Genome-Wide Identification of the Phytocyanin Gene Family and Its Potential Function in Salt Stress in Soybean (Glycine max (L.) Merr.)

Round 1

Reviewer 1 Report

Phytocyanins play a major role in different stages of plant development, are also involved in plant response to abiotic and biotic stresses. Therefore, the relevance of this study is high.

Phytocyanins gene family of soybean was identified and characterized at the whole genome level, including the gene number and structures, conserved domains and motifs, chromosomal locations, phylogenetic relations. Thus, this work is almost 100% theoretical (except RT-qPCR analysis) and is based on database work.

 L. 78 The abbreviation GmPC should be given.

L. 90-94 How correct is it to conduct "Sequences of GmPC 91 genes were compared with PC genes in Arabidopsis thaliana", especially since "soybean has more members of the PC gene family than Arabidopsis thaliana" (L. 172)? The correct comparison would be with a species in the legume family.

L. 126. It should be stated which gene-specific primers for amplification of target genes and reference genes were used.

L. 156 The authors write that "...analysis indicated that most GmPCs were located in...". It should be pointed out that they are talking about proteins, not GmPCs genes.

Author Response

Dear Reviewer,

We do appreciate your time spent reviewing our manuscript entitled "Genome-wide identification of phytocyanin gene family and their potential function in salt stress in soybean (Glycine max)", and your insightful comments and suggestions, which have helped us improve our manuscript.

We have carefully revised the manuscript as suggested. Revisions are marked in red in the revised manuscript. Here are the point-by-point responses to your comments.

Yours sincerely.

Author Response File: Author Response.pdf

Reviewer 2 Report

The authors performed genome-wide screening and identification (both genomics and transcriptomics) to characterize the Phytocyanin gene family in soybean. Phytocyanin plays an important role in plant development as well as responses to abiotic and biotic stresses. The research addresses a specific gap that these genes, which are related to agricultural productivity, were never comprehensively explored, although the gene family was relatively well characterized in model species such as Arabidopsis and there are some reports on members of the gene family in the legume (e.g. ENODL gene members with high expression in nodules). The conclusions are consistent with the evidence and arguments presented and they address the main question posed. Here are some additional comments authors might consider for improvement:

 

Introduction:

Line 34-35: I would start the introduction with PC and explain the relationship of it to BCP.

 

Methods:

Line 90: Pfam database literature should also be cited https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965110/

 

Line 91: For annotation of PCs in soybean, I would also use other species, especially any PCs with functional validations, to do the comparative analysis for annotation purposes (“orthologous mapping”). This also will link those members introduced in the Introduction to the soybean PCs discussed in the results and discussion section.

 

Line 102: NCBI (https://pubmed.ncbi.nlm.nih.gov/34850941/) and MEME (https://pubmed.ncbi.nlm.nih.gov/19458158/) should also be cited.

 

Line 121 – 125: The authors may provide more details of the transcriptome datasets they used in the database, in addition to citing the database.

 

Results:

“Soybean” and “Glycine max” were used interchangeably. Depending on the style authors may want to use, I would either define Glycine max ­(Soybean, and hereafter) and use soybean for later text or keep using Glycine max across the whole manuscript.

Section 3.4-3.6 Each of these parts was solid as supports that certain members of PCs/certain regulatory elements are related to development and stress responses. Authors may consider doing some more analyses, trying to link them together, Specific tasks authors may consider:

1.    Co-expression network analysis (WGCNA or even K-means clustering) on these genes, using public datasets to find gene expression modules and potential TF regulators of these PC genes.

2.    Potential regulatory elements related to expression changes (linking 3.4 with 3.5 and 3.6), whether there is a strong correlation between expression and regulatory elements.

 

Discussion:

 

The discussion further dives into the literature and the presented study, supporting some of these PC genes are very important. Authors may also want to discuss the limitations of the current study, e.g. what kinds of functional validation experiments can be done to further test the importance of these genes, etc. Also, what is the bigger gap in research for PC study in general?

 

Author Response

Dear Reviewer,

We do appreciate your time spent reviewing our manuscript entitled "Genome-wide identification of phytocyanin gene family and their potential function in salt stress in soybean (Glycine max)", and your insightful comments and suggestions, which have helped us improve our manuscript.

We have carefully revised the manuscript as suggested. Revisions are marked in red in the revised manuscript. Here are the point-by-point responses to your comments.

Yours sincerely.

Author Response File: Author Response.pdf

Reviewer 3 Report

The manuscript is well written and executed. Frankly, I would not change much.

I would only suggest to proofread it, as there are many places with typos and spelling mistakes, but not too bad overall.

Author Response

Dear Reviewer,

We do appreciate your time spent reviewing our manuscript entitled "Genome-wide identification of phytocyanin gene family and their potential function in salt stress in soybean (Glycine max)", and your insightful comments and suggestions, which have helped us improve our manuscript.

We have carefully revised the manuscript as suggested. Revisions are marked in red in the revised manuscript. Here are the point-by-point responses to your comments.

Yours sincerely.

Author Response File: Author Response.pdf

Reviewer 4 Report

see the file

Comments for author File: Comments.pdf

see the file

Author Response

Dear Reviewer,

We do appreciate your time spent reviewing our manuscript entitled "Genome-wide identification of phytocyanin gene family and their potential function in salt stress in soybean (Glycine max)", and your insightful comments and suggestions, which have helped us improve our manuscript.

We have carefully revised the manuscript as suggested. Revisions are marked in red in the revised manuscript. Here are the point-by-point responses to your comments.

Yours sincerely.

Author Response File: Author Response.pdf

Reviewer 5 Report

Summary:

The manuscript titled "Genome-wide Identification of Phytocyanin Gene Family and Their Potential Function in Salt Stress in Soybean (Glycine max)" presents an in-depth analysis of the phytocyanin gene family in soybeans and explores their potential role in salt stress tolerance. The authors employ a comprehensive bioinformatics approach to identify and characterize phytocyanin genes in the soybean genome and subsequently investigate their expression patterns under salt stress conditions. Overall, the study provides valuable insights into the potential involvement of phytocyanin genes in salt stress response in soybean.

Rephrase the sentence line 82-84 according to your hypothesis. Under different stresses or one stress.

Correct the scientific name soybean in the title.

Comprehensive Genome-wide Analysis: The manuscript offers a thorough genome-wide analysis of phytocyanin genes in soybeans, which is essential for understanding the gene family's composition and evolutionary history. The use of multiple databases and bioinformatics tools for gene identification and classification is commendable.

Expression Profiling under Salt Stress: The study delves into the expression patterns of phytocyanin genes in response to salt stress, which is a relevant and significant aspect of the research.

Functional Annotation and Prediction: The authors discuss the potential functions of phytocyanin genes in soybeans, particularly in the context of salt stress tolerance. The functional annotation and enrichment analysis provide a valuable starting point for further research in this area. For more reliability of the results, authors should add Co-expression analysis.

Graphical Representation and Figures: The figures and tables included in the manuscript are clear and well-organized, aiding in the understanding of the data presented. However, Figure 1 needs more visibility and different color contrast for clarity.

Figure 2: Name of the genes in bold for more visibility.

Minor Points:

Future Directions: It would be helpful to conclude the manuscript with a section discussing potential future directions for this research, such as functional validation experiments or exploring the regulatory mechanisms of phytocyanin genes in salt stress response.

Language and Clarity: The manuscript is generally well-written, but some sections could benefit from improved clarity and organization. Additionally, a thorough proofreading for grammatical and typographical errors is recommended.

Line 39-42: need a reference to support your statement.

All genes in italic form i.e., OsUCL23

 

 

minor English editing requires

Author Response

Dear Reviewer,

We do appreciate your time spent reviewing our manuscript entitled "Genome-wide identification of phytocyanin gene family and their potential function in salt stress in soybean (Glycine max)", and your insightful comments and suggestions, which have helped us improve our manuscript.

We have carefully revised the manuscript as suggested. Revisions are marked in red in the revised manuscript. Here are the point-by-point responses to your comments.

Yours sincerely.

Author Response File: Author Response.pdf

Round 2

Reviewer 4 Report

See the paper

Reviewer 5 Report

Thanks to the author's response to all the suggested comments for the improvement of MS.