PONE-D-23-37042Integrated transcriptome and proteome analysis reveals the unique nutritional composition on the muscles in Chinese Taihe Black-bone Silky Fowl (Gallus gallus domesticus Brisson)PLOS ONE

Dear Dr. Liao,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please submit your revised manuscript by Jan 13 2024 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

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We look forward to receiving your revised manuscript.

Kind regards,

Tomoyoshi Komiyama, Ph.D

Academic Editor

PLOS ONE

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In addition, we noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed:

- https://medlineplus.gov/genetics/gene/agpat2/

- https://www.ncbi.nlm.nih.gov/gene/136319

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Additional Editor Comments:

Dear Authors,

Your research analyzed the unique nutritional composition of the muscles in Chinese Taihe Black-bone Silky Fowl.

For the research, you performed a comprehensive analysis of the muscle transcriptome and proteome in order to investigate the molecular mechanisms underlying chicken growth.

You suggested that these findings collectively support the concept that the Taihe black-bone cocoon chicken exhibits unique properties in mitochondrial energy metabolism and muscle tissue antioxidant capacity.

In the attached reviews, the reviewers have given feedback your manuscript.

I have carefully considered your manuscript.

Unfortunately, I decided major revision is required based on the three reviewer’s comments.

I think that it is necessary to strengthen the reliability of your results by adding as much information as possible.

I believe these comments will be very helpful in the revision of your study.

If your results become clear, I think your research will be important for the future of any researchers who aim to better understand this subject.

In its current state, I am unable to accept this manuscript. After revision, please feel welcome to resubmit.

Thank you for your understanding.

I have an additional comment.

Please include the results of the RNA sample quality test in the methods or supplemental section to prove the reliability of the data.

For example, nanodrop and bioanalyzer tests.

Tomoyoshi Komiyama

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: No

Reviewer #2: Partly

Reviewer #3: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: No

Reviewer #3: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: No

Reviewer #2: No

Reviewer #3: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Review of PONE-D-23-37042, Integrated transcriptome and proteome analysis reveals the unique nutritional composition on the muscles in Chinese Taihe Black-bone Silky Fowl (Gallus gallus domesticus Brisson) by Guanghua Xiong et al.

The manuscript describes results of the integrated analysis of the transcriptome and proteome of muscles of two native Chinese chicken breeds with unique nutritional values. In itself such studies are interesting, even when the breeds themselves are of limited (commercial) value.

Major comments

1. The present manuscript lacks language clarity and should be revised. Usually, I provide a list of language suggestions, but here the list would have been 10 pages or so…… So, I suggest to contact a language editing company to improve the English presentation of the results.

2. The Discussion section needs extensive rewriting, basically to the level of setting up an entire new Discussion section. Part of the results section need to be moved to the Discussion section, the results need to be removed from the Discussion section, and conclusions need to be drawn from the results after discussing them with the existing literature. Most of these points are either lacking from the present Discussion section, or the readability is such that I did not get it.

Minor comments

Line (L)17: nutritional components: What do you mean? What the chicken eats? What the nutritional value is for consumers? Please be specific.

L18: Biomarkers for what?

L19: Growth: general growth, or muscle development in specific?

L23: laid green-shelled eggs: only later it became known to me that this is possibly a breed, it is unclear here. Just add “chicken” or “breed” and the reader is not confused anymore.

L35: Overlapped: what do you mean by overlapped? transcriptome and proteome? What about the others? Are they false positives?

L62-64: Please rewrite sentence

Section 3.1 seems to contain no experimental results of this study. correct? Please delete.

L231-235: This is Materials ands Methods. Please delete here. If necessary, move to the Materials and Methods section.

L264-267: Not in the Results section

L283-285: Move to the Discussion section.

L301: micro-organs? Do you mean organelles?

L336-339: Move to the Discussion section.

L346-348: Move to the Discussion section.

L372-278: What is the meaning of this? It is so unclear to me that I cannot make a suggestion what to do with it.

L398-400: Repetition of results is no discussion. What are the meanings of your results? Please discuss that.

References: no given names of authors

Reviewer #2: General comments: The authors have put together an interesting data on the muscle of Chinese Taihe Black-bone Silky Fowl. However, there are some modifications to be made to this manuscript before is suitable for publication.

1. Line1-2: What is the unique nutritional composition of muscle in Chinese Taihe Black-bone Silky Fowl? I can not find that in the manuscript.

2. Line 23: What does ‘Black Feathered chicken and laid green-shelled eggs’ mean? Black Feathered chicken? laid green-shelled eggs?

3. Line 23: Why was Black Feathered chicken selected for transcriptome and proteome analysis? Which breed does Black Feathered chicken belong to?

4. Line 102: abdominal muscle tissues?

5. Line 115-116: ‘all the chickens were randomly selected’ should be modified to ‘all the chickens were selected’

6. Line 117: How were the chicken euthanized?

7. Line 201-202: Which statistical analyses in the study were performed using the SPSS 20.0 software?

8. Line 214-215: where was the data on eggs obtained from?

9. Line 218: What does ‘data not shown’ mean? Is that your result?

10. Line 221-224: Why did proteomic quantitative analysis was performed using four biological replicates of muscle samples but RNA-Seq three biological replicates?

11. Which part of result does the Figure 7 belong to? I did not find Figure 7 in the results and and legend of Figure 7 of manuscript.

12. Please upload your original sequencing data.

Reviewer #3: The manuscript is written clearly with the exception of some few areas that need to be addressed as follows:

1. there are several grammatical errors- L40-41, 62, 68, and112.

2. avoid repeating methods in results-L210-212, 231-233, and 367-374.

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Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

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While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

PONE-D-23-37042R1Integrated transcriptome and proteome analysis reveals the unique molecular features and nutritional components on the muscles in Chinese Taihe black-bone silky fowl chickenPLOS ONE

Dear Dr. Liao,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please submit your revised manuscript by Mar 07 2024 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Tomoyoshi Komiyama, Ph.D

Academic Editor

PLOS ONE

Additional Editor Comments:

Dear authors,

Thank you for submitting your revised manuscript.

I think it is easier to understand than the previous manuscript.

However, it received some additional questions from a reviewer.

Please answer these questions.

Tomoyoshi Komiyama

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #2: All comments have been addressed

Reviewer #3: All comments have been addressed

Reviewer #4: (No Response)

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: No

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: Yes

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #2: The authors have put together an interesting data on the muscle of Chinese Taihe Black-bone Silky Fowl.

Minor comment:

1.Line140-141: |fold changes| or |log2(fold change)| ?

Reviewer #3: The manuscript has been revised adequately. All the issues raised have been adequately addresses including depositing of data in the NCBI.

Reviewer #4: In your research, you performed RNA-Seq, transcriptome, and proteome analyses using Black-Bone silky fowl chicken.　You identified genes from these analyses that were associated with improving the antioxidant status of muscles.　However, I have some suggestions.

1. Please make the abstract section a little more concise.

2. Please include the results of the RNA sample quality test in the methods or supplemental section to prove the reliability of the data.　For example, nanodrop and bioanalyzer tests.

3. Please add a conclusions section with your results included.

4. Please revise the discussion section to clearly show the relevance of your results.

Currently, it is difficult to understand the relationship between your results and references to previous studies.

5. You note the “unique economic value of Taihe BB-sfc chickens in the future”

Please explain in more detail. Why and how is it useful?

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7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #2: No

Reviewer #3: Yes: Samuel Nahashon

Reviewer #4: No

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[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

Integrated transcriptome and proteome analysis reveals the unique molecular features and nutritional components on the muscles in Chinese Taihe black-bone silky fowl chicken

PONE-D-23-37042R2

Dear Dr. Liao,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.

If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Tomoyoshi Komiyama, Ph.D

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Dear authors,

Thank you for submitting your revised manuscript.

I think it was much easier to understand than the original manuscript.

I am satisfied with the responses and the edits, I am happy to accept this manuscript.

The authors have replied to my remaining questions satisfactorily from four reviewers.

Therefore, I have no further comments to make, all of my previous concerns were adequately addressed.

This manuscript will be satiating the reader's interest.

Tomoyoshi Komiyama

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #4: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #4: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #4: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #4: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #4: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #4: Dear authors,

Thank you for submitting your revised manuscript.

The authors revised the sentences according to my comments.

Therefore, I have no further questions.

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7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #4: No

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