Integrated Phylogenomics and Expression Profiling of the Peptide Deformylase Gene Family in Oryza sativa Reveals Their Role in Development and Stress Tolerance

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Manuscript Title

Integrated Phylogenomics and Expression Profiling of the Peptide Deformylase Gene Family in Oryza sativa Reveals Their Role in Development and Stress Tolerance

This manuscript presents a comprehensive analysis of the OsPDF gene family in rice, combining bioinformatics, promoter analysis, and qRT-PCR validation under abiotic stress. The topic is relevant and fits well within plant molecular biology and stress physiology. The study provides useful insights into gene family evolution and stress-responsive expression.

However, while the work is well-organized and scientifically sound, there are several issues related to clarity, redundancy, methodology description, and interpretation depth that should be addressed before publication.

1. The manuscript mainly confirms already known features of PDF genes (e.g., stress response, chloroplast function).
2. The authors should clearly state:

• What is new compared to previous studies (especially Moon et al., 2008).
• What gap this study fills.

3. Several sections repeat the same ideas:

• Introduction and Discussion overlap heavily
• Results are partially repeated in Discussion

4. The study relies heavily on bioinformatics + expression data, but:

• No functional validation (mutants, overexpression)
• Conclusions about “roles in stress tolerance” are overstated

5. 5. qRT-PCR Methodology Needs More Detail

The experimental section lacks clarity:

• Number of technical replicates
• Reference gene(s) used
• Primer validation
• Efficiency of PCR

6. Figures Need Improvement

Several figure issues:

• Figure 1 caption is duplicated
• Figures lack sufficient explanation
• No statistical significance indicators (e.g., *, **)

7. Language and Grammar Issues

There are many grammatical problems

8. References

• Some references appear irrelevant or incorrectly formatted

 

 

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

This manuscript examines the Peptide deformylase family, which is responsible for protein maturation. The authors comprehensively present the functional significance of this family in the Introduction section. Interesting results were obtained in identifying cis-acting elements associated with ABA, MeJA, GA, and auxin. Based on these results, it was concluded that the three members of the PDF family have different functional activities. This is also supported by gene expression data in response to various abiotic stresses. However, the conclusion about closer evolutionary relationships between rice and monocotyledonous wheat is hasty; more thorough study on a larger number of plants is needed, especially since the three members of the rice PDF family differ from each other.
The manuscript is carefully formatted, with some minor comments.
Figure 1 caption should be repeated.
Figure 3 caption should provide a more detailed description.
Figures 5-8 can be combined under the title "The relative expression analysis of the OsPDFs under abiotic stresses."

Author Response

Please see the attachment.

Author Response File: Author Response.pdf