Review Reports

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

General Comments

• The English quality can be improved for better comprehension by native speakers. Check the punctuations.
• The authors should carefully review and revise the Materials and Methods to ensure clarity and completeness.
• The results section is well structured; however, most figures need better resolution and formatting.
• A thorough revision of the Discussion and Conclusion is recommended to enhance scientific interpretation.

 

Title

The writing formats (rule) of titles in MDPI, including Agronomy, should have every main word in capital letters as follows:

Genome-Wide Identification, Expression Profile and Evolution Analysis of Importin α Gene Family in Glycine max’

 

Abstract

Overall, the abstract wasn’t well presented

Comments:

• GmIMPα, in some places wrote in italic and other places wrote in normal. Please check them throughout the manuscript.
• Line 27, Cpllectively, spelling check.
• The main methodologies should be clearly presented.
• Overall, the abstract requires revision to improve clarity and alignment with journal standards.

Introduction

Comments

• The referencing format within the text does not comply with journal guidelines and should be corrected.
• Add global production of soybean according to the FAO stat.
• Revisions are needed in punctuation, spacing, and the use of abbreviations to ensure consistency and clarity

Materials and Methods                             

• The methodology was not clear for example how many soybean genotypes were taken for this study. Please indicate.
• The methodology was not clear, please present in a clear way.
• Overall, the materials and methods should be revised.

 

Results

• While the results are clearly presented, most of the figures lack sufficient resolution and clarity.

Discussion

Overall, the discussion should be revised and indicate the main mechanisms.

 

Conclusion

The conclusion is good and provide future direction.

References

References should be revised  

 

Best Regards

Comments on the Quality of English Language

The quality of English Language is low, the authors should revise the manuscript carefully for clarity. 

Author Response

Reviewer 1

General Response

We sincerely appreciate the reviewer’s thorough evaluation and constructive feedback. We have carefully revised the manuscript in accordance with all comments. All changes are highlighted in yellow in the revised version.

Title

Comment: The title should follow MDPI capitalization rules.

Response: Revised to “Genome-Wide Identification, Expression Profile and Evolution Analysis of Importin α Gene Family in Glycine max” (highlighted in yellow in the title).

Abstract

Comments: GmIMPα formatting inconsistent (italic vs. normal).

Response: All gene symbols GmIMPα are now consistently italicized, while protein names are set in regular font (all revisions are highlighted in yellow in the amended document).

 

Comment: Line 27: “Cpllectively” misspelled.

Response: The spelling error “Cpllectively” has been corrected to “Collectively.”

 

Comment: Methodologies not clearly presented.

Response: We have revised the abstract to include a concise yet comprehensive description of the main analytical procedures. Specifically, we now outline the genome-wide identification of GmIMPα genes, followed by gene structure and conserved motif analyses, chromosomal distribution and duplication inference, synteny and selection (Ka/Ks) analyses, and expression profiling across tissues and stress conditions using public RNA-seq datasets and expression browsers. These revisions allow readers to clearly understand the principal bioinformatics approaches applied in this study directly from the abstract.

 

Comment: Abstract needs improved clarity and journal conformity.

Response: The abstract has been rewritten to improve clarity and alignment with MDPI standards (highlighted in yellow in the Abstract).

Introduction

Comment: In-text referencing does not follow journal guidelines.

Response: In-text citations have been standardized to the MDPI numeric format throughout the manuscript.

 

Comment: Add global soybean production data (FAO).

Response: Global soybean production data from FAOSTAT have been incorporated to emphasize the agricultural and economic importance of soybean (highlighted in yellow in the Introduction). Revised text (Lines 37–40). “According to the latest statistics from the Food and Agriculture Organization of the United Nations (FAO) (https://www.fao.org/home/en/, accessed on 30 October 2025), global soybean production exceeded 371 million metric tons in 2023, highlighting its central role in the global supply of vegetable oil and protein.”

 

Comment: Ensure punctuation, spacing, and abbreviation consistency.

Response: Punctuation, spacing, and abbreviation formats have been thoroughly revised and standardized (highlighted throughout the manuscript).

Materials and Methods

Comments: Methodology unclear, including number of genotypes used.

Response: The sources, versions, and database links for all 27 genomes are now provided in the Methods section and listed in Table S1 (highlighted in yellow) (Lines 95–98).

 

Comments: The section should be clarified and better organized.

Response: The Materials and Methods section has been thoroughly revised to improve clarity, logical flow, and organization. Each subsection now provides a detailed description of the analytical procedures, software tools, and parameters used. Clear subtitles (e.g., Identification and Characterization of GmIMPα Genes, Pan-Genome Categorization, Expression Analysis under Stress Conditions) have been added to guide readers through the methodology. For the reviewer’s convenience, all modifications and newly added details are highlighted in yellow in the revised manuscript.

Results

Comment: Figures lack sufficient resolution.

Response: All figures have been re-exported in 600–900 dpi high resolution, labels enlarged, and color contrast optimized for clarity. Figure 3C has been specifically corrected for legibility.

Discussion

Comment: The discussion needs to focus more clearly on key mechanisms.

Response: The Discussion section has been thoroughly revised to emphasize the key molecular mechanisms underlying the function and diversification of the GmIMPα gene family. We have reorganized the content for greater coherence and depth, integrating explicit mechanistic interpretations that link our results to nuclear import regulation and stress signaling. Specifically, we now discuss how the conserved ARM-repeat architecture and the prevalence of purifying selection across duplicated GmIMPα pairs constrain classical NLS-dependent nuclear import, while motif variations and selective expression suggest paralog-specific cargo recognition under stress. The revised text also highlights the integration of hormone and stress signaling through cis-regulatory elements and differential gene activation, proposing that GmIMPα paralogs may fine-tune nuclear transport pathways in response to environmental stimuli.

Conclusion

Comment: The conclusion is good and provides future direction.

Response: Thank you.

References

Comment: References should be revised.

Response: All references have been checked and reformatted according to MDPI reference style, with correct journal names, volume, pages, and DOIs (highlighted in yellow in the References section).

 

Author Response File: Author Response.docx

Reviewer 2 Report

Comments and Suggestions for Authors

In this manuscript, the authors were seeking to identify IMPα genes in soybean, and understand their evolution, structure, and functions. This was done using existing genomic data, transcriptomic data, expression profiler tools, and comparative genomics. Overall, this seems like a good study, and much of the methods and results are made clear by the authors. There are some minor issues that should be addressed before publication though.

General comments:

• There are a few typos throughout the manuscript. One obvious one is misspelling “collectively” in the abstract. Please go through one more time to detect any typos.
• At the start of the intro, the authors used numbers for the references. By line 39, they were using the name and year format. I believe this journal generally uses the number format.
• When the name and year in-text citation format was used, there was always a missing space before the opening parenthesis of the citation.

Materials & Methods:

• Thank you for clearly including all the version numbers of reference genomes mentioned in the methods. Many authors forget to include the version numbers, and I appreciate authors being proactive and clear on this.
• In the results, it is mentioned that 27 soybean genomes were used to find the distribution of IMPα genes. No mention of these 27 genomes is in the methods. Please clarify where these came from.

Results:

• The terms of core, softcore, dispensable, and private genes in reference to pangenomes is still a relatively recent occurrence, and many readers might not yet know these terms. Please add in greater clarification of these terms. Either where they first appear in the results, or in the methods. I recommend citing a paper that further defines these, such as this pangenome review paper: https://doi.org/10.1186/s12864-024-10931-w
• For Figure 1, please add more text to the caption so it can stand alone. Add greater clarification to this figure. Such as indicating what 0 and 1 are. I assume it is absence and presence in the genome, respectively. Also include what core, softcore, etc mean here. Make it so a reader can look at the figure alone and understand what is going on without having to find the information in text.
• In Figure 3, panel C it hard to read due to size. Even when zooming in fully, the numbers cannot be read due to pixelation.
• Pertaining to section 3.9. Given that the data used is from published data from other studies and in the expression browser, are the samples coming from the same types of tissues? Are there different tissue types depending on the stress factor? Please clarify this, with the results mentioning what types of tissues had differential gene expression for the IMP genes in each stress treatment.

Author Response

Reviewer 2

General Response

We appreciate the reviewer’s careful reading and helpful comments. All issues have been addressed, and changes are marked in yellow in the revised manuscript.

General Comments

Comment: There are a few typos throughout the manuscript. One obvious one is misspelling “collectively” in the abstract. Please go through one more time to detect any typos.

Response: Typographical errors (e.g., “collectively”) have been corrected. We apologize for this error and have carefully rechecked the entire manuscript to ensure there are no similar spelling mistakes.

 

Comment: At the start of the intro, the authors used numbers for the references. By line 39, they were using the name and year format. I believe this journal generally uses the number format.

When the name and year in-text citation format was used, there was always a missing space before the opening parenthesis of the citation.

Response: In-text citation format has been unified to numeric style; missing spaces and punctuation before parentheses have been fixed.

Materials & Methods

Comment: In the results, it is mentioned that 27 soybean genomes were used to find the distribution of IMPα genes. No mention of these 27 genomes is in the methods. Please clarify where these came from.

Response: We appreciate the reviewer’s observation. The revised Materials and Methods section now clearly describes the origin and handling of the 27 soybean genomes used in this study (Lines 95–98). Specifically, we have added detailed information on the sources, versions, and database links for all genomes, which are now summarized in Table S1 (highlighted in yellow). As described, a total of 27 Glycine max genomes representing diverse cultivars and lines were retrieved from the SoyOmics database (https://ngdc.cncb.ac.cn/soyomics/index, accessed on 15 July 2025) and used for comparative and pangenome analyses. The revised text also outlines the bioinformatic workflow, including the use of HMM profiles from the InterPro database to identify IMPα domains, validation via SMART and the NCBI Conserved Domain Database, and classification of IMPα genes into core, soft-core, dispensable, and private categories based on presence/absence patterns across the 27 accessions. These additions ensure that the source, rationale, and analytical steps associated with the 27 soybean genomes are explicitly described, enhancing both methodological transparency and reproducibility. All newly added information is highlighted in yellow in the revised Methods section.

Results

Comments: The terms of core, softcore, dispensable, and private genes in reference to pangenomes is still a relatively recent occurrence, and many readers might not yet know these terms. Please add in greater clarification of these terms. Either where they first appear in the results, or in the methods. I recommend citing a paper that further defines these, such as this pangenome review paper: https://doi.org/10.1186/s12864-024-10931-w.

Response: Response: We thank the reviewer for this valuable suggestion. To improve clarity for readers unfamiliar with pangenome terminology, we have added brief definitions of “core,” “soft-core,” “dispensable,” and “private” genes in the Materials and Methods section, where these terms first appear. Specifically, we now clarify that core genes are present in all analyzed accessions, soft-core genes occur in most but not all genomes, dispensable genes appear in only a subset of accessions, and private genes are unique to a single accession. In addition, we have cited the recommended review paper — “A stepwise guide for pangenome development in crop plants: an alfalfa (Medicago sativa) case study” (https://doi.org/10.1186/s12864-024-10931-w) — to provide readers with a comprehensive reference on the conceptual framework and application of these definitions. The corresponding text and citation have been added to the Methods section and are highlighted in yellow in the revised manuscript.

 

Comments: For Figure 1, please add more text to the caption so it can stand alone. Add greater clarification to this figure. Such as indicating what 0 and 1 are. I assume it is absence and presence in the genome, respectively. Also include what core, softcore, etc mean here. Make it so a reader can look at the figure alone and understand what is going on without having to find the information in text.

Response: We appreciate the reviewer’s helpful suggestion. The caption for Figure 1 has been substantially revised to provide sufficient context and clarity so that the figure can stand alone. The updated caption now explicitly defines the meaning of “0” and “1” (representing gene absence and presence, respectively) and includes concise explanations of core, soft-core, dispensable, and private genes according to established pangenome classifications. The revised figure caption has been highlighted in yellow in the manuscript.

 

Comments: In Figure 3, panel C it hard to read due to size. Even when zooming in fully, the numbers cannot be read due to pixelation.

Response: Figure 3C has been re-rendered at high resolution, with enlarged text and scale bars for readability.

 

Comments: Pertaining to section 3.9. Given that the data used is from published data from other studies and in the expression browser, are the samples coming from the same types of tissues? Are there different tissue types depending on the stress factor? Please clarify this, with the results mentioning what types of tissues had differential gene expression for the IMP genes in each stress treatment.

Response: We thank the reviewer for this insightful comment. The revised Results section (Section 3.9) now clearly specifies the tissue types analyzed for each stress and hormone treatment, in accordance with the original data sources from published studies and the expression browser. Specifically, we now state that leaf tissues were used for drought, heat, and combined drought–heat treatments (Figure 10), whereas root tissues were analyzed for salt and hormone (IAA, JA, ETH) treatments (Figure 11). We also clarified that cold treatment expression data were derived from leaf samples, allowing consistent interpretation of stress-specific expression responses across tissues. In addition, we expanded the figure captions for Figures 10 and 11 to indicate both the tissue type and sampling time points (e.g., 0 h, 1 h, 8 h, 24 h) for each stress condition, making these datasets self-explanatory. The revised results now highlight which GmIMPα genes exhibit tissue-specific or condition-specific induction patterns—for instance, the strong upregulation of GmIMPα2/3/6/8 in leaves under drought, versus rapid induction of GmIMPα2/4/6/8 in roots under salt stress—thereby clarifying the spatial and temporal expression dynamics of the family. All newly added clarifications are highlighted in yellow in the revised manuscript text and figure captions.