled “Study on revealing peanut related disease prevention gene clusters by whole transcriptome sequencing”. In general, the manuscript was satisfactory well presented, however some issues need attention.
(Suggestions to improve)
1- Introduction needs to be significantly improved, indicating the scientific contribution to the response mechanism of peanut plants to F. oxysporum stress induced by the microbial pesticide B. thuringiensis
2- Improve the Introduction using recent publications.
3- Check the English grammar and structure throughout the manuscripts.
4- Use more descriptive and precise expressions in the conclusion part.
- None
Author Response
Dear teacher,
Thank you very much for your suggestions for revising the manuscript, which have greatly benefited me. Your affirmation is my greatest support and assistance. In response to your guidance, I have made the following modifications.
Please see the attachment.
Once again, I would like to express my gratitude to the teacher. It is my greatest blessing to have the guidance and support of the teacher throughout my long journey of life.
Kind regards,
Yours, Hongbo
July 29 , 2023
Author Response File: 
Author Response.pdf
Reviewer 2 Report (New Reviewer)
The manuscript is well-written and organized. It presents the results of original research and makes a valuable contribution to knowledge and understanding of the studied topic. Sections of the manuscript are well organized. The methods are well elaborated and presented. Results are presented in a clear way throughout the text, as well as in figures. The discussion is presented in a proper way and supported with the adequate citations from the literature.
Author Response
Dear teacher,
Thank you very much for your suggestions for revising the manuscript, which have greatly benefited me. Your affirmation is my greatest support and assistance.In future research and learning, I hope to receive guidance from teacher again.
Once again, I would like to express my gratitude to the teacher. It is my greatest blessing to have the guidance and support of the teacher throughout my long journey of life.
Kind regards,
Yours, Hongbo
July 29, 2023
Reviewer 3 Report (New Reviewer)
Du et al. presented the work to probe disease prevention gene clusters of peanuts by RNA-seq. The question asked was interesting and was straightforwardly addressed by systematic approaches such as transcriptome profiling. The techniques were well-established and justified, and the data generated were great resources—definitely, the story is worthwhile to be published. However, the manuscript may need major revisions before it can be reconsidered for publication.
1. The biggest concern of mine: It is hard to follow the manuscript, and the scientific writing in English should be largely improved throughout the whole manuscript, and from my point of view, before reconsidering it for publication. To use an “English polishing” service or to invite a native English scientific writer for revision would be highly appreciated.
e.g., the Second sentence in the Introduction: “transcriptome methods related genes have received more and more attention”. The second sentence of Material and Methods: “Watered thoroughly and managed the emergence of seedlings normally for 14 days” – this is not even a complete sentence. It is very hard to read sentences like this, throughout the manuscript.
2. Method section: how did authors count the read (use software like Stringtie?)
3. Line 171: Gene Expression Level Analysis: the authors did not write detailed results, which makes it more like a method section.
4. Figures: quality of some figures needs to be improved, e.g., Figure 11, which is very blurry. Figure 5 is too busy, and authors may want to reduce the content to highlight key points and put extra information as supplemental figures. Also, there are 11 figures in total, I suggest that authors revisit the figure settings, and some of the figures might be better combined (e.g., Figures 8-10 all describing peanut disease resistance genes), with key points highlighted and the remaining information presented as supplements.
5. More data-driven approaches are recommended to be used to probe functional modules, instead of discussing genes separately:
Integral methods such as WGCNA: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-559
This can be easily implemented in TBtools (authors can also use this to polish their figures such as heatmap): https://www.sciencedirect.com/science/article/pii/S1674205220301878
The current presentation of data focuses more on a gene-by-gene style (e.g., the Conclusions part), though the authors did some pathway enrichment analysis which is great. WGCNA may facilitate the integration of different layers of cellular functions (TFs, receptors, enzymes, etc., together with the physiology such as in Figure 2. Changes in chlorophyll can be used as a variable like gene).
The manuscript might need to be revisited sentence by sentence, and figure by figure.
Author Response
Dear teacher,
Thank you very much for your suggestions for revising the manuscript, which have greatly benefited me. Your affirmation is my greatest support and assistance. In response to your guidance, I have made the following modifications.
Please see the attachment.
Once again, I would like to express my gratitude to the teacher. It is my greatest blessing to have the guidance and support of the teacher throughout my long journey of life.
Kind regards,
Yours, Hongbo
July 29, 2023
Author Response File: Author Response.pdf
Round 2
Reviewer 3 Report (New Reviewer)
Response 1: To use an “English polishing” service and then the manuscript have been revisited sentence by sentence, and figure by figure.
There is certainly a big improvement which I really appreciate. I feel the English is still needed to be further polished, significantly, by an agent or English native writer.
Response 2: Illumina platform software was used to convert BCL files to FASTQ file data through the bcl2fastq package. After the original reads data was filtered, the residual data of low-quality was removed to obtain clean reads data.
I asked about the transcript quantification method after read mapping. Methods for this step are used to quantify the expression level based on mapped read (e.g. .bam file). Popular ones include Stringtie. What software did the authors use? Also, I think authors may also want to state the software used for reads quality control (if has been done), mapping, and the versions of the software used.
Response 4: Use Figure 5 as supplementary data. Fig. 6 and Fig 7 merge into one image. as shown in the original manuscript merge Fig 8-10 into a new image with prominent emphasis, and revise Fig 11 to make it clear and prominent focus.
Certainly, this got improved, but still unsatisfactory. I appreciate it if the authors can further address:
1) All figures like Figure 2: Making figures in Excel is a good way, but these three subfigures should be made with consistent font and size and background. Please check those publications with appealing bar graphs and improve the figures accordingly. This won’t take much time but will significantly improve the readers’ experience.
2) All figures like Figure 3: Authors may want to export figures into .png using high dpi. Since this is generated in R.
3) Figure 4. The labels on the right are collapsed with each other.
Response 5: Thank you for your good question. Your suggestions are constructive, but in this manuscript, analysis methods such as WGCNA and TBtools were not included in the research plan. In the following research, we will refer to your suggestions. Thank you very much for your concern and help.
Certainly, this is still recommended to make the whole discovery as a coherent story. However, I am less concerned about this if authors can address my other points satisfactorily, especially the overall scientific writing in English and figure quality improvement.
Need to be significantly further improved
Author Response
Dear teacher,
Thank you very much for your suggestions for revising the manuscript, which have greatly benefited me. Your affirmation is my greatest support and assistance. In response to your guidance, I have made the following modifications.
Please see the attachment.
Once again, I would like to express my gratitude to the teacher. It is my greatest blessing to have the guidance and support of the teacher throughout my whole journey of life.
Kind regards,
Hongbo
Aug1, 2023
Author Response File: 
Author Response.docx
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
1. Authors should rewrite the entire manuscript for better presentation
2. Scientific names should be italicized
3. Some critical points asked in the attached file should be corrected.
4. Supplementary data should be provided
Comments for author File: Comments.pdf
Scientific writing in english language must be improved
Author Response
Please refer to the attachment
Author Response File: Author Response.pdf
Reviewer 2 Report
Dear Authors,
I enjoyed reviewing this article on the peanut disease resistance clusters by transcriptome sequencing. I think this study has a great scope to understand the underlying resistance mechanisms and the biological pathways. But the article lacks several basic components and experimental descriptions to support objectives. It needs a lot of grammar improvement for example this article is written in present tense while it should be in past tense.
This manuscript is on the disease related genes in peanut, but it has too intensive introduction describing almost all gene classes starting from the cell differentiation and proliferation regulation, flavonoid and anthocyanin genes, abiotic stresses (nitrogen, phosphorus, and potassium) and plant growth, drought, and Ultraviolet stresses. All this information has nothing to do with disease resistance mechanisms in plants or specifically in peanuts. I suggest to more focus on the disease resistance gene clusters, resistance mechanism and regulation. Add more detail on Fusarium oxysporum pathogenicity and pathogen role in the disease triangle.
Materials and Methods:
This section needs a lot of improvement, for example for sequencing how DNA was extracted, what genotyping platform was used, what SNP calling pipeline was used, what was the reference genome for alignment, how many raw reads were obtained, what was the read filtration criteria etc. Furthermore, how, GO function analysis, Pathway function analysis, cluster analysis, protein interaction network, and transcription factor coding ability prediction on the selected differentially expressed genes was performed. There is not even a single citation.
Discussion:
Most of the discussion is irrelevant to the results described in the current study. Please add on your commentary on the specific results for your experiments and their justification with supporting evidence from the literature.
Comments for author File: Comments.pdf
It needs a lot of grammar improvement for example this article is written in present tense while it should be in past tense. I have highlighted in yellow at some places directly in the manuscript PDF file
Author Response
Please refer to the attachment.
Author Response File: Author Response.pdf
Round 2
Reviewer 1 Report
I think authors should read the manuscript and correction asked by reviewers properly before submission as no corrections were incorporated and no question were addressed. Kindly check the previous correction file also.
Comments for author File: Comments.pdf
Many grammatical mistakes has been noticed in this manuscript. Kindly improvised it.
Reviewer 2 Report
I can see that the manuscript has not even considered improving the basic English grammar mistakes which I highlighted in the previous review. Please find attached my comments on lines from 65-75 and it can show how serious are the writing concerns on this manuscript. I will highly recommend and appreciate if authors can carefully review this manuscript and ask an English native speaker to make corrections before submitting for publication.
Comments for author File: Comments.pdf
I can see that the manuscript has not even considered improving the basic English grammar mistakes which I highlighted in the previous review. Please find attached my comments on lines from 65-75 and it can show how serious are the writing concerns on this manuscript. I will highly recommend and appreciate if authors can carefully review this manuscript and ask an English native speaker to make corrections before submitting for publication.
