Using Integrated Multi-Omics to Explore the Differences in the Three Developmental Stages of Thelephora ganbajun Zang
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsReview Reports
The article “Using Multi-Omics Integration to explore the differences in the three developmental stages of Thelephora ganbajun Zang” is interesting because the species has edible and medicinal value. However, its inability to be artificially cultivated poses a challenge to production. The experimental and analysis methodology were adequate. Statistical and multivariate analyzes were well conducted, contributing to support the conclusions. Therefore, in my opinion, this article is suitable for publication for the reasons mentioned above and I therefore recommend acceptance.
Comments/suggestions:
- In Table 1, explain the abbreviation: GPP_vs_GSP; GP_vs_GPP and GP_vs_GSP
- Figure 2 and Figure 3, improve the description of the figures, they should be self-explanatory.
Comments for author File: 
Comments.pdf
Author Response
Dear Editors and Reviewers:
　　Thank you for your comments concerning our manuscript entitled “Using integrated multi-omics to explore the differences in the three developmental stages of Thelephora ganbajun Zang” (ID: applsci-2882409). The comments are all valuable and very helpful for revising and improving our paper, as well as providing important guiding significance for our research. We have studied the comments carefully and have made corrections, which we hope meet you’re your approval. We have uploaded the point-by-point responses to the reviewers’ comments, the revised manuscript, and the clean manuscript. Please see the attachment.
Yours sincerely,
The Authors
Author Response File: Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsThe current article is not appropriate for publication in the current format as there are several mistakes and it seems like the manuscript is written by the third person and not by authors on this manuscript. Major points are as follows:
1. In the introduction, line 43, "The findings of this study are summarized in the following table". What do authors try to imply here? There is no table provided/referred.
2. Line 101: "Multi-omics analysis effectively filters out a vast amount of 101 invalid and interfering information.". This is not true/doesn't support the findings.
3. Line 102: "In certain cases, Gene ID transformation through databases such as NCBI can precisely pinpoint the target gene's location in the genome". This sentence doesn't make sense.
4. Line 110: "We then carried out a comprehensive analysis with the transcriptome, exploring gene expression and its corresponding 111 downstream metabolites". How could transcriptome provides information about metabolites?
5. Materials and Methods is poorly written. Major English and scientific formatting needs to be done. Following are some major points.
a. From line 126: It is not clear how mycelium was processed.
b. Line 139: "absorbance values were measured at 595 nm 139 with an enzyme marker."
c. The mass spectrometry section is a disaster which is evident by line: 149 "Evaluation of identification and quantification results encompassed standard curve OD values"
And the list goes on...
Comments on the Quality of English Language
Dear
Author Response
Dear Editors and Reviewers:
　　Thank you for your comments concerning our manuscript entitled “Using integrated multi-omics to explore the differences in the three developmental stages of Thelephora ganbajun Zang” (ID: applsci-2882409). The comments are all valuable and very helpful for revising and improving our paper, as well as providing important guiding significance for our research. We have studied the comments carefully and have made corrections, which we hope meet you’re your approval. We have uploaded the point-by-point responses to the reviewers’ comments, the revised manuscript, and the clean manuscript. Please see the attachment.
Yours sincerely,
The Authors
Author Response File: Author Response.pdf
Reviewer 3 Report
Comments and Suggestions for AuthorsThe authors present an interesting study on an uncultivable fungus, Thelephora ganbajun Zang. Using multi-omics analyses they have identified proteins and metabolites of interest during transition from mycelium to primordium to fruiting body. This research facilitates the design of artificial environments to culture the fungus, which is known for its nutrition and health benefits. However there are several issues outlined below, that need to addressed before the article can be published:
L26: Suggest not using acronyms here. Please mention full names of genes
L149-152: The details should be provided. The section ands with “etc.” which is unacceptable in a scientific article. Pertinently, the discussion section should include why the (presumptively) quantile normalization method was used.
L152: The term DDA is not explained anywhere. Please mention the full form of the method name and include a reference.
L160-169: Appears to be a protocol capture. Please make consistent with style of the rest of the methods section. The number and type of replicates should be mentioned
L205: Is “transcriptome” a typing error? If not, details must be included
L256, L376: The heatmap conveys little to the reader and is more for the original researchers’ visualization. Suggest removal from the manuscript.
L209,342: The rationale for choosing the thresholds for log2(FC) should be discussed. It is also not clear how the FDR was calculated. Lastly, the choice of 0.05 as the significance level for the t-test appears to not consider repeated measures.
In supplementary tables S1,S3 (ABC) and S4, error estimates need to be provided.
Comments on the Quality of English LanguageSuggest professional english editing services for minor errors in usage of words. Grammar is acceptable.
Author Response
Dear Editors and Reviewers:
　　Thank you for your comments concerning our manuscript entitled “Using integrated multi-omics to explore the differences in the three developmental stages of Thelephora ganbajun Zang” (ID: applsci-2882409). The comments are all valuable and very helpful for revising and improving our paper, as well as providing important guiding significance for our research. We have studied the comments carefully and have made corrections, which we hope meet you’re your approval. We have uploaded the point-by-point responses to the reviewers’ comments, the revised manuscript, and the clean manuscript. Please see the attachment.
Yours sincerely,
The Authors
Author Response File: 
Author Response.docx
Round 2
Reviewer 2 Report
Comments and Suggestions for AuthorsThe authors have made changes to the manuscript but there are still several concerns that need to be addressed.
1. Abstract: Lines 18, and 19 are incorrect as proteins are not small molecules and need rephrasing
2. The Introduction section is too unrelated. It can be shortened to provide precise information about the background of the study.
3. The mass spectrometer information is incorrect for the proteomics analysis or referred incorrectly to Table S3. Need to be clarified.
4. The background database to search the data is Human as provided in the supplementary table which is incorrect.
5. "with sampling performed by the double-antibody sandwich method" Line 181 is incorrect
6. The mass spectrometry section under methods for proteomics is too vague and the obvious portion needs to be shortened such as the background of DDA method and data acquisition.
7. Authors are referring to gene data at multiple places throughout the manuscript instead of proteomics data which needs correction.
8. Total number of proteins identified in Table 1 for the GPP_vs_GSP category is 44 which is less than the other two categories. Can the author explain the potential cause for that? Also, the number of differentially expressed proteins in all categories is more than 55%. This raises concerns about the samples and data normalization.
9. The volcano plots in figure 2 have a lot more points than the total identified proteins reported also the number of points that are differentially expressed doesn't match with the reported numbers from Table 2. This raises the concern about the authenticity of the data. The same is true about heatmap.
10. Lines 281-283 are incorrect and need to rewrite.
11. Volcano plots for GM vs GSM and GPM vs GSM look similar while GM vs GPM looks completely different. Can authors provide a possible explanation for this?
12. The source for the interaction network for metabolites identified is not clear. Which tool was used to generate these networks and what is the evidence for them?
Comments on the Quality of English Language
Need to be improved.
Author Response
Dear Editors and Reviewers:
　　Thank you for your comments concerning our manuscript entitled “Using integrated multi-omics to explore the differences in the three developmental stages of Thelephora ganbajun Zang” (ID: applsci-2882409). The comments are all valuable and very helpful for revising and improving our paper, as well as providing important guiding significance for our research. We have studied the comments carefully and have made corrections, which we hope meet you’re your approval. We have uploaded the point-by-point responses to the reviewers’ comments, the revised manuscript, and the clean manuscript. Please see the attachment.
Yours sincerely,
The Authors
Author Response File: Author Response.pdf
Reviewer 3 Report
Comments and Suggestions for AuthorsSatisfactory changes have been made and the paper now reads much clearer. However, the text on several figures is too small and therefore hard to read. I recommend fixing these and using more space for each of the problematic figures.
Comments on the Quality of English LanguageA professional editor should be able to fix any remaining issues with the language.
Author Response
Dear Editors and Reviewers:
　　Thank you for your comments concerning our manuscript entitled “Using integrated multi-omics to explore the differences in the three developmental stages of Thelephora ganbajun Zang” (ID: applsci-2882409). The comments are all valuable and very helpful for revising and improving our paper, as well as providing important guiding significance for our research. We have studied the comments carefully and have made corrections, which we hope meet you’re your approval. We have uploaded the point-by-point responses to the reviewers’ comments, the revised manuscript, and the clean manuscript. Please see the attachment.
Yours sincerely,
The Authors
Author Response File: Author Response.pdf
