Genome-Wide Identification of Nucleotide-Binding Site–Leucine-Rich Repeat Gene Family in Cymbidium ensifolium and Expression Profiles in Response to Fusarium Wilt Infection

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The article submitted for review is interesting. However, in my opinion, it cannot be published in its current form.

There are some inaccuracies in the introduction. For example, viruses are not microorganisms. Also, the text implies that genes have CC, TIR domains, etc., whereas, it should refer to the proteins encoded by those genes.

Unfortunate phrases appear, such as "the CC coil domain accompanies" or "genes are exclusively found."

In the “R-genes” phrase, R should be italicized.

What is meant by "positive regulation of Fusarium wilt"?

The last sentence in introduction does not determine a goal but is a conclusion.

Subhead in section 2.1 is not relevant to the content; results should not be included in the methodology section. I believe that the phylogenetic analysis should be enriched with the ML method.

In section 2.3 Authors do not mention the conducted analysis of cis-elements.

In section 2.4 it should be "MEME," not "meme," and a reference to the website and parameters used during the analysis is missing.

The phrase "the final images were beautified" seems like a lapse or a mistranslation.

Section 2.5 lacks the information on how many plants were subjected to the experiment. The name of the RT kit is missing.

Section 2.6 lacks the information about the annealing temperature of primers. In my opinion, two reference genes should be chosen instead of one.

In section 3.2: nucleotides do not build proteins, as implied in the text, which I suspect might be a mistranslation. Aliphatic index refers to proteins, not genes.

According to Table 2, only one protein is located in chloroplasts, not several of them.

Fig. 2 - why do all the indicated chromosomes not align from 0 Mbp? What do the different colors of the bars mean?

Section 3.4 lacks Table S2.

Section 3.5 lacks Table S3. Fig. 6 is illegible.

Section 3.6 lacks Table S4. The description of methodology includes completely no information about the transcriptome analysis. This part could not be assessed as it lacks tabular data.

It's not the genes that increased/decreased but their expression.

In the discussion, there are shortcuts that need to be corrected (see the introduction for example). Wheat, tomato, rice, etc. do not need to be italicized.

The Conclusion section seems more like an abstract and needs improvement.

Comments on the Quality of English Language

The text contains a lot of mental shortcuts and linguistic slips that require correction.

Author Response

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Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

1. What is the main question addressed by the research?

 What are the features of Nucleotide-binding site leucine-rich repeat (NBS-LRR) genes in Cymbidium ensifolium? How does the expression of NSB-LRR genes relate to plant stress in Cymbidium ensifolium?

2. Do you consider the topic original or relevant in the field? Does it

address a specific gap in the field?

The topic is original and provides useful fundamentals for further studies on identifying disease-resistant genes in plants.

3. What does it add to the subject area compared with other published

material?

This study added novel information about the genetic diversity of NBS-LRR genes and disease-resistant genes of Cymbidium ensifolium in China.

4. What specific improvements should the authors consider regarding the

methodology? What further controls should be considered?

The authors used appropriate methods for obtaining the results; therefore, no further improvements are needed.

5. Are the conclusions consistent with the evidence and arguments presented and do they address the main question posed?

The results supported the conclusions of this study and all aims were achieved.

6. Are the references appropriate?

The references are suitable to the content of the manuscript. 

7. Please include any additional comments on the tables and figures.

The tables and figures were used correctly and presented the results.

 Please check my comments below for minor issues.

1/ Line 156, suction 2.6: "Eight candidate genes were selected for expression validation."Please clarify the criteria for selecting these eight genes.

2/ In Figure 1, Please increase the sizes of Bootstrap values and Type (at the upper right corner). 

3/ There are no Table S2, S3, S4 in the submission. Please add them in the revised manuscript.

Thank you.

Author Response

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Author Response File: Author Response.pdf

Reviewer 3 Report

Comments and Suggestions for Authors

In this study titled "Genome-wide Identification and Expression Profiling of the NBS-2 LRR Gene Family in Cymbidium ensifolium," the authors conducted a comprehensive analysis of the NBS-LRR gene family within the genome of the Orchidaceae Cymbidium ensifolium, particularly following infection by the phytopathogenic agent. Through transcriptomic and bioinformatic analyses, the authors identified two genes that play key roles in resisting pathogen-induced stress. The objectives are clearly outlined, and the obtained results significantly contribute to the field of this economically important species. The manuscript is well-written and structured; however, some improvements are suggested:

1. It would be beneficial to mention in the title that the investigated NBS-2 LRR gene family serves as key regulatory factors in plant disease resistance responses.

2. Similarly, this point should also be reflected in the keywords.

3. The abstract should explicitly mention the biotic stress agent used in this study (Fusarium wilt) and avoid general statements for clarity.

4. Section 2.5, "Plant Material and Gene Expression Analysis," should include information about the used plant material such as variety name, developmental stage, plant culture conditions, and replicates.

5. Throughout the manuscript, the analyzed part of plant material (including abstract) should be mentioned.

6. The reasons behind the selection of the eight NBS-LRR genes for real-time fluorescence quantitative experiments should be presented.

7. Improvements should be made to the quality of the figures, considering that the figures in the supplementary data are clearer.

8. Finally, English typesetting errors should be corrected for improved readability.

Author Response

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Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

Thank you for considering my comments during the revision of the manuscript. The only point of uncertainty is regarding the annealing temperature of the primers (were the values set to the hundredths?).

Author Response

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Author Response File: Author Response.pdf