Characterization of Drought-Responsive miRNAs in Peanut Through Integrated Transcriptomic Approaches
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsThe manuscript (agriculture-3907715) submitted by Zhang et al. describes the identification and functional analysis of miRNAs (specifically, ahy-miR398 and ahy-miR408) responsive to drought stress in peanuts using sRNA sequencing and degradome sequencing. They demonstrated that ahy-miR398 and ahy-miR408 negatively regulate drought stress in peanuts via targeting their respective target genes. Overall, the manuscript is well written, and the conclusion is supported by the presented data. However, I noticed some issues in the current version of the manuscript. The authors need to address the issues before the manuscript can be published.
- In Figure 3 legend, no description of Panel A and B is provided. Similarly, in Figure 5 legend, the description of Panel A, B, and C does not match the figures and there is no description for D, E, and F. In Panels A, C, and E, I believe the top panels are normal conditions and the bottom panels are drought stress. But the authors did not mention this.
- Line 271-271, “Cleaved transcripts were classified into five categories (0–4) based on the abundance and positional confidence of cleavage signatures”, the authors need to provide more information about the five categories.
- Line 246-248, the authors stated that “Notably, although ahy-miR395 was upregulated in both mock and treatment groups, its expression at T24 showed a 21.96-fold increase compared to baseline”. However, in Line 251-252, they stated that “Surprisingly, ahy-miR395 exhibited stable, high-level expression despite predicted differential patterns”. It is about the same ahy-miR395, but the description is totally different.
- Line 333, the authors stated that “ahy-miR408 and ahy-miR398 exert antagonistic regulatory roles”. However, both ahy-miR408 and ahy-miR398 are down-regulated under drought stress, and overexpression of both ahy-miR408 and ahy-miR398 in Arabidopsis shows the same phenotypes.
- Minors: Line 65, “Populus” should be italicized; Line 145, “Agrobacterium tumefaciens” should be italicized; Line 342, “Peg-treated” should be “PEG-treated”.
Author Response
Response to Reviewer1 Comments
We sincerely appreciate the reviewer’s careful reading of our manuscript (agriculture-3907715) entitled “Integrated Multi-omics Analysis Reveals Drought-Responsive miRNAs in Peanut (Arachis hypogaea L.)” and their valuable comments and suggestions, which have helped us improve the clarity and quality of the paper. We have revised the manuscript accordingly, and our detailed responses to each comment are provided below.
Reviewer Comment 1:
In Figure 3 legend, no description of Panel A and B is provided. Similarly, in Figure 5 legend, the description of Panel A, B, and C does not match the figures and there is no description for D, E, and F. In Panels A, C, and E, I believe the top panels are normal conditions and the bottom panels are drought stress. But the authors did not mention this.
Response:
The legends for Figures 3 and 5 have been thoroughly revised to provide clear and accurate descriptions for each panel. Specifically: Figure 3: The legend now includes explicit descriptions of Panels A and B, indicating that the top panels represent expression under control conditions and the bottom panels under drought (PEG) treatment. Figure 5: The legend has been corrected to accurately describe Panels A–F, including clear identification of control and drought stress panels and the corresponding quantitative analyses.
Revision made: pages 9 lines 269-279, Figure 3 and page 11-12 lines 340-355, Figure 5. These changes ensure that figure legends fully correspond to the visual data.
Reviewer Comment 2:
Line 271-271, “Cleaved transcripts were classified into five categories (0–4) based on the abundance and positional confidence of cleavage signatures”, the authors need to provide more information about the five categories.
Response:
The description of degradome classification has been expanded in the Materials and Methods (Section 2.3) as follows: Category 0 represents the highest confidence, where the cleavage site has the most abundant tag and a single maximum. Category 1 has multiple sites with maximum abundance. Category 2 and 3 correspond to sites with tag abundance above or below the transcript median, respectively. Category 4 indicates sites supported by only one read. These categories reflect decreasing confidence in miRNA-guided cleavage.
Revision made: Materials and Methods, page 3-4 lines 132-138. This addition clarifies the classification criteria for degradome sequencing results.
Reviewer Comment 3:
Line 246-248 and Line 251-252: The description of ahy-miR395 is inconsistent — once described as upregulated (21.96-fold increase) and then as “stable, high-level expression”.
Response:
To clarify, the 21.96-fold upregulation at T24 compared to baseline (Table 2 and Table S1) reflects the sequencing data, which initially suggested a drought stress response. However, northern blot validation revealed that ahy-miR395 maintained stable, high-level expression across the experimental conditions (Figure 3B), which contrasts with the predicted differential patterns from sequencing. This discrepancy between sequencing predictions and northern blot results will be addressed in the revised manuscript by explicitly noting the divergence and discussing potential reasons for the inconsistency. Therefore, ahy-miR395 will not be considered a candidate drought responsive sRNA. It is true that the original sentence "although ahy-miR395 was upregulated in both mock and treatment groups, its expression at T24 showed a 21.96-fold increase compared to baseline." is ambiguous. We have revised it to "Notably, although sequencing results revealed that ahy-miR395 was upregulated in both mock and treatment groups, its expression at T24 showed a 21.96-fold increase compared to baseline."
Revision made: Result, page 8 lines 259-261.
Reviewer Comment 4:
Line 333, the authors stated that “ahy-miR408 and ahy-miR398 exert antagonistic regulatory roles”. However, both are down-regulated under drought stress, and overexpression of both in Arabidopsis shows the same phenotype.
Response:
We appreciate the reviewer’s insightful comment regarding the use of the term “antagonistic regulatory roles.” Upon careful re-evaluation of our results, we agree that this wording may not accurately reflect the functional relationship between ahy-miR398 and ahy-miR408.
Our integrated multi-omics data and transgenic validation indicate that both ahy-miR398 and ahy-miR408 are downregulated under drought stress and that their overexpression reduces drought tolerance in Arabidopsis. Specifically, ahy-miR398 targets Cu/Zn-superoxide dismutase chaperones (CCSs), influencing oxidative stress responses, whereas ahy-miR408 regulates laccase (LAC12) and copper transporter (COPA/PCL) genes involved in copper homeostasis and ROS modulation. Thus, both miRNAs act as negative regulators of drought tolerance but function through distinct molecular pathways rather than directly opposing each other. The previous use of “antagonistic” could imply opposite biological effects, which is not supported by our data. To enhance scientific accuracy, we have revised the sentence as follows:
“Integrated multi-omics analysis demonstrated that ahy-miR408 and ahy-miR398 exert distinct but functionally convergent regulatory roles through separate molecular path-ways”
Revision made: Discussion, page 12 lines 357-370.
Reviewer Comment 5 (Minor Issues):
Line 65, “Populus” should be italicized;
Line 145, “Agrobacterium tumefaciens” should be italicized;
Line 342, “Peg-treated” should be “PEG-treated”.
Response:
All minor issues have been corrected as suggested: Populus and Agrobacterium tumefaciens are now italicized. “Peg-treated” has been changed to “PEG-treated” throughout the manuscript.
Revision made: Introduction, page 2 line 79; Discussion, page 12 lines 378.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsZhang et al performed a study to determine mi RNAs involve in drought response in Arachis hypogaea. I think this descriptive study is interesting and well conducted. However, i have some comments:
Major comments:
1.- In the title, authors declare an integrated multi-omics analysis, however, the termn "Multiomics" is usually used to the integration of data from different omic sciences like proteomics, genomics, metabolomics and transcriptomics. But, here is just different transcriptomic approaches. There is not data from other omic sciences. Please review https://www.mdpi.com/2223-7747/14/6/865#
2.- Figure 3 is poorly described. Even the figure legend does not mention anything about figures A and B.
3.- The same happens to Figure 5 where even Figures 5D to 5F are not explained at all. In addition, figures 5A to 5C are not properly explained. Just as an example. What is the difference between top and bottom figures in figure 5C? The same for figures 5A and 5B. What is the difference between the right and left sides of figures 5B, 5D and 5F?
4.- In figure 1B legend is mentioned that the outermost ring shows selected chomosomes. But just as an example: which chromosome is arahy.tifrunner.gnm2.arahy.14? What is the biological meaning of these codes?
Other few minor comments are included in the attached file.
Comments for author File: Comments.pdf
Author Response
Response to Reviewer 2 Comments
Thank you for your valuable feedback and insightful comments on our manuscript. We appreciate your time and effort in reviewing our work. Below, we provide our detailed responses to your major and minor comments:
Major Comments:
- Title and Multi-Omics Terminology:
We appreciate your observation regarding the use of the term "multi-omics." You are absolutely right that "multi-omics" typically refers to the integration of data from different omic platforms such as genomics, proteomics, metabolomics, and transcriptomics. In our study, we only employed various transcriptomic approaches (e.g., small RNA sequencing and degradome sequencing), so we acknowledge that the use of "multi-omics" was not accurate. We have revised the title and the abstract accordingly to reflect that this study focuses on a multi-approach transcriptomic analysis of drought-responsive miRNAs in Arachis hypogaea. Thank you for pointing this out.
Revision made: Article and Full text.
- Figure 3 Description:
We apologize for the lack of clarity in the figure legend of Figure 3. We have now updated the figure legend to provide a more detailed explanation of Figures 3A and 3B, including a clear description of the experimental setup and the key findings illustrated in the figure. Additionally, we have made sure that all aspects of the figure are properly explained to enhance its readability and understanding.
Revision made: Result, page 9 lines 268-279
- Figure 5 Explanation:
We appreciate your comments on Figure 5. Upon review, we noticed that the legend was insufficient in explaining the differences between the top and bottom figures in 5C, as well as the left and right sides of figures 5A, 5B, 5D, and 5F. We have now revised the figure legend to provide a clearer explanation of these details. Specifically, we have explained the differences in experimental conditions and data presentation for each figure panel. We believe these clarifications will help make the figure more understandable to the readers.
Revision made: Result, pages 11-12 lines 339-355
- Figure 1B Legend and Chromosome Codes:
We appreciate your comment on the biological meaning of the chromosome codes shown in Figure 1B. The codes like "arahy.tifrunner.gnm2.arahy.14" represent specific chromosomes in the Arachis hypogaea genome based on the Tifrunner reference genome (v2). In the revised figure legend, we have now included an explanation of these codes and their biological significance. We also added a brief note about the genomic assembly version to help readers understand the reference genome used in this study.
Revision made: Result, pages 5-6 lines 196-211
Minor Comments:
We have carefully reviewed the manuscript and made necessary revisions accordingly. Specific changes include: 1, Adjusting the phrasing for clarity in several sections of the manuscript. 2, Correcting minor typographical and grammatical errors. 3, Ensuring consistency in the formatting of figure legends and references.
Once again, we thank you for your constructive feedback, which has helped us improve the quality and clarity of our manuscript. We believe the revisions we have made address your concerns, and we hope that the revised manuscript will meet your expectations.
Thank you for your time and consideration.
Author Response File: Author Response.pdf
Reviewer 3 Report
Comments and Suggestions for AuthorsGeneral comments
The publication offers a multi-omics investigation of drought-responsive miRNAs in peanut, nevertheless, it lacks distinct novelties and comprehensive functional insights, especially as the major miRNAs (miR398 and miR408) are already extensively characterized in stress responses. The lack of a thorough regulatory framework and inadequate statistical information reduces the study's value. Significant modifications are necessary to enhance mechanistic depth, data display, and biological interpretation.
Major points
Lack of clarity on novelty of findings
Lines 14–33: The manuscript presents a multi-omics analysis of drought-responsive miRNAs in peanut, focusing on miR398 and miR408. However, both miRNAs have been previously linked to drought stress in multiple species. The study does not clearly establish what is new in the context of peanut or what mechanistic insights have not been previously reported. The novelty should be explicitly emphasized in both the abstract and the discussion.
Functional validation limited to heterologous system
Lines 295–327 (Section 3.6): The study uses Arabidopsis for overexpression analysis. While this provides preliminary functional validation, it is a heterologous system. Given species-specific miRNA processing differences, the conclusions drawn should be cautiously interpreted. The authors themselves note this limitation (Lines 394–396), but it should be addressed more critically and future directions toward validation in peanut should be proposed in the conclusion.
Missing integration of omics data into a regulatory model
Throughout results and discussion: The manuscript would benefit significantly from a summarizing model or diagram integrating miRNA expression, target gene networks, phenotypic outcomes, and stress-response pathways. Currently, the results remain fragmented. A final figure or schematic model summarizing the entire regulatory pathway would improve reader understanding and impact.
Figures and tables lack detail and clarity
Figure 4 is not clear, as too many subsets of figures are compressed in one panel.
p-values and statistical tests used are reported clearly.
Incomplete description of statistical methods: Lines 215–227, 267–274, and 300–326: Details of the statistical methods used to determine differential expression, target validation, and phenotypic differences are incomplete or missing. Clearly define Fold change cutoffs, the TPM normalization procedure, software/tools used, and statistical tests applied to germination and growth comparisons.
Minor points
Line 25–26: Overuse of technical terms in a single sentence: “P-type ATPase copper transporters (COPAs), and a blue copper protein-like (PCL) gene…” Consider breaking into simpler components.
Line 38: “Photosynthetic system disruption…” could be rephrased as “disruption of photosynthesis” for clarity.
Line 57–60: Multiple examples are packed into one sentence. Consider splitting into separate lines for ROS, hydraulic architecture, and ABA signaling.
Line 74: Avoid using both “PEG6000-simulated” and “osmotic stress” interchangeably. Clarify the simulation method consistently throughout.
Line 104: Typo: “RNA purity was checked…” should be followed by a full stop instead of a comma at the end of the sentence.
Line 140: Method: "Expression levels were quantified using ImageJ as instructed." This is vague. Specify if normalization and background subtraction were applied.
Line 213: Header: “3.3. Revealed differential miRNA expression profiling…” Suggest rephrasing as “Differential Expression Profiling of miRNAs.”
Line 226: phrase “integrative analysis identified…” is ambiguous. Specify the tool or statistical method used for the integration.
Line 255: “100 μg of total RNA was loaded.” This looks quite high. Confirm if the information is correct or a typo.
Line 261: Degradome sequencing section lacks the reference genome version. Include the version and date of download.
Line 274: Sentence “We selected genes with categories < 2 as candidate targets.” What is <2?; Add justification or citation for this threshold.
Line 295: “Arabidopsis thaliana lines heterologously overexpressing…” Consider simplifying to “Transgenic Arabidopsis lines overexpressing…”
Line 404–412 (Conclusion): conclusion restates findings well but could benefit from a clearer summary of practical applications (e.g., molecular breeding or marker-assisted selection).
Throughout: Consistent italicization of Arachis hypogaea and Arabidopsis thaliana.
miRNA naming should be standardized (e.g., “ahy-miR398” vs “miR398”).
Author Response
Response to Reviewer 3 Comments
Summary
We sincerely thank the reviewer for the detailed and constructive comments. We have carefully revised the manuscript to address each concern. Below we provide a point-by-point response, with the corresponding revisions implemented in the revised version.
Point-by-point Response
Comment 1: Lack of clarity on novelty of findings
Lines 14–33: The manuscript presents a multi-omics analysis of drought-responsive miRNAs in peanut, focusing on miR398 and miR408. However, both miRNAs have been previously linked to drought stress in multiple species. The study does not clearly establish what is new in the context of peanut or what mechanistic insights have not been previously reported. The novelty should be explicitly emphasized in both the abstract and the discussion.
Response 1:
We sincerely thank the reviewer for highlighting this important point. We fully agree that the initial version of the manuscript did not explicitly emphasize the novelty of our study. In response, we have substantially revised the Abstract (Lines 15–35) and expanded the Discussion (Lines 357–37-) to clearly articulate the unique contributions and novel mechanistic insights of our work.
Revision made: Page 1, Abstract, Lines 15–35; Page 1, Discussion, Lines 357–370
Comment 2: Functional validation limited to heterologous system
Lines 295–327 (Section 3.6): The study uses Arabidopsis for overexpression analysis. While this provides preliminary functional validation, it is a heterologous system. Given species-specific miRNA processing differences, the conclusions drawn should be cautiously interpreted. The authors themselves note this limitation (Lines 394–396), but it should be addressed more critically and future directions toward validation in peanut should be proposed in the conclusion.
Response 2:
We agree that Arabidopsis serves as a heterologous system and that species-specific differences in miRNA processing could affect the interpretation of our findings. To address this concern, we have revised the Result and Discussion sections to more critically acknowledge this limitation and propose future directions for further validation in peanut. We have now emphasized that the findings based on Arabidopsis overexpression are preliminary, and that species-specific differences in miRNA processing may influence the observed results. These limitations are clearly stated, and we caution that the full biological relevance of these findings will require confirmation in the native peanut system.
Revision made: Result, page10 lines 320-326 and Discussion, page 13-14 lines 433-443.
Comment 3: Missing integration of omics data into a regulatory model
Throughout results and discussion: The manuscript would benefit significantly from a summarizing model or diagram integrating miRNA expression, target gene networks, phenotypic outcomes, and stress-response pathways. Currently, the results remain fragmented. A final figure or schematic model summarizing the entire regulatory pathway would improve reader understanding and impact.
Response 3:
Thank you for your insightful comment. We appreciate your suggestion to integrate the omics data into a more cohesive regulatory model. To address this, we plan to include a schematic diagram in the revised manuscript that will consolidate the miRNA expression, target gene networks, phenotypic outcomes, and stress-response pathways into a unified model (Figure 6). This diagram will help to visually illustrate the interactions and provide a clearer representation of the regulatory pathways. We believe this addition will enhance the reader's understanding and improve the overall impact of the manuscript. Thank you again for your valuable feedback.
Revision made: Discussion, page14 lines 444-455 (Figure 6).
Comment 4: Figures and tables lack detail and clarity
Figure 4 is not clear, as too many subsets of figures are compressed in one panel.
Response 4:
Thank you for your valuable feedback. We fully agree that the clarity of Figure 4 and the corresponding results section can be improved. In the revised manuscript, we have refined the description of Section 3.5 to make the target identification process and results more structured and easier to follow. Additionally, Figure 4 has been reorganized by separating panels (A–B) and (C–F) for better visualization, enlarging key elements, and clearly labeling the cleavage sites, p-values, and categories. The revised figure caption and result section now provide a more coherent and detailed explanation of the degradome analysis, highlighting how ahy-miR398 and ahy-miR408 regulate drought-responsive target genes. We believe these revisions significantly enhance the figure’s readability and strengthen the interpretation of the data.
Revision made: Result, page 9-10 lines 298-308 and page 10 lines 310-318, Figure 4
Response toMinor points
Line 25–26: Overuse of technical terms in a single sentence: “P-type ATPase copper transporters (COPAs), and a blue copper protein-like (PCL) gene…” Consider breaking into simpler components.
Response: We have revised this sentence for clarity by splitting it into simpler components. The revised sentence now reads: “In contrast, ahy-miR408 targets laccase 12 (LAC12), P-type ATPase copper transporters (COPAs), and a blue copper protein-like (PCL) gene. These targets are involved in copper homeostasis and the regulation of reactive oxygen species (ROS), suggesting that ahy-miR408 plays a role in oxidative stress management.”
Revision made: Abstract , page 1 lines 25-29.
Line 38: “Photosynthetic system disruption…” could be rephrased as “disruption of photosynthesis” for clarity.
Response: We have rephrased this sentence for clarity, and it now reads: “disruption of photosynthesis…”
Revision made: Introduction, page 1 lines 41-42.
Line 57–60: Multiple examples are packed into one sentence. Consider splitting into separate lines for ROS, hydraulic architecture, and ABA signaling.
Response: We have split this sentence into separate lines to improve readability. The revised version reads: “Unlike transcriptional regulators exhibiting 2-4 hour response delays, miRNAs demon-strate rapid stress perception, activating within 30 minutes, and precise targeting, with each miRNA regulating 3-5 genes. Their spatiotemporal expression dynamics co-ordinate drought resilience through modulating ROS homeostasis, such as in Arabidopsis, where miR398-mediated suppression of CSD1/2 reduces oxidative damage; optimizing hydraulic architecture, as seen in rice, where miR408 enhances xylem lignification to improve embolism resistance; and fine-tuning ABA signaling, exemplified by barley miR159a, which regulates stomatal closure”
Revision made: Introduction, page 2 lines 57-65.
Line 74: Avoid using both “PEG6000-simulated” and “osmotic stress” interchangeably. Clarify the simulation method consistently throughout.
Response：We have clarified this by specifying that “PEG6000-simulated” refers to osmotic stress induced by polyethylene glycol (PEG6000). The term "osmotic stress" has been used consistently to describe the simulated conditions in the revised manuscript.
Revision made: Introduction, page 2 lines 77.
Line 104: Typo: “RNA purity was checked…” should be followed by a full stop instead of a comma at the end of the sentence.
Response: We have corrected the typo, and the sentence now ends with a full stop as follows: “RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA).”
Revision made: Materials and Methods, page 3 lines 107-108.
Line 140: Method: "Expression levels were quantified using ImageJ as instructed." This is vague. Specify if normalization and background subtraction were applied.
Response: We have revised this for precision, adding details regarding normalization and background subtraction.
Revision made: Materials and Methods, page 3 lines 151-152.
Line 213: Header: “3.3. Revealed differential miRNA expression profiling…” Suggest rephrasing as “Differential Expression Profiling of miRNAs.”
Response: We have rephrased this section title to: “Differential Expression Profiling of miRNAs.” This rephrasing provides a clearer and more concise description of the section.
Revision made: Result, page 7 lines 226-227.
Line 226: phrase “integrative analysis identified…” is ambiguous. Specify the tool or statistical method used for the integration.
Response: We have clarified this sentence by specifying the tool used for integrative analysis: “In the end, integrative analysis using the DESeq2 statistical method identified 10 con-served peanut miRNAs exhibiting significant differential expression”.
Revision made: Result, page 7 lines 239-240.
Line 255: “100 μg of total RNA was loaded.” This looks quite high. Confirm if the information is correct or a typo.
Response: There is no issue; we used 100 μg of total RNA to ensure that miRNAs could be detected. Using too little total RNA could result in some miRNAs not being detected.
Line 261: Degradome sequencing section lacks the reference genome version. Include the version and date of download.
Response: Thank you for your valuable feedback. We have now included the reference genome version and the date of download for the degradome sequencing analysis. The reference genome used in our study is the Tifrunner gnm1 (v2) assembly Tifrunner gnm2 (v2), GenBank accession GCF_003086295.3, NCBI Annotation Release 106, which was downloaded on May 12, 2023. This information has been added to the revised manuscript.
Revision made: Materials and Methods, page 3 lines 128-130
Line 274: Sentence “We selected genes with categories < 2 as candidate targets.” What is <2?; Add justification or citation for this threshold.
Response: We have now added clarification regarding the selection of genes with categories < 2 as candidate targets. Genes categorized as 0 and 1 represent the highest-confidence cleaved targets based on the abundance and positional accuracy of the cleavage signatures. These categories were chosen to minimize the risk of false positives and ensure that the identified targets have high reproducibility and precision in their cleavage events. The rationale for this threshold is that categories 0 and 1 reflect the most reliable cleavage sites with the highest tag abundance.
We hope this clarification resolves the concern, and we appreciate your careful review of our manuscript.
Revision made: Result, page 9 lines 293-297.
Line 295: “Arabidopsis thaliana lines heterologously overexpressing…” Consider simplifying to “Transgenic Arabidopsis lines overexpressing…”
Response: We have simplified the phrasing as follows: “Transgenic Arabidopsis lines overexpressing…”
Revision made: Result, page 10 line 321.
Line 404–412 (Conclusion): conclusion restates findings well but could benefit from a clearer summary of practical applications (e.g., molecular breeding or marker-assisted selection).
Response: We sincerely appreciate the reviewer’s thoughtful suggestions and constructive feedback. In particular, we have addressed the points regarding the practical applications of our findings in the conclusion. Based on the reviewer’s suggestion, we have revised the conclusion to more clearly emphasize the practical relevance of ahy-miR398 and ahy-miR408 in molecular breeding, particularly in marker-assisted selection (MAS) for developing drought-tolerant peanut varieties. The revised conclusion now highlights how these miRNAs can be leveraged to improve climate resilience in arid regions, where conventional breeding methods face limitations due to environmental constraints such as water scarcity.
Revision made: Conclusions, page 14 -15 lines 457-473.
Throughout: Consistent italicization of Arachis hypogaea and Arabidopsis thaliana.
Response: We have ensured that both Arachis hypogaea and Arabidopsis thaliana are consistently italicized throughout the manuscript as per standard nomenclature conventions.
miRNA naming should be standardized (e.g., “ahy-miR398” vs “miR398”).
Response: We have standardized the miRNA naming throughout the manuscript to ensure consistency in the format. For example, "ahy-miR398" is now consistently used for peanut, instead of simply "miR398," to avoid confusion. Similarly, for miR398 in other crops, we have used the appropriate species-specific names, such as "gma-miR398" for Glycine max and "osa-miR398" for Oryza sativa.
Author Response File: Author Response.pdf
Round 2
Reviewer 1 Report
Comments and Suggestions for AuthorsIn the revised version of the manuscript, the authors made extensive changes, including my comments and comments from other reviewers. I am glad to see that the authors have satisfactorily addressed all my comments. Therefore, I recommend acceptance for publication.
Author Response
Dear Reviewer,
We would like to express our sincere gratitude for your thoughtful and constructive feedback on our manuscript. Your comments were invaluable in improving the quality and clarity of our work. We appreciate the time and effort you invested in reviewing our submission.
Reviewer 2 Report
Comments and Suggestions for AuthorsAuthors performed all suggested changes, improving the manuscript. T do not have any extra comments.
Author Response
Dear Reviewer,
We would like to express our sincere gratitude for your thoughtful and constructive feedback on our manuscript. Your comments were invaluable in improving the quality and clarity of our work. We appreciate the time and effort you invested in reviewing our submission.
Reviewer 3 Report
Comments and Suggestions for AuthorsWhile the authors have made significant efforts to revise the text, the figures remain too low. For example, when I try to enlarge Figure 1B, Figure 2, and Figure 4 to read the axis and depth information, they look blurred, and I cannot get any information. The authors should present high-resolution figures.
Author Response
Dear Reviewer,
Thank you for your valuable feedback on our manuscript. We appreciate your positive remarks regarding our revisions. Regarding your comment on the figures, we apologize for the low resolution of some of the images. We understand that this affects the clarity of important details, such as the axis and depth information in Figures 1B, 2, and 4. We will replace the current figures with high-resolution versions to ensure that all information is clearly visible.
Thank you once again for your insightful comments, and we are grateful for your support in improving the quality of our manuscript. Best regards
Author Response File: Author Response.pdf
