An Analysis of the Potential Regulatory Mechanisms of Sophora Flower Development and Nutritional Component Formation Using RNA Sequencing
Round 1
Reviewer 1 Report
1. There is no flowering time phenotype of Sophora japonica in the study, so the flowering or flowering regulation in the text is not accurate, flower development should be better.
2. The detail information of nutritional components at different flower development stages should be given or described, it would be also better to describe the process of flower development, it would help readers to get the purpose and conclusion of the study.
3. In the title, "quality formation" changed to "nutrional compenents" would be better. "quality" results in misunderstanding of other values.
4. The name of Sophora(S.) japonica in the text should be Italic.
Author Response
Reviewer 1:
Comments and Suggestions for Authors
- There is no flowering time phenotype of Sophora japonica in the study, so the flowering or flowering regulation in the text is not accurate, flower development should be better.
Answer: We appreciate your suggestion which is helpful for the revision of this manuscript. We have now modified the contents related to flowering time and corresponding phenotypes. The sampling period is based on the results of the previous research from our team (Wang JR, Li LY, Tan J, et al. Variations in the Components and Antioxidant and Tyrosinase Inhibitory Activities of Styphnolobium japonicum (L.) Schott Extract during Flower Maturity Stages. Chem Biodivers. 2019;16(3):e1800504. https://doi.org/10.1002/cbdv.201800504.), and we also cited the article in this manuscript. Figure 1 shows the phenotypes of the different flowering stages used in this experiment. Thanks again for your advice.
- The detail information of nutritional components at different flower development stages should be given or described, it would be also better to describe the process of flower development, it would help readers to get the purpose and conclusion of the study.
Answer: We appreciate your professional advice. Because the main medicinal components of Sophora japonica flowers are flavonoids, the contents of total flavonoids, rutin, and narcissin were detected at different flowering stages in the early stage of the experiment. In this paper, the results of flavonoid content are associated analysis with the RNA-Seq data (WGCNA), rather than presented separately. I'm very sorry for the misunderstanding. We believe that WGCNA analysis will better reveal the results of metabolic compound synthesis and regulate gene expression.
- In the title, "quality formation" changed to "nutrional compenents" would be better. "quality" results in misunderstanding of other values.
Answer: Thank you very much for your advice. We have revised the title according to your suggestion.
- The name of Sophora(S.) japonica in the text should be Italic.
Answer: Thank you very much for your advice. We have revised the manuscript according to your suggestion.
Author Response File: 
Author Response.docx
Reviewer 2 Report
At RESULTS, subsection 3.1. Appearance characteristic of S. japonica flowers.
There is no need to make such a subsection under Results and Discussion. This aspect is more related to the biological material used which can be found in Material and working method.
To DISCUSSIONS
We understand that there are no reporters on the transcriptome exploration of the molecular mechanism of development of Huaihua, and there are few transcriptome studies on continuous flowering. However, for comparative analyses, it is requested that the authors refer to the existing data in the specialized literature, even if they are few.
Author Response
Reviewer 2:
Comments and Suggestions for Authors
At RESULTS, subsection 3.1. Appearance characteristic of S. japonica flowers.
There is no need to make such a subsection under Results and Discussion. This aspect is more related to the biological material used which can be found in Material and working method.
Answer: We appreciate your professional advice. The description in Section 3.1 of this article differs from the materials and methods. In materials and methods, we focus on describing the details of sampling, processing, and treatment, such as sampling time, location, sample repetition, etc. In the results, we focused on the phenotypes and characteristics of S. japonica flowers at different periods, which echoed the results of our subsequent RNA-Seq analysis. Therefore, we think this is essential, but also in order to better present the analysis content of this paper to readers. Thank you again for your advice and patience.
To DISCUSSIONS
We understand that there are no reporters on the transcriptome exploration of the molecular mechanism of development of Huaihua, and there are few transcriptome studies on continuous flowering. However, for comparative analyses, it is requested that the authors refer to the existing data in the specialized literature, even if they are few.
Answer: Thank you very much for your advice. We have revised the manuscript according to your suggestion. In the discussion section, we add the reported results of previous studies and discuss the results of this manuscript.
Author Response File: Author Response.docx
Reviewer 3 Report
The manuscript entitled “The Potential Regulatory Mechanisms Analysis of Sophora Flower Development and Quality Formation by RNA Sequencing” described the results of RNA-seq analysis on five developmental stages of flower in S. japonica. They also performed DEG and WGCNA analyses to investigate the mechanism of nutritional quality and flower development of S. japonica. This manuscript is well written and is useful for plant scientists relevant to this field.
However, I have a concern for this manuscript. They have previously published their work (Metabolic analysis reveals dynamic changes in secondary metabolites of Sophora japonica L. during flower maturation). Thus, they will compare the results of RNA-seq data analyzed in this study with their previous work and then will include this point in the Discussion part. After that, I could recommend to publish in Horticulturae.
Author Response
Reviewer 3:
Comments and Suggestions for Authors
The manuscript entitled “The Potential Regulatory Mechanisms Analysis of Sophora Flower Development and Quality Formation by RNA Sequencing” described the results of RNA-seq analysis on five developmental stages of flower in S. japonica. They also performed DEG and WGCNA analyses to investigate the mechanism of nutritional quality and flower development of S. japonica. This manuscript is well written and is useful for plant scientists relevant to this field.
Answer: Thank you very much for your recognition of the research content of this manuscript and for giving us the opportunity to revise it. We took all the reviewers' professional suggestions seriously and made detailed revisions to the manuscript.
However, I have a concern for this manuscript. They have previously published their work (Metabolic analysis reveals dynamic changes in secondary metabolites of Sophora japonica L. during flower maturation). Thus, they will compare the results of RNA-seq data analyzed in this study with their previous work and then will include this point in the Discussion part. After that, I could recommend to publish in Horticulturae.
Answer: Thank you very much for your advice. We carefully read the article you recommended (which is also one of the results of our team). And, we have revised the manuscript according to your suggestion. Thank you again for your patience and professional advice.
Author Response File: Author Response.docx
Round 2
Reviewer 3 Report
Dear authors,
I satisfied the revised manuscript. I recommend this manuscript for publication in Horticulturae.
