Genome-Wide Analysis of SPL Gene Families Illuminate the Evolution Patterns in Three Rubber-Producing Plants
Round 1
Reviewer 1 Report
Comments to the Author
The manuscript entitled “Genome-wide Analyses illuminate evolution of SPL gene families of three rubber-producing plants, Taraxacum kok-saghyz, Hevea brasiliensis and Eucommia ulmoides” presents the identification of the SPL gene family through a combination of phylogenetic analysis, cis-acting element analysis, and gene expression analysis. This study provides insights into the distribution and structure of the SPL gene family in these three rubber plants. However, the specific aim of the study and the rationale for selecting these particular rubber-producing plants for SPL gene family are not clearly stated.
Find below more specific comments:
1. Line 18-19:
“A phylogenetic analysis of 90 SPL proteins from 25 TkSPLs, 16 HbSPLs, 13 EuSPLs, 17 AtSPLs, and 19 OsSPLs was divided into eight groups”. This statement is not accurate.
2. Line 51-54:
In this sentence, SPL9 and AtSPL9 are different genes? If so, which species did SPL9 and SPL15 come from?
3. Introduction:
Why were three rubber-producing plants selected for SPL gene family analysis? What role does SPL play in the biosynthesis of natural rubber? The purpose of the study was not clearly stated.
4. Line 178-181:
“The species Taraxacum kok-saghyz and Eucommia ulmoides were more similar in terms of the number of Exons, Intron, and CDS, as well as the number of amino acids and molecular weight.” Why do you think these numbers are more similar for the two species? Are genes on the same evolutionary clad more similar?
5. Line 200:
Arabidopsis thaliana is not monocotyledon.
6. Figure 2:
It's better to mark eight subfamily branches on the evolutionary tree.
7. Line 218:
“NLS” The abbreviation that appear for the first time should be marked with the full name.
8. Line 224:
SCR, RRR, and CQQC sequences should be marked in the Figure 3.
9. Line 231:
Why only investigate the gene functions and expression regulation patterns of EuSPLs?
10. Line 245-247:
“It is speculated that SPL genes may perform crucial functions in stress response, growth, hormone regulation, and photoperiodic regulation of three rubber-producing plants.” This result cannot be used to speculate on three rubber-producing species, as only Eucommia ulmoides was examined here. And what about species that don't produce rubber? Is the discovery of these cis-acting elements unique to rubber-producing species?
Comments for author File: 
Comments.pdf
Author Response
Contents
Dear editor,
Thanks a lot for your comments and kind suggestions of our manuscript. According to the comments, we have carried out all essential revisions suggested by reviewer to make it readability and more clearly. The revisions were marked in yellow in the revised manuscript.
Reviewer 1
Comment 1: Line 18-19: “Aphylogenetic analysis of 90 SPL proteins from 25 TkSPLs, 16 HbSPLs, 13 EuSPLs, 17 AtSPLs, and 19 OsSPLs was divided into eight groups”. This statement is not accurate.
Response: Thank you for your feedback on our paper. After carefully considering your comments, we have revised the content based on your suggestions. In light of your concerns regarding the accuracy of the statement, we have made the necessary changes. The revised sentence now reads as follows: " The phylogenetic analysis of 90 SPL proteins from 25 TkSPLs, 16 HbSPLs, 13 EuSPLs, 17 AtSPLs, and 19 OsSPLs resulted in their classification into eight distinct groups."
Comment 2: Line 51-54: In this sentence, SPL9 and AtSPL9 are different genes? If so, which species did SPL9 and SPL15 come from?
Response: I apologize for the lack of clarity in my previous statement. The genes SPL9 and AtSPL9 mentioned here refer to the same gene from Arabidopsis. Similarly, SPL9 and SPL15 are also genes derived from Arabidopsis. In the revised manuscript, the terms have been modified to AtSPL9 and AtSPL15 for consistency.
Comment 3: Introduction: Why were three rubber-producing plants selected for SPL gene family analysis? What role does SPL play in the biosynthesis of natural rubber? The purpose of the study was not clearly stated.
Response: We appreciate your valuable feedback on the introduction section of our manuscript. SPL genes are transcription factors that are part of the SBP-box gene family. They play a crucial role in various aspects of plant growth and development, including the regulation of secondary metabolites. Natural rubber is a terpenoid secondary metabolite of rubber-producing plants. The exact role of SPL genes in rubber biosynthesis is not fully understood, but it is believed that they may regulate the expression of genes involved in the mevalonate (MVA) pathway or the methylerythritol phosphate (MEP) pathway, both of which contribute to the synthesis of the isoprenoid precursor for rubber molecules. The selection was based on the fact that these three plants, namely Hevea brasiliensis, Taraxacum kok-saghyz, and Eucommia ulmoides, are known to be significant natural rubber producers. By analyzing the SPL gene family in these plants, we aimed to explore potential insights into the involvement of SPL genes in the biosynthesis of natural rubber. The revised version of this section can be found in lines 81 to 92 of the "Introduction" section in the paper.
Comment 4: Line 178-181: “The species Taraxacum kok-saghyz and Eucommia ulmoides were more similar in terms of the number of Exons, Intron, and CDS, as well as the number of amino acids and molecular weight.” Why do you think these numbers are more similar for the two species? Are genes on the same evolutionary clad more similar?
Response: Thank you for your valuable feedback regarding the statement in line 178-181 of our manuscript. The statement was intended to highlight the observed similarities in gene structure and protein characteristics between Taraxacum kok-saghyz and Eucommia ulmoides as reported in our analysis. The expression should have been as follows: "In terms of the data range of exons, introns, and CDS, as well as the data range of amino acids and molecular weight, Taraxacum kok-saghyz and Eucommia ulmoides exhibit a higher degree of similarity." However, after careful consideration of your suggestion, we indeed found inaccuracies in the description. Therefore, this sentence has been removed from the article.
Comment 5: Line 200: Arabidopsis thaliana is not monocotyledon.
Response: I apologize for the oversight made in my previous text. I have now rectified it by specifying two model plants (Arabidopsis thaliana and Oryza sativa).
Comment 6: Figure 2: It's better to mark eight subfamily branches on the evolutionary tree.
Response: Thank you for your suggestion, it is indeed an improvement. The modifications in Figure 2 have already been marked.
Comment 7: Line 218: “NLS” The abbreviation that appear for the first time should be marked with the full name.
Response: Your suggestion is imperative and I have already incorporated it as a bidirectional nuclear localization signal (NLS).
Comment 8: Line 224: SCR, RRR, and CQQC sequences should be marked in the Figure 3.
Response: I have carefully considered your suggestion to mark the SCR, RRR, and CQQC sequences in Figure 3. I agree that highlighting these specific sequences will enhance the clarity and understanding of the figure. I will revise Figure 3 accordingly by including clear annotations or labels to indicate these sequences.
Comment 9: Line 231: Why only investigate the gene functions and expression regulation patterns of EuSPLs?
Response: We appreciate your time and effort in reviewing our work. Regarding your comment on Line 231, we apologize for any confusion caused. We chose to investigate the gene functions and expression regulation patterns specifically in EuSPLs due to their significant contribution to rubber production in the selected plant species. Our objective was to understand the specific mechanisms underlying rubber biosynthesis, and focusing on EuSPLs allowed us to achieve this goal. Based on your suggestions, we have now added the relevant data for Taraxacum kok-saghyz and provided descriptions and explanations from line 305 to 314 in the document.
However, we acknowledge the importance of considering other SPL gene subfamilies, and we will take your suggestion into account for future research or revisions. By exploring the functions and expression patterns of other SPL subfamilies, we can gain a more comprehensive understanding of the entire SPL gene family in rubber-producing plants.
Comment 10: Line 245-247: “It is speculated that SPL genes may perform crucial functions in stress response, growth, hormone regulation, and photoperiodic regulation of three rubber-producing plants.” This result cannot be used to speculate on three rubber-producing species, as only Eucommia ulmoides was examined here. And what about species that don't produce rubber? Is the discovery of these cis-acting elements unique to rubber-producing species?
Response: Thank you for your feedback and for pointing out the concerns regarding the statement in line 245-247 of the manuscript. I appreciate your attention to detail and raising these important questions.
We have added additional data on Taraxacum kok-saghyz to further supplement and support this section, as you have pointed out. To address this issue, we will revise the sentence in the paper to clarify that this speculation only involves two species: Eucommia ulmoides and Taraxacum kok-saghyz.
Additionally, your question about the uniqueness of the discovered cis-acting elements to rubber-producing species and their relevance to non-rubber producing species is very pertinent. We acknowledge that further research is required to determine the extent of conservation or specificity of these elements across different plant species, both rubber-producing and non-rubber producing. This point will be duly acknowledged and discussed in the revised version of the manuscript.
Thank you for bringing these issues to our attention. Your comments have been instrumental in improving the accuracy and clarity of our work. If you have any further suggestions or concerns, please do not hesitate to let us know.
Author Response File: 
Author Response.docx
Reviewer 2 Report
Genome-wide Analyses illuminate evolution of SPL gene families of three rubber-producing plants, Taraxacum kok-saghyz, Hevea brasiliensis and Eucommia ulmoides
The authors have presented good work on economically important plants
Queries-
Why only three trees chosen
The abstract must be restructured
Write more roles of SPL in recent context
Please see these articles and may use in discussion
https://doi.org/10.1016/j.ijbiomac.2012.05.014
Differential transcript accumulation in chickpea during early phases of compatible interaction with a necrotrophic fungus Ascochyta rabiei | SpringerLink
The conclusion must summarise the whole work , so please see
The redundancy in figures and tables must be removed
Satisfactory
Author Response
Contents
Dear editor,
Thanks a lot for your comments and kind suggestions of our manuscript. According to the comments, we have carried out all essential revisions suggested by reviewer to make it readability and more clearly. The revisions were marked in yellow in the revised manuscript.
Reviewer 2
Comment 1: Why only three trees chosen
Response: Thank you for reviewing my paper and providing feedback. I appreciate your questions regarding the selection of only these three species in our research. The selection of these three species is based on specific criteria and research goals. Our aim is to focus the investigation on representative rubber-producing species and the Taraxacum kok-saghyz,Hevea brasiliensis, and Eucommia ulmoides are the three most commonly used rubber-producing plants. Additionally, due to the lack of available genomic data for other rubber-producing species at the moment, they cannot be included in this study. However, I understand your concern for the inclusiveness of the research. Indeed, considering diverse species in future studies is crucial to provide a more comprehensive analysis. I will take this into consideration and explore the possibility of including other species to broaden the scope of our research.
Comment 2: The abstract must be restructured
Response: Regarding your suggestion to restructure the abstract, I would like to express my gratitude for bringing attention to this aspect. In response to your comment, I will revise the abstract to ensure clarity and coherence. I will carefully consider how to restructure it to provide a more concise and effective summary of the research presented in the paper. Once again, I appreciate your valuable feedback and am dedicated to addressing your concerns to improve the quality of my work.
Comment 3: Write more roles of SPL in recent context
Response: Thank you for providing valuable feedback on my paper. I greatly appreciate your suggestion to incorporate additional roles of the SPL in recent contexts. I will thoroughly consider this recommendation and make the required additions to the manuscript.
Comment 4: Please see these articles and may use in discussion
https://doi.org/10.1016/j.ijbiomac.2012.05.014
Differential transcript accumulation in chickpea during early phases of compatible interaction with a necrotrophic fungus Ascochyta rabiei | SpringerLink
Response: Thank you for your valuable feedback on my paper. I appreciate your suggestion to refer to the following articles: "Differential transcript accumulation in chickpea during early phases of compatible interaction with a necrotrophic fungus Ascochyta rabiei".
I have carefully reviewed the suggested article and found it to be relevant to our research topic. The research suggested for your reference demonstrates that transcription level analysis can identify genes involved in plant regulation. Similarly, this study aims to identify key SPL genes involved in the regulation of rubber plant growth through transcriptome analysis. The information provided in this study will undoubtedly contribute to a more comprehensive and robust discussion in my paper.
Thank you again for your recommendation. I have incorporated this article into the discussion section of my research paper. Please refer to lines 368 to 372 for specific details.
Comment 5: The conclusion must summarise the whole work, so please see
Response: Thank you for your feedback on my paper. I appreciate your suggestion to ensure that the conclusion summarizes the entire work. I will revise the conclusion accordingly to provide a comprehensive summary of the research conducted and the main findings obtained.
Currently, the conclusion section of the article has been revised: This work combines genome-wide data from three rubber-producing plants to conduct a comprehensive bioinformatics investigation of the SPL transcription factor family. As a result, a total of 54 SPL transcription factor family genes were identified and classified into eight groups based on evolutionary tree analysis. The members of the SPL family exhibit the typical SBP structural domains. Furthermore, a thorough analysis of the gene structure, conserved domain, chromosome location, cis-acting element, and expression pattern of the SPL genes in the three rubber-producing plants was conducted. Additionally, the expression patterns of the EuSPLs gene family were analyzed, revealing that the EuSPL8 gene was highly expressed in bark, EuSPL3 and EuSPL7 were highly expressed in fruit, and EuSPL4 was highly expressed in both fruit and leaf. This article focuses on the genome-wide investigation of SPL gene families in rubber-producing plants. These findings will facilitate a better understanding of the biological function and molecular mechanisms of SPL genes in rubber-producing plants.
I sincerely appreciate your valuable input and will make the necessary changes to improve the quality of the paper.
Comment 6: The redundancy in figures and tables must be removed
Response: I have carefully considered your suggestion to remove redundancy in figures and tables. I acknowledge the importance of presenting concise and clear information in the paper. Upon re-evaluating the figures and tables, I will make necessary revisions to eliminate any unnecessary replication or duplication, ensuring that they serve a meaningful purpose in supporting the research findings.
Author Response File: Author Response.docx
Reviewer 3 Report
Comments
Renping et al. provided a Research article on “Genome-wide Analyses illuminate evolution of SPL gene families of three rubber-producing plants, Taraxacum kok-saghyz, Hevea brasiliensis, and Eucommia ulmoides” Though the topic is of current interest, the manuscript needs a substantial revision to be published. I have mentioned a few points of the manuscript that can be considered by the authors.
Ø Revised line no.109.
Ø Elaborate result 3.1 in the text.
Ø Elaborate the caption of Fig. 4.
Ø You are suggested to check the title of the research article, in terms of either sentence case or capitalization of each word, and reframe it.
Ø You are also advised to validate gene, expression patterns resulting from 3.5.
Ø Recheck all the references.
Comments
Renping et al. provided a Research article on “Genome-wide Analyses illuminate evolution of SPL gene families of three rubber-producing plants, Taraxacum kok-saghyz, Hevea brasiliensis, and Eucommia ulmoides” Though the topic is of current interest, the manuscript needs a substantial revision to be published. I have mentioned a few points of the manuscript that can be considered by the authors.
Ø Revised line no.109.
Ø Elaborate result 3.1 in the text.
Ø Elaborate the caption of Fig. 4.
Ø You are suggested to check the title of the research article, in terms of either sentence case or capitalization of each word, and reframe it.
Ø You are also advised to validate gene, expression patterns resulting from 3.5.
Ø Recheck all the references.
Author Response
Contents
Dear editor,
Thanks a lot for your comments and kind suggestions of our manuscript. According to the comments, we have carried out all essential revisions suggested by reviewer to make it readability and more clearly. The revisions were marked in yellow in the revised manuscript.
Reviewer 3
Comment 1: Revised line no.109.
Response: Thank you for your review. Regarding the suggested revision on line 109, I will make the necessary changes to provide a clearer expression of my intended meaning. I will rephrase the sentence to describe the physicochemical characterization of proteins and the methods employed for structural analysis, ensuring that readers can better comprehend this section. Currently, this sentence has been modified to "Physicochemical Characterization and Structural Analysis of the Protein". I appreciate your valuable suggestion, as it will help improve the accuracy and readability of the paper.
Comment 2: Elaborate result 3.1 in the text.
Response: Thank you for your valuable feedback on our paper. To address your comment regarding result 3.1, we will provide a more comprehensive explanation of this particular result in the text. We will expand on the details and provide additional supporting information to make it clearer and more understandable for readers.
Comment 3: Elaborate the caption of Fig. 4.
Response: Thank you for your review comments. Regarding the title of Figure 4, I will provide further explanation and clarification. I will include more details to ensure that readers can better understand the meaning and importance of the chart. I will provide appropriate annotations and explanations so that readers have a clearer understanding of the content of the figure. Thank you very much for your valuable suggestions, which will help improve the quality of the paper.
Comment 4: You are suggested to check the title of the research article, in terms of either sentence case or capitalization of each word, and reframe it.
Response: Thank you for providing valuable feedback on the title of our research article. We appreciate your suggestion to review the capitalization and sentence case in the title and reframe it accordingly. Considering your advice, we have revised the title of the research article as follows: "Genome-Wide Analyses Illuminate the Evolution of SPL Gene Families in Three Rubber-Producing Plants: Taraxacum kok-saghyz, Hevea brasiliensis, and Eucommia ulmoides." This revised title accurately reflects the content of our study while adhering to the appropriate capitalization style. We sincerely value your input and hope that this revision meets your expectations.
Comment 5: You are also advised to validate gene, expression patterns resulting from 3.5.
Response: Thank you for providing feedback on my paper. I greatly appreciate your suggestion to verify the gene expression patterns resulting from 3.5. I will thoroughly contemplate this advice and intend to conduct additional experiments in order to validate the discovered results.
Comment 6: Recheck all the references.
Response: Thank you greatly for the reviewers' comments. We have thoroughly examined all the references once more and implemented the required revisions.
Author Response File: Author Response.docx
