Unveiling Transcriptional Dynamics Across Five Developmental Stages of the Edible Mushroom Oudemansiella raphanipes

Round 1

Reviewer 1 Report

General Comments

This study presents a stage-resolved transcriptomic analysis of Oudemansiella raphanipes across five developmental stages. The dataset is extensive, and the overall analytical framework is appropriate for describing transcriptional dynamics during development. The work provides a useful resource for understanding developmental transitions in this species.

Major Concerns
1. The manuscript proposes associations between transcriptional programs in mature fruiting bodies and the nutritional characteristics of O. raphanipes. At present, these interpretations are primarily based on pathway-level correlations. The authors are encouraged to clearly state that these links are inferential and to moderate the language so that these associations are not interpreted as demonstrated causal relationships. Expressions such as “associated with” or “may relate to” would be more appropriate in these sections.

2. The numbers of DEGs reported for some stage transitions are very large, particularly in early developmental comparisons. While large-scale transcriptional reprogramming is expected, a brief clarification would be helpful regarding how biological variability was managed, how normalization may influence DEG counts, and how such extensive DEG sets were functionally prioritized beyond pathway enrichment. Adding several explanatory sentences in the Methods or Discussion would improve interpretability.

3. The Discussion would benefit from a clearer statement of what distinguishes the findings in O. raphanipes from those reported in other edible fungi. In addition to highlighting shared developmental patterns, the authors are encouraged to summarize any pathways, gene groups, or transcriptional trends that appear particularly characteristic of this species.

1. The Introduction provides a broad overview of related studies, but the specific biological questions addressed in this study could be stated more explicitly. Clarifying the distinction between mapping developmental transcriptional programs and exploring their potential links to nutritional traits would help define the study focus.

2. The RNA-seq data quality and DEG thresholds are appropriate. However, a brief note on how the proportion of unannotated genes might influence pathway-based interpretation would help readers understand the scope and limitations of functional analysis.

3. PCA results show clear separation among stages, but including a short comment on the dispersion of biological replicates within each stage would strengthen confidence in reproducibility.

4. The analysis of stage-exclusive genes is interesting, but the very small numbers identified in later stages should be interpreted with caution. The authors may consider briefly noting that detection limits or low expression levels could influence this result.

5. In the Discussion, the sections linking transcriptional patterns to nutritional advantages are engaging but should be framed more explicitly as potential associations rather than demonstrated mechanisms.

Author Response

First of all, I would like to express my sincere thanks for your review. Your comments have greatly contributed to the improvement of our manuscript. Thank you very much again for devoting your valuable time to reviewing our work. All corrections and changes (highlighted in yellow in the manuscript) were made in accordance with your suggestions, and details are provided in the attached PDF "Responses to Reviewer1".

Author Response File: Author Response.pdf

Reviewer 2 Report

General comment:

The manuscript entitled: „Unveiling Developmental Dynamics and Molecular Signatures Across Five Stages of the Edible Mushroom Oudemansiella raphanipes“ presents a valuable and ambitious multi-stage transcriptomic investigation of Oudemansiella raphanipes, an understudied but nutritionally important edible mushroom. The integration of developmental RNA-seq profiling with nutritional characterization is original and potentially impactful, offering a systems-level perspective that is rarely attempted in edible fungi research. I suggest minor revision.

Abstract

Delete subheadings in abstract.

Add methodology

Introduction

Put the family name in italic

Lines 80 – 102: Too much information regarding other species, please shorten this part.

Figure 1 must be removed from Introduction part

Results

Line 236: Paraphrase the subheading, it should not be stated as result, for example write only „Nutritional profile of edible mushrooms“ or something like that

Discussion

Section 4.2. What is novel for O. raphanipes?

Line 435: Were NsdD and SEC4 validated by qPCR or only RNA-seq?

Line 450: “nitrogen fixation” is incorrect terminology for fungi (they assimilate, not fix atmospheric nitrogen)

Overall, discussion is well written. However try to avoid overstating causal links between gene expression patterns and measured nutritional traits, which are inferred rather than experimentally validated. 

Author Response

First of all, I would like to express my sincere thanks for your review. Your comments have greatly contributed to the improvement of our manuscript. Thank you very much again for devoting your valuable time to reviewing our work. All corrections and changes (highlighted in yellow in the manuscript) were made in accordance with your suggestions, and details are provided in the attached PDF "Responses to Reviewer2".

Author Response File: Author Response.pdf