Genome-Wide Identification and Expression Analysis of eIF Family Genes from Brassica rapa in Response to TuMV Resistance
, Shaoxing Wang 1,2,†, Shifan Zhang 1, Fei Li 1, Hui Zhang 1, Rifei Sun 1, Shujiang Zhang 1,* and Guoliang Li 1,*
Round 1
Reviewer 1 Report
Dear Authors,
I had great opportunity to review the manuscript entitled: “Genome-Wide Identification and Expression Analysis of eIF Family Genes From Brassica rapa in Response to TuMV Resistance” which is considered for publication in Plants Journal. The article itself presets new and interesting insights in resistance against TuMV . However some results presented on Figures are bad quality and some figures are overloaded with data which makes them difficult to read. I present a specific comments in a form of list:
1. General comments (less problematic):
Authors must check once again the publication rules of Plants journal because in many points article is not good prepared. This is easy spotted for example in reference list in which any of 65 positions is not prepared according journal rules. Other problems also any of citation in main text of manuscript is not correct the manuscript should have number not names in square bracket [] not in ()
2. Introduction section
This part of manuscript should be ended with clearly presented aim or and hypothesis of the study currently any of that is not present
3. Results
As mentioned before some results presented on Figures are bad quality and some figures are overloaded with data which makes them difficult to read. The problem occurs in the case of
Figure 2 is to small very big number of pad pixels low quality
Figure 5 Present the whole structures of different eiFs. In my humble opinion the authors should also compare the active domain or elements /the most crucial parts of eiFs not only whole structures. Moreover, Authors must also add markings on the structures which will show the important/crucial parts of eiF domains/active elements etc.
Figure 7 must be split to two separately figures now this figure is difficult to read
Figure 8 analyses of expression must have add information about statistical analyses. The significant expression values must be mark on charts bars. Now the results have low scientific meaning
Table 2 The results is lite strange because authors did not detect any metabolites which be element of resistant reaction like H2O2 or other reactive forms or vital antioxidant molecules. Moreover the presence of benzen is also strange it suggest that the plants was cultivated on soil or base with contamination of industry waste.
Sincerely,
Author Response
Response to Reviewer 1 Comments
Point 1: Authors must check once again the publication rules of Plants journal because in many points article is not good prepared. This is easy spotted for example in reference list in which any of 65 positions is not prepared according journal rules. Other problems also any of citation in main text of manuscript is not correct the manuscript should have number not names in square bracket [] not in ()
Response: Thank you for your advice, and I am sorry for my carelessness. The formatting errors in the article have been corrected.
Point 2: This part of manuscript should be ended with clearly presented aim or and hypothesis of the study currently any of that is not present
Response: Thank you very much for your comments, and I have added the purpose of the study to the introduction section of the article.
Point 3 :Figure 2 is to small very big number of pad pixels low quality
Response: Thank you for your suggestion, and I have replaced Fig. 2 in the article with a high resolution version.
Point 4 : Figure 5 Present the whole structures of different eiFs. In my humble opinion the authors should also compare the active domain or elements /the most crucial parts of eiFs not only whole structures. Moreover, Authors must also add markings on the structures which will show the important/crucial parts of eiF domains/active elements etc.
Response: Thank you for your suggestion, and Fig. 5 shows the 3D structure of the protein in this subsection of the article to introduce each eIF protein, because the 3D structure is shown, and if the key structural domains circled in the picture may lead to inaccurate circled structure, so the key structural domains are not circled in the picture.
Point 5 : Figure 7 must be split to two separately figures now this figure is difficult to read.
Response: Thank you for your proposal, and Fig. 7 shows the gene family heat map of eIF, and these two figures are the comparison results of different transcripts, which are more visual, intuitive and accurate.
Point 6: Figure 8 analyses of expression must have add information about statistical analyses. The significant expression values must be mark on charts bars. Now the results have low scientific meaning
Response: Thank you very much for your comments and we have added specific values for the expression of each gene in disease-resistant and disease-susceptible plants at the top of the graph in Fig. 8 to more clearly show the differences in expression.
Point 7: Table 2 The results is lite strange because authors did not detect any metabolites which be element of resistant reaction like H2O2 or other reactive forms or vital antioxidant molecules. Moreover the presence of benzen is also strange it suggest that the plants was cultivated on soil or base with contamination of industry waste.
Response: In our previous study (Lu et al., 2022, horticulturae), there are differences in volatile organic compounds between disease-resistant and susceptible plants may be due to changes in metabolism of susceptible plants resulting in changes in these volatile organic compounds to attract aphids for virus transmission.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
Journal: Plants
Manuscript: Manuscript ID: plants-1845582
Title: Genome-Wide Identification and Expression Analysis of eIF Family Genes From Brassica rapa in Response to TuMV Resistance
Dear Editor
Thank you for inviting me to review the manuscript “
Genome-Wide Identification and Expression Analysis of eIF Family Genes From Brassica rapa in Response to TuMV Resistance”
The publication requires addition of information.
Kind regards
Title:
1. Latin names should be italicised throughout the manuscript.
2. The species name should be supplemented with the name of the discoverer.
Abstract:
3. What „metabolite substances” were detected?
Key words:
4. Eliminate phrases appearing in the title of the manuscript.
Introduction
l. 32-52.
5. Provide information on the proteins “…can combine different eIF proteins,…”
6. Indicate other functions in addition to those mentioned “…could present various functions,…”
7. l. 45-47. This fragment is not associated with the issues studied in the present work. Please stick to the topic of the study with reference to the family and the closest order.
8. While citing two literature references, consider the use of an expression “Many studies have found ..”
9. Instead of the expression “and so on:”, specify for which the other “eIF genes” are responsible.
l. 52 – 66.
Table 1.
10. Eliminate the repetitions.
a. E.g. “eIF4E” column 2; this can be combined.
b. „Resistance to” column 3 etc.; please consider reediting the titles of the column.
l. 94-100
11. Specify the research theses.
12. Clarify the aim of the study.
Results
l. 101 – 122
13.Uniform the notations “(Figure 2)”, “(Fig. 3)”, l. 147, l. 187
14. The Results section is not a proper section to cite literature references. 151-153, 157-161, 224-248,
Discussion and conclusion
15. The guidelines for authors indicate the following division: Introduction, Results, Discussion, Materials and Methods, Conclusions …. (l. 357).
16. Eliminate repeated citations of the figures in the discussion (l. 408, 409).
17. The description is repeated – is this necessary? (l. 508-525).
Conclusion
18. Draw logical and concrete conclusions from the present study
Materials and Methods
19. Please provide detailed information in the "Materials and Methods” section.
One (l. 460-463) or two (l. 440-445, 446-450) sentences cannot constitute a subsection
References
20. Comment 1. (l. 593-597, 604-607 e.t.c)
21. Check the list of references and the entire text so that they follow the guidelines for authors.
Author Response
Response to Reviewer 2 Comments
Point 1: Latin names should be italicised throughout the manuscript.
Response: Thank you for your suggestion, and I am sorry for my carelessness, and the error has been corrected in the article.
Point 2: The species name should be supplemented with the name of the discoverer.
Response: Thank you very much for your comments. B. rapa is a vegetable that has been popular for a long time, and it is difficult to verify the exact discoverer, if added with uncertainty.
Point 3: What metabolite substances” were detected?
Response: Thanks for your comments, and an introduction to the detected metabolites has been added to the Introduction.
Point 4: Eliminate phrases appearing in the title of the manuscript.
Response: Thank you very much for your opinion, and I have tried to remove the phrases that appeared in the title of the keywords, after which the keywords could not accurately express the key information expressed by the article.
Point 5: Provide information on the proteins “…can combine different eIF proteins,…”
Response: Thank you very much for your comments, and I have added the proteins and efficacy that can bind eIF to the text.
Point 6: Indicate other functions in addition to those mentioned “…could present various functions,…”
Response: Thank you very much for your comments, which have been added to the article.
Point 7: 45-47. This fragment is not associated with the issues studied in the present work. Please stick to the topic of the study with reference to the family and the closest order.
Response: Thank you very much for your comments. This article is to study the function and conserved structure of the eIF gene family in B. rapa. Both animals and plants contain the eIF gene family. The verified function of the eIF gene family of animals and plants is used as a reference to speculate in this article.
Point 8: While citing two literature references, consider the use of an expression “Many studies have found ..”
Response: Thank you very much for your comments. I have used many research findings in the article citing two literatures, but in order to ensure that the article uses this sentence many times, I use other sentences with similar meanings.
Point 9:Instead of the expression “and so on:”, specify for which the other “eIF genes” are responsible.
Response: Thank you very much for your comments, and I have added the specific efficacy of the eIF gene in the text.
Point 10: Eliminate the repetitions.
a.E.g. “eIF4E” column 2; this can be combined.
b.Resistance to” column 3 etc.; please consider reediting the titles of the column.
Response: Thank you very much for your comments. Table 2 is based on other published articles in the eIF family, so that it can more accurately express the different eIF genes of this species. At the same time, the title name of the third column has been changed to effect, which could represent the eIF gene functions in this species.
Point 11: Specify the research theses.
Response: Thank you very much for your comment, and your request has been added there.
Point 12: Clarify the aim of the study.
Response: Thank you very much for your comment, and your request has been added there.
Point 13: Uniform the notations “(Figure 2)”, “(Fig. 3)”, l. 147, l. 187
Response: Thank you for your suggestion, and I am sorry for my carelessness, the error has been corrected in the article.
Point 14: The Results section is not a proper section to cite literature references. 151-153, 157-161, 224-248.
Response: Thanks for your valuable comments, and I have corrected the references correctly.
Point 15: The guidelines for authors indicate the following division: Introduction, Results, Discussion, Materials and Methods, Conclusions …. (l. 357).
Response: Thank you for your reminder, and I have revised it according to the article submission requirements.
Point 16: Eliminate repeated citations of the figures in the discussion (l. 408, 409).
Response: Thanks for your suggestion, and I have edited it.
Point 17: The description is repeated – is this necessary? (l. 508-525).
Response: Thanks for the reminder, and I have removed the duplicate.
Point 18: Draw logical and concrete conclusions from the present study.
Response: Thanks for the suggestion, and I've added specific conclusions to the conclusion.
Point 19: One (l. 460-463) or two (l. 440-445, 446-450) sentences cannot constitute a subsection
Response: Thanks for the reminder, and I've combined these two edits into one summary.
Point 20: Comment 1. (l. 593-597, 604-607 e.t.c)
Response: Thank you for your suggestion, and I am sorry for my carelessness. The error has been corrected in the article.
Point 21: Check the list of references and the entire text so that they follow the guidelines for authors.
Response: Thanks for your suggestion, and it has been checked and revised according to the submission requirements.
Author Response File: Author Response.pdf
Round 2
Reviewer 1 Report
Dear Authors,
Thank for changes but some problems still persist. Added aim of the study bad formulated I suggest correction by native speaker. Figure 2 still is bad quality with big number bad pixels. Figure 7 must be split to two separately figures now this figure is still difficult to read. Figure 5 Present the whole structures of different eiFs. The authors should also compare the active domain or elements /the most crucial parts of eiFs not only whole structures. Moreover, Authors must also add markings on the structures which will show the important/crucial parts of eiF domains/active elements etc. The explanation presented in response is little illogical in context importance of eiF structures. Without deeper analyzes the figure has little meaning for scientific aim. I understand the changes in organic metabolites but lack changes in reactive oxygen species (like H2O2) is problematic because is first and firm confirmation of well characterized resistant reaction in measurement of H2O2.
Sincerely,
Author Response
Point 1: Authors Added aim of the study bad formulated I suggest correction by native speaker.
Response: Thank you for your suggestion, and the sentence has been revised.
Point 2: Figure 2 still is bad quality with big number bad pixels.
Response: Thank you for your suggestion, and I have replaced Fig. 2 in the article with a high resolution version.
Point 3:Figure 7 must be split to two separately figures now this figure is still difficult to read.
Response: Thank you very much for your comments, and Figure 7 has been split into two separate figures.
Point 4:Figure 5 Present the whole structures of different eiFs. The authors should also compare the active domain or elements /the most crucial parts of eiFs not only whole structures. Moreover, Authors must also add markings on the structures which will show the important/crucial parts of eiF domains/active elements etc. The explanation presented in response is little illogical in context importance of eiF structures. Without deeper analyzes the figure has little meaning for scientific aim.
Response: In our previous study, the structure of the eIF(iso)4E protein is highly similar to that of the eIF4E protein, including eight β-strands, three α-helices, and three extended loops, which could form an inwardly depressed hydrophobic core structure that could be combined with the mRNA cap structure (Li et al., 2018), and the key amino acid F36L was marked in the eIF(iso)4E and eIF4E proteins structure (white arrow). However, we are very sorry that the functions of the other eIF proteins structure (eIF3B, eIF6A, eIF5B, and eIF4A) were not reported, and we just predicted the protein structure modal using Phyre2 software, and we could not link which one active elements/domains to the resistance in B. rapa, which need other experiment to provide evidence. Through the protein structure analysis, some special structure modals were found, which were relate to resistance in plants, but the active elements were not predicted.
Point 5:I understand the changes in organic metabolites but lack changes in reactive oxygen species (like H2O2) is problematic because is first and firm confirmation of well characterized resistant reaction in measurement of H2O2.
Response: We agree with you that the resistance was related to the changes of the reactive oxygen species (like H2O2). However, we are sorry that the metabolites analysis were conducted in our previous study, and we just detected the volatile organic compounds (VOCs), not including the reactive oxygen species (like H2O2). So in this study, we could not show the changes of the reactive oxygen species.
Author Response File: 
Author Response.docx
Round 3
Reviewer 1 Report
Dear Authors,
All my comments was added. I recomend publication.
Sincerely,
