Review Reports

Round 1

Reviewer 1 Report

The manuscript is very well written and clear. I enjoyed reading it and could not find significant problems except minor issues and simple typing errors, such as the missing space between bracket signs and the neighbor words in some sentences.

Other minor issues

pI is an estimated pI value. Please correct. What was the resolution used to calculate the pI? Was it average or Monoisotopic? Please add this information to the manuscript.

Line 112: There is no need to mention the link for the ProtParam tool (https://web.expasy.org/protparam/) in the Results section. Apply the same concept to other web links in the Results section since you already mentioned that in the Materials and Methods section.

Line 122: Please specify what yeast species you mean. Saccharomyces cerevisiae? Please add this information to the manuscript.

Line 148: Please correct “The tree was constructed usingconstru”

Line 149: I can not see the 1000 boots on the phylogenetic tree. Please clarify.

Line 160: “The results(Figure 2B)” Please cite the Figures at the end of the sentences. Apply this concept to the rest of the manuscript.

Line 176 (Figure 2C). Please find a suitable way to show the different cis elements and their identities using a clearer illustration.

Figure 2D is unclear. Why do you not use a separate Figure for each type of analysis?

Line 254: “Among them, BrATG1a/1b/1c/3a/3c/8d/10/11b/18d/VTI12c were significantly induced..” What is the p-value used to show this statistical significance? Please add this information to the manuscript each time you show “significant changes, increase, decrease …etc.”

Figure 5. Please mention the p-value used in the statistical analysis of the qPCR data.

Author Response

Response to Reviewer 1 Comments

 

Point 1: pI is an estimated pI value. Please correct. What was the resolution used to calculate the pI? Was it average or Monoisotopic? Please add this information to the manuscript.

 

Response 1: PI here refers to the theoretical isoelectric point, calculated by using the online ProtParam tool (http://web.expasy.org/ compute_pi/) for the theoretical pI (isoelectric point) of BrATG, which is monomeric. For better expression, we have added a note for this abbreviation at the end of Table 1.

 

Point 2: Line 112: There is no need to mention the link for the ProtParam tool (https://web.expasy.org/protparam/) in the Results section. Apply the same concept to other web links in the Results section since you already mentioned that in the Materials and Methods section.

 

Response 2: Yes, we have removed this part.

 

Point 3: Line 122: Please specify what yeast species you mean. Saccharomyces cerevisiae? Please add this information to the manuscript.

 

Response 3: In this case it refers to Saccharomyces cerevisiae (scientific name: S. cerevisiae), which we have added in the article.

 

Point 4: Line 148: Please correct “The tree was constructed usingconstru”

 

Response 4: We modified "The tree was constructed usingconstru" to read: A phylogenetic tree of 169 ATG protein sequences from four species was constructed using MEGA11 software.

 

Point 5: Line 149: I can not see the 1000 boots on the phylogenetic tree. Please clarify.

 

Response 5: Here it means that the neighbor-joining method was used in MEGA 11.0 software and 1000 repetitions of bootstrap tests were performed to construct the evolutionary tree. Since we have already talked about it in detail in the method, repeating the elaboration here may be somewhat redundant. So we have removed this part.

 

Point 6: Line 160: “The results(Figure 2B)” Please cite the Figures at the end of the sentences. Apply this concept to the rest of the manuscript.

 

Response 6: Yes, we checked the article and quoted all the diagrams in it to the end of the sentence.

 

 

 

Point 7: Line 176 (Figure 2C). Please find a suitable way to show the different cis elements and their identities using a clearer illustration.

 

Response 7: Instead of the original diagram, we have applied a stacked bar chart that shows more clearly and visually the different homeopathic components and their identities.

 

Point 8: Figure 2D is unclear. Why do you not use a separate Figure for each type of analysis?

 

Response 8: The original Figure 2D protein interaction network (PPI) plot was too cluttered, so we have re-specified a higher confidence level and labeled each type of analysis using red circles.

 

Point 9: Line 254: “Among them, BrATG1a/1b/1c/3a/3c/8d/10/11b/18d/VTI12c were significantly induced..” What is the p-value used to show this statistical significance? Please add this information to the manuscript each time you show “significant changes, increase, decrease …etc.”

 

Response 9: We have revised and shown P values (P<0.05) where significant increases or decreases were addressed in line 254 of the article.  

 

Point 10: Figure 5. Please mention the p-value used in the statistical analysis of the qPCR data.

 

Response 10: Yes, we have added the P-values used in the statistical analysis of qPCR data (P<0.05) in the notes below Figure 5.

Author Response File: Author Response.docx

Reviewer 2 Report

In the manuscript entitled "Genome-wide identification and expression analysis of BrATGs and their different roles in response to abiotic stresses in Chinese cabbage" the authors describe the new 64 autophagy-associated genes of Chinese cabbage. This is a well-known group of genes in many plants; however, they have not been previously described for Chinese cabbage, which makes this work relevant. I liked the approach of the authors to the design of experiments, such methods of plant molecular biology as the RNAseq, qRT‒PCR and a wide range of bioinformatics approaches were applied. The design of experiments is correct and understandable. Materials and methods are not fully developed, but enough to understand the basic meaning and find detailed information on the links provided. The results obtained look logical and do not raise big questions in my opinion, the discussion is also logical and understandable. In general, I liked this work, but it is not without flaws. The main disadvantage of this work is how the data are presented, namely the design of the figures and the poor elaboration of the text of the work. More detailed remarks follow.

The saddest thing is the lack of spaces where they should be. For example: lines 14,47,49,51,52,55,56,57,59,62,54,66,69,71,73,74,75,78,81,84,87,90, 111,112,124,129,131,133 and so on Further. I don't see the point in listing all the cases. I advise the authors to read the work carefully again and fill in the gaps where they are required. As I noticed, most often they are missing before brackets or quotes, but not always. It is also worth paying attention to the correct placement of punctuation marks: for example, line 93 “drought and high and low-temperature stresses seriously limit” there were extra commas here.

Line 106. Maybe we should remove "Based on two identification methods" and go straight to the results? The methods can be found later in the text and in the corresponding chapter.

 

Table 1. In the caption to the table, decipher the abbreviations used to denote the columns in the table (MW, AA, pI) and indicate for which database Gene IDs are typical.

Figure 2 and 3. The presentation is simply awful, all the symbols are presented in an extremely small way, which makes it impossible to understand what is written. I propose to divide the drawing, which will make it possible to present the designations in a larger font. Or just make the inscriptions readable. In Figure 3A, it is generally difficult to understand the location of genes on chromosomes, since the names of the genes are very small.

Line 265. BrACTIN7. The letter I is missing.

What is the reason for the choice of the indicated concentrations of cadmium? It is also interesting why the authors used during stress time points that were quite close to each other, but the expression analysis was not carried out after 24 hours of stress exposure? It is possible that some BrATG genes are activated at a later date and the authors did not have time to notice a possible interesting result. I recommend taking this remark into account in future experiments and doing more time-experimented experiments.

In general, it was interesting and pleasant for me to get acquainted with this work, and I believe that it is worthy of publication, but after a slight revision. I hope my comments will help improve this work.

Author Response

Response to Reviewer 1 Comments

 

Point 1: The saddest thing is the lack of spaces where they should be. For example: lines 14,47,49,51,52,55,56,57,59,62,54,66,69,71,73,74,75,78,81,84,87,90, 111,112,124,129,131,133 and so on Further. I don't see the point in listing all the cases. I advise the authors to read the work carefully again and fill in the gaps where they are required. As I noticed, most often they are missing before brackets or quotes, but not always. It is also worth paying attention to the correct placement of punctuation marks: for example, line 93 “drought and high and low-temperature stresses seriously limit” there were extra commas here.

 

Response 1: Yes, we noticed this too. We have read through the entire text and filled in the gaps where needed based on your suggested changes. The extra punctuation was removed.

 

Point 2: Line 106. Maybe we should remove "Based on two identification methods" and go straight to the results? The methods can be found later in the text and in the corresponding chapter.

 

Response 2: Yes, I recognize that too. We have removed that part from the article.

 

Point 3:Table 1. In the caption to the table, decipher the abbreviations used to denote the columns in the table (MW, AA, pI) and indicate for which database Gene IDs are typical.

 

Response 3: Here, PI is the theoretical isoelectric point, MW is the abbreviation for molecular weight, and AA is the number of amino acids. We have added the meanings of these abbreviations in the headings of Table 1 for better expression and understanding. In the article we add the provenance of the gene IDs in the Brassicaceae Database (BRAD), a typical gene database, and point them out accordingly.

 

Point 4: Figure 2 and 3. The presentation is simply awful, all the symbols are presented in an extremely small way, which makes it impossible to understand what is written. I propose to divide the drawing, which will make it possible to present the designations in a larger font. Or just make the inscriptions readable. In Figure 3A, it is generally difficult to understand the location of genes on chromosomes, since the names of the genes are very small.

 

Response 4: Yes, we also found this problem and we are very much in favor of your suggestion. We have adjusted and optimized the presentation and text size of the original Figure 2C and Figure 2D. We split Figure 2 into 3 parts (Figure 2, Figure 3 and Figure 4A/4B). We also readjusted the font for the very small names of genes.

 

Point 5: Line 265. BrACTIN7. The letter I is missing.

 

Response 5: Since we have a very large number of primer sequences, including the internal gene BrACTN7 and other BrATGs genes, in order to make the article more concise and readable, we are going to put the total primer list (Table S1) in the appendix and add how they are obtained in the text, which can be downloaded through the link to Table S1.

 

 

Point 6: What is the reason for the choice of the indicated concentrations of cadmium? It is also interesting why the authors used during stress time points that were quite close to each other, but the expression analysis was not carried out after 24 hours of stress exposure? It is possible that some BrATG genes are activated at a later date and the authors did not have time to notice a possible interesting result. I recommend taking this remark into account in future experiments and doing more time-experimented experiments.

 

Response 6: We are very sorry that we forgot to add the cadmium stress treatment time on the article, unlike the other treatments cadmium stress treatment time was 7 days. It is based on the fact that it takes some time for plants to absorb cadmium and respond, and different cadmium concentration treatments are making the plant body face different concentration stresses. It is also based on other literature and our previous studies on cadmium damage in cabbage, when the cadmium concentration exceeds 6 mg/L, the growth and development of cabbage will be significantly limited and serious toxic effects (leaf shrinkage and browning necrosis, etc.) will occur. It would also be very interesting to do more time experiment (0-24h or 0-32 days) studies in future experiments, and I think we will explore this suggestion carefully and do further studies in future experiments.

Author Response File: Author Response.docx