Leveraging Functional Genomics and Engineering Approaches to Uncover the Molecular Mechanisms of Cnidarian–Dinoflagellate Symbiosis and Broaden Biotechnological Applications

Round 1

Reviewer 1 Report (Previous Reviewer 1)

Comments and Suggestions for Authors

I have reviewed the manuscript entitled "Leveraging Functional Genomics and Engineering Approaches to Uncover the Molecular Mechanisms of Cnidarian-Dinoflagellate Symbiosis and Broaden Biotechnological Applications", submitted to Phycology. I had also reviewed the manuscript in its previous submission, which was rejected with an invitation for resubmission. This new version demonstrates enhanced scientific robustness, and all the concerns raised in the previous review have been properly addressed. Although the text still requires some attention in terms of formatting and punctuation, I believe these issues will be readily resolved by the MDPI editorial/proofreading team. Therefore, I feel confident in recommending this manuscript for publication.

Author Response

We sincerely thank the reviewer for their thoughtful re-evaluation of our manuscript and for recognizing the improvements made since the previous submission. We are especially grateful for the positive feedback regarding the enhanced scientific robustness and the resolution of earlier concerns.

We also appreciate the note regarding minor formatting and punctuation issues and revised them accordingly, as addressed by other reviewers.

Thank you once again for your support and recommendation for publication.

Reviewer 2 Report (Previous Reviewer 2)

Comments and Suggestions for Authors

The MS by Mannur etc. reviewed the functional genomics and engineering approaches to analyze molecular mechanisms for the cnidarian-dinoflagellate symbiosis and the biotechnological application. The authors explored the directions in functional genomics as applied to coral-algal symbiosis, and focused on uncovering the molecular pathways that govern photosynthesis and stress tolerance. Also, the challenges and opportunities in applying functional genomics to support coral health, improve ecosystem resilience and inform biotechnological applications in agriculture and medicine, were discussed. Generally, this paper was interesting, it may posit the potential for engineered symbioses as a needed focus in mitigating biodiversity loss and supporting sustainable ecosystem management in the face of accelerating environmental change. But, there are minor issues still need to be corrected, and listed as follow.

 

• Add the email addressee for each author.
• Please exchange the potions of line 7 and line 8.
• If necessary, suggest to use some subsections for each section of the MS.
• Line 24-25, use the lowercase first letter for the keywords.
• Line 27, suggest use ....1. Introduction..  as the beginning of the MS.
• Please recheck the references, for format errors, such as, line 335, the journalname; line 341, doi; line 381, doi; line 442-445 for Ref 59; line 534, the journal 
• Section Author Contributions and Conflicts of Interest are both Please add them and refer to the format of the journal and Guide for Authors.
• Line 324-325, may add into section Funding

Author Response

We sincerely thank the reviewer for their positive feedback towards the improvements made from the previous submission. 

• Comment 1: Add the email addresses for each author. 
  • Response: We thank the reviewer’s comment and have revised the author line to include their respective email addresses. Lines 5-6  
• Comment 2: Please exchange the potions of line 7 and line 8.
  • Response: We thank the reviewer’s comment and have exchanged these lines' positions. Lines 8-9
• Comment 3: If necessary, suggest to use some subsections for each section of the MS.
  • Response: We thank the reviewer’s comment and have included subsections where appropriate. Lines 48, 84-85, 134, 167, 220, 255, 297, 315
• Comment 4: Line 24-25, use the lowercase first letter for the keywords.
  • Response: We thank the reviewer’s comment and have revised the case of the list of keywords. Lines 25-26
• Comment 5: Line 27, suggest use ....1. Introduction..  as the beginning of the MS.
  • Response: We thank the reviewer’s comment and have revised the beginning section of the manuscript to "1. Introduction". Line 28
• Comment 6: Please recheck the references, for format errors, such as, line 335, the journalname; line 341, doi; line 381, doi; line 442-445 for Ref 59; line 534, the journal
  • Response: We thank the reviewer’s comment and have revised the reference list for DOI links, journal names, and punctuation. Line 344-345, 385-386, 452-453, 446-447, 535-536  
• Comment 7: Section Author Contributions and Conflicts of Interest are both Please add them and refer to the format of the journal and Guide for Authors.
  • Response: We thank the reviewer’s comment and have added the Author Contribution section and reorganized the Conflict of Interest line to reflect the template/format. Lines 334, 343  
• Comment 8: Line 324-325, may add into section Funding
  • Response: We thank the reviewer’s comment and have included the Funding line in the appropriate location. Line 336

This manuscript is a resubmission of an earlier submission. The following is a list of the peer review reports and author responses from that submission.

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

I have reviewed the manuscript entitled "Leveraging Functional Genomics and Engineering Approaches to Uncover the Molecular Mechanisms of Cnidarian-Dinoflagellate Symbiosis and Broaden Biotechnological Applications," submitted to Phycology. The manuscript provides a comprehensive review of recent advances in genomics and genetic engineering to explore endosymbiotic relationships and expand the emerging biotechnological applications of dinoflagellates from the family Symbiodiniaceae. Although the text is well-written and well-structured, several modifications are required before potential publication in Phycology.

1.    The abstract submitted in the Susy system is too simple and does not adequately cover the vast range of topics addressed in the review.
2.    The first section of the manuscript delves directly into a highly specific topic. I suggest including an introductory paragraph providing background on the growing interest in endosymbiotic dinoflagellates, both from an environmental perspective (their association with cnidarians, coral bleaching, and ocean warming) and a biotechnological standpoint (due to various bioactive metabolites already reported). It is essential to consult relevant references such as: https://doi.org/10.3390/publications8040050 and https://doi.org/10.1007/s00253-022-12131-6
3.    The number of references in the manuscript is disproportionately high compared to the limited amount of text presented. For example, in lines 28–29, five references (12–16) are cited for a short and basic piece of information, despite all covering the same topic. It is imperative to reduce excessive citations and avoid unnecessary self-citations in some cases.
4.    Conversely, if the authors wish to maintain this number of citations, they must expand the content of the review. Many relevant studies are cited but not adequately explored in the topic discussion. In several instances, citations are merely listed, without a proper analysis of their findings.
5.    Finally, the document does not follow the MDPI template and does not use the journal’s required citation format. Other formatting issues are also present, and the authors should consult the journal's Instructions for Authors page (https://www.mdpi.com/journal/phycology/instructions) to ensure compliance.

Reviewer 2 Report

Comments and Suggestions for Authors

I don’t think the MS by Gagan et al. provide a qualified manuscript for efficient reviewing.

1. Section abstract is missing.
2. Suggest the authors prepare the MS according to the format of the journal.
3. Please check the format of the References
4. For the review article, I think only five pages and 3 figures, seems not to provide enough information for this important topic.

Comments on the Quality of English Language

The English Language is generally OK.