Proteomic Approach during the Induction of Somatic Embryogenesis in Coffea canephora

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

I have carefully reviewed the manuscript titled "Proteomic approach during the induction of somatic embryogenesis in Coffea canephora" submitted to Plants. My assessment of the manuscript's quality and suitability for publication is detailed below.

 

Summary:

The manuscript investigates somatic embryogenesis (SE) in Coffea canephora, focusing on the role of plant growth regulators (PGR) using a proteomic approach. It explores the changes in protein expression during different stages of SE induction and identifies proteins associated with auxin and cytokinin metabolism, among others.

 

Critical Evaluation:

 

Scientific Contribution: The manuscript aligns with the scope of Plants, as it employs proteomic techniques to study SE in Coffea canephora. However, the manuscript has several shortcomings that need to be addressed.

 

Clarity and Presentation: The manuscript lacks clarity and precision in several areas:

 

Abstract: The abstract should succinctly convey the study's objectives, methods, and key findings. It currently contains redundant information and should be revised for clarity.

Introduction: The introduction is inadequate. It should provide a clearer rationale for the study, explaining why proteomic analysis is crucial for understanding SE in Coffea canephora and summarizing existing knowledge in the field.

Conclusion: The conclusion section is too brief and lacks depth. It should summarize the main findings and their implications for the field of SE in Coffea canephora.

Experimental Design and Results: The methodology and results sections need further elaboration. The authors should provide a detailed description of the proteomic techniques used, including sample preparation and data analysis. Additionally, the results should be discussed in greater depth, with a focus on their significance and implications.

 

Recommendations:

 

The manuscript requires substantial revisions to address the issues identified in this review.

The abstract should be rewritten to provide a clear and concise summary of the study.

The introduction should be expanded to better justify the study and provide context.

The conclusion section should be enhanced to summarize the key findings and their implications.

 

 

Author Response

Reviewer 1

Dear reviewer. We appreciate the time you took to review our paper and thank you for your comments that have improved our manuscript.

Answers

Dear Reviewer, we carefully reviewed and agree with your suggestions. We have made the requested changes in all sections (please, see the changes in the manuscript). We appreciate your comments, as they undoubtedly greatly improved our manuscript.

 

have carefully reviewed the manuscript titled "Proteomic approach during the induction of somatic embryogenesis in Coffea canephora" submitted to Plants. My assessment of the manuscript's quality and suitability for publication is detailed below.

Summary:

The manuscript investigates somatic embryogenesis (SE) in Coffea canephora, focusing on the role of plant growth regulators (PGR) using a proteomic approach. It explores the changes in protein expression during different stages of SE induction and identifies proteins associated with auxin and cytokinin metabolism, among others.

Critical Evaluation:

Scientific Contribution: The manuscript aligns with the scope of Plants, as it employs proteomic techniques to study SE in Coffea canephora. However, the manuscript has several shortcomings that need to be addressed.

Clarity and Presentation: The manuscript lacks clarity and precision in several areas:

 Abstract: The abstract should succinctly convey the study's objectives, methods, and key findings. It currently contains redundant information and should be revised for clarity.

Introduction: The introduction is inadequate. It should provide a clearer rationale for the study, explaining why proteomic analysis is crucial for understanding SE in Coffea canephora and summarizing existing knowledge in the field.

Conclusion: The conclusion section is too brief and lacks depth. It should summarize the main findings and their implications for the field of SE in Coffea canephora.

Experimental Design and Results: The methodology and results sections need further elaboration. The authors should provide a detailed description of the proteomic techniques used, including sample preparation and data analysis. Additionally, the results should be discussed in greater depth, with a focus on their significance and implications.

Recommendations:

The manuscript requires substantial revisions to address the issues identified in this review.

The abstract should be rewritten to provide a clear and concise summary of the study.

The introduction should be expanded to better justify the study and provide context.

The conclusion section should be enhanced to summarize the key findings and their implications.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

In this manuscript, the authors used label-free quantitative proteomics to monitor proteome changes during somatic embryogenesis induction. They found that some proteins in specific pathways were enriched. The conclusions are, for the most part, supported by the data. However, there are several concerns that should be addressed prior to publication.

 

Major points:

 

1.    The Methods section lacks detail. There is a lot of missing information. For example: How many biological replicates were performed? How did the authors harvest the tissues? Was protein extraction conducted at room temperature or 4°C? Can 50 mM ammonium bicarbonate with 0.1% SDS dissolve all the pellets? Was overnight digestion conducted with rotation? How did the authors perform fractionation? What are the settings for MS?

 

2.    The authors used plantlets that were harvested 14 days before induction as a control. Did the authors mean the use of whole plants? To compare with leaf explant on day 0, day 7, and day 21, using only leaves would be a better design.

 

Minor points:

 

1.    In Line 466, it should be "log fold change of 1."

 

2.    Figure 3B: The text is too small to read.

Author Response

Dear reviewer. We appreciate the time you took to review our paper and thank you for your comments that have improved our manuscript.

 

Reviewer 2

In this manuscript, the authors used label-free quantitative proteomics to monitor proteome changes during somatic embryogenesis induction. They found that some proteins in specific pathways were enriched. The conclusions are, for the most part, supported by the data. However, there are several concerns that should be addressed prior to publication.

 

Major points:

 

1. The Methods section lacks detail. There is a lot of missing information. For example: How many biological replicates were performed? How did the authors harvest the tissues? Was protein extraction conducted at room temperature or 4°C? Can 50 mM ammonium bicarbonate with 0.1% SDS dissolve all the pellets? Was overnight digestion conducted with rotation? How did the authors perform fractionation? What are the settings for MS?

 

Dear reviewer, we appreciate having noticed the errors. Your corrections have undoubtedly improved the understanding of the manuscript, and we have covered them all. Please see the correction in the manuscript.

 

2. The authors used plantlets that were harvested 14 days before induction as a control. Did the authors mean the use of whole plants? To compare with leaf explant on day 0, day 7, and day 21, using only leaves would be a better design.

 

Thanks for your observation. In each case, we use the leaves of the plants. We have clarified this information in the methodology section.

 

Minor points:

 

1. In Line 466, it should be "log fold change of 1."

We agree with the observation; the correction has been made. 

2. Figure 3B: The text is too small to read.

          Thank you for the suggestion. We have corrected the Figure.

Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

Comments and Suggestions for Authors

All the concerns have been addressed.