PONE-D-25-28327

Genome-Wide Identification and Characterization of m6A Regulatory Genes in Soybean: Insights into Evolution, miRNA Interactions, and Stress Responses

PLOS ONE

Dear Dr. Ghosh,

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Academic Editor

PLOS ONE

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2. We noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed:

https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-024-04813-2

In your revision ensure you cite all your sources (including your own works), and quote or rephrase any duplicated text outside the methods section. Further consideration is dependent on these concerns being addressed.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: No

Reviewer #2: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: In this article, the authors report the identification of genes encoding 12 m6A writer, 11 eraser and 19 reader proteins in soybean. They characterized the gene and domain structures, and their interactomes. They also showed that expression of these genes might be controlled by light exposure, stress, or plant growth. Overall, they authors provided the first characterization of m6A effector proteins in soybean highlighting potential key role in plant development, especially when experiencing stress. Here are some comments I would like to see addressed:

1) Table 1 and 2 were not included in the manuscript. These are key to the manuscript, and therefore I was not able to thoroughly review this manuscript. Please ensure they are included.

2) Please discuss previous literature results from reference 40. They identified 13 writers, including two HAKAI-containing ones. Can you comment on the differences? Are there HAKAI-containing writers in soybean? Please double check your results and add clear discussion of the reference results. Also modify lines 414-415 accordingly.

3) Figure 7 and 8: Please add significance evaluation for expression levels. Are these differences significant?

4) Lines 365-373: Please add rationale for looking at miRNA target

5) All Figures: When downloaded the quality was good, however when added to the PDF the quality prevented clear reading. Ensure the sizing of your figure matches the final size in the article to prevent reduced quality.

6) Figure 1: Ensure the color-coding of the legend matches the figure

7) Figure 3: Please label legend in the figure: what is the scale showing?

8) Figure 4: Do the color of the gene bubbles represent something? Please clarify.

9) Figure 8: Please label legends in the figure.

10) Lines 330-332: Please remove unnecessary capital letters.

11) Lines 411-412: “are regulated by three types of m6A regulatory genes” is incorrect. Methylation is regulated by proteins, or gene expression but not gene themselves.

12) Line 455: Typo “sheath” should be “sheets”

13) Line 482: “combines” Please removed unnecessary capital letter.

Reviewer #2: This manuscript presents a comprehensive and well-structured genome-wide analysis of m6A regulatory genes in soybean, including writers, erasers, and readers. Through an integrative bioinformatic pipeline, the authors examine gene structure, evolutionary relationships, duplication events, protein-protein interactions, miRNA targeting, and expression profiles under abiotic and biotic stress conditions.

The work addresses a relevant knowledge gap in plant epitranscriptomics, particularly in soybean, a crop of major agricultural importance. The study is timely, methodologically sound, and provides valuable data that will be of interest to the plant biology and epigenetics communities.

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Reviewer #1: No

Reviewer #2: No

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Genome-wide identification and characterization of m6A regulatory genes in Soybean: Insights into evolution, miRNA interactions, and stress responses

PONE-D-25-28327R1

Dear Dr. Ghosh,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

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Kind regards,

Kai Huang

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: (No Response)

Reviewer #2: Yes

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: (No Response)

Reviewer #2: Yes

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4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: (No Response)

Reviewer #2: Yes

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5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: (No Response)

Reviewer #2: Yes

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: (No Response)

Reviewer #2: The revised manuscript presents a comprehensive genome-wide identification and characterization of m6A regulatory genes in soybean, integrating evolutionary analysis, domain architecture, gene duplication, miRNA targeting, and stress-responsive expression profiling. The authors have provided detailed responses to all prior reviewer and editor comments and have appropriately revised the manuscript to address the raised concerns.

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7. PLOS authors have the option to publish the peer review history of their article (what does this mean? ). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy .

Reviewer #1: No

Reviewer #2: Yes:  Haozhou Tan

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