Comprehensive Bioinformatics and Expression Analysis of the TLP Gene Family Revealed Its Role in Regulating the Response of Oryza sativa to Nilaparvata lugens, Laodelphax striatellus, and Jinggangmycin

Round 1

Reviewer 1 Report

 

1. Lines 28-29 are not clear what you want to say.
2. remove unnecessary acronyms in the abstract i.e. JGM
3. Section 2.6 section title is not useful.
4. Materials and methods should be completely reorganized plant materials should come first, then biotic stress treatment, etc etc.
5. The study lacks control. Why you didnt take samples from rice without infestation?
6. In several studies, RNA extraction was done 14 days after infestation. In your case RNA was extracted at 42, 44, and 48-day-old plants. What's the basis for this?
7. Figure 10, genes tested varied in terms of expression. Are they significantly different in-between days? This should. be highlighted.
8. Font for references seems diffent from the main body of the manuscript. Please change for uniformity. 

Author Response

Reviewer 1

1. Lines 28-29 are not clear what you want to say.

Our response: The sentence has been revised according to the reviewer suggestion.

 

2. remove unnecessary acronyms in the abstract i.e. JGM

My response: Changes have been made according to the reviewer suggestion.

 

3. Section 2.6 section title is not useful.

Our response: Thanks for your suggestion. However, we believe that it is useful in the context of this paper. The contents in section 2.6 provide valuable information about the performed experiment. Therefore, we apologetically disagree with the reviewer's comment.

 

4. Materials and methods should be completely reorganized plant materials should come first, then biotic stress treatment, etc etc.

Our response: Changes have been made according to the reviewer suggestion.

5. The study lacks control. Why you didn't take samples from rice without infestation?

Our response: Thank you for the comment. We have used control for all the treatments with the name (CK) in Fig.10. 

 

6. In several studies, RNA extraction was done 14 days after infestation. In your case, RNA was extracted at 42, 44, and 48-day-old plants. What's the basis for this?

Our response: Thank you for the comment. We have revised that particular section. The revised text is as follows (Forty days old, rice plants were exposed to BPH, and SBPH stress and samples were taken at 2, 4 and 8 days after infestation. Similarly, JGM was sprayed on the rice plants and samples were taken at 2, 4 and 8 days after treatment. Following that, RNA was extracted from the samples using Trizol reagent (Invitrogen, Carlsbad, CA, United States). 

7. Figure 10, genes tested varied in terms of expression. Are they significantly different in-between days? This should. be highlighted.

Our response: Thanks for the comment. We have revised the figures by applying student t-test. The difference has been pointed out with different alphabets.

 

8. Font for references seems different from the main body of the manuscript. Please change for uniformity. 

Our response: Changes have been made according to the reviewer's suggestion.

 

Author Response File: Author Response.docx

Reviewer 2 Report

Overall, the manuscript is easy to read. However, the methodology misses several important details that prevent any replication of this study. For instance, in the first part of this study, the authors searched several online databases but the specific details of the searches have been omitted. The same occurs in the programs/servers used. For instance, the authors have used string to retrieve the interactive network of proteins. That is fine! But the results vary quite substantially depending on the parameters used to retrieve the networks. So, please detail the methods used. I am sure that the authors can easily update the text.

In relation to the expression of genes, it is very hard to follow what is new from what has come from published studies. In fact, I only realized that after reading the results (nothing is said about that in M%Ms). In this sense, those results are tricky because the reader cannot follow the conditions of those experiments, unless, I have misunderstood this part. Could you please explain this better?

Author Response

 

Reviewer 2

Overall, the manuscript is easy to read. However, the methodology misses several important details that prevent any replication of this study. For instance, in the first part of this study, the authors searched several online databases, but the specific details of the searches have been omitted. The same occurs in the programs/servers used. For instance, the authors have used string to retrieve the interactive network of proteins. That is fine! But the results vary quite substantially depending on the parameters used to retrieve the networks. So, please detail the methods used. I am sure that the authors can easily update the text.

Our response: Thanks for the comment. The M&M section has been rearranged in the pattern. We believe the revised version will be easy for the readers to follow our work. For the string database, we selected one reference gene from the TLP family and used its protein sequence to identify its potential interactive partners. There were no specific parameters as such. We downloaded the interactive map and tabulated its key interactive partners.

In relation to the expression of genes, it is very hard to follow what is new from what has come from published studies. In fact, I only realized that after reading the results (nothing is said about that in M%Ms). In this sense, those results are tricky because the reader cannot follow the conditions of those experiments unless I have misunderstood this part. Could you please explain this better?

Our response: Thanks for highlighting this crucial mistake. We have made amendments to the M&M section as per the reviewer's suggestion. The revised changes are as follows (Forty days old, rice plants were exposed to BPH and SBPH stress, and samples were taken at 2, 4, and 8 days after infestation. Similarly, JGM was sprayed on the rice plants, and samples were taken at 2, 4, and 8 days after treatment. Following that, RNA was extracted from the samples using Trizol reagent (Invitrogen, Carlsbad, CA, United States).  

Note: Dear reviewer, additionally, we have revised the manuscript in "track changes" that has changed line numbers; kindly find the revised changes.

Note: Dear reviewer, additionally, we have revised the manuscript in "track changes" that has changed line numbers; kindly find the revised changes.

 

Author Response File: Author Response.docx

Round 2

Reviewer 1 Report

The authors have addressed my comments and suggestions. Although I am endorsing this manuscript for publication, several minor grammatical errors should be corrected in the manuscript during the proofing stage. 

Reviewer 2 Report

I believe the authors have addressed all the concerns raised in the previous version.