PONE-D-23-05086A pilot-scale comparison between single and double-digest RAD markers generated using GBS strategy in sesame (Sesamum indicum L.)PLOS ONE

Dear Dr. Rangan,

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.

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Tzen-Yuh Chiang

Academic Editor

PLOS ONE

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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: Partly

Reviewer #2: Partly

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

Reviewer #1: Yes

Reviewer #2: No

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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

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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: Yes

Reviewer #2: No

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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: Line 435. How many basse pair was used for size selection

Line 440. why you were select these enzymes. Do you have any pre-experiment for efficiency of enzymes

Line 442. Size selection. Length of size???

Line 444. What is your length of product. 150 x2 ? and single or paired?

Line 447. What is your parameters in trimmomatic

Line 465. ….genes as described in (Ruperao et al., 2021). Missing sentence???

Line 175…..and ddRAD-seq datasets, respectively

Line 272-273. Please add related references

Line 383-392. There is one study has been conducted sesame for diversity analysis with the use of ddRAD-Seq approach. You should discuss the study

Basak, M., Uzun, B., and Yol, E. (2019). Genetic diversity and population structure of the mediterranean sesame core collection with use of genome-wide SNPs developed by double digest RAD-Seq. PLoS one 14:e0223757. doi: 10.1371/journal.pone.0223757

Line 396. Identifying 8 samples as a core collection is not scientific approach. It is not suitable for core collection idea. Please delete all about core collection

--Discussion is a weak. Please discuss these methods advantages and disadvantages compared to other sequencing approach

Reviewer #2: In their manuscript "A pilote-scale comparison between single and double-digest markers generated using GBS strategy in sesame (Sesamus indicus)", P. Ruperao and colleagues use both single and double digest RAD-sequencing to assess the genetic diversity of multiple sesame strain.

This Work provide interesting genetic resources for sesame cultivators, however some caveats in the approach used and their description maked me think that the manuscript does not reach the standards for scientific publications.

Please find bellow some of the main pitfall I found in the actual version of the manuscript.

Some major comments :

- My first point concern the absence consideration of the fact that rad-sequencing (sd or sd) is highly dependent on the coverage of each samples. This mean that samples with less coverage will de-facto have information, either because some locus were not sequenced, or because the coverage in some locus might not be sufficient to call SNPs.

In the actual manuscript, this aspect is not discuss while it might have a huge impact on the diversity parameter inferred, either with the kmer approach or with the SNPs calling part.

- The introduction claims that genetic information exist for the species, but do not list them (at least if information about populations exist), nor discuss the results of this study in perspectives with previous experiments.

- The choice of the enzymes, that will have a great impact on the number of locus is not explained nor discussed.

- The choice of the strains considered in this study, what is know about their history and how the are related is absent in the actual document and does not allow to grasp the pertinence of the study.

- The choice of the methods chose to “evaluate the genetic diversity” is not explained. Why use a Kmer approach ? How does the number of reads per samples affect the results of this approach ?

- The description of the methods used does not allow the reproducibility of the experiment (Few examples : authors did not describe the size of the fragments selected, nor the parameters for trimming in trimomatic, nor the ones for SNP calling in STACKS)

- Data are not made available, or at least, this is not stated in the manuscript.

-Multiple statement through the document needs references.

Some minor comments :

- Check reference line 431

- Check tense through the document (example line 64: “were” is used wile present tense is used in the rest of the paragraph)

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Reviewer #1: No

Reviewer #2: No

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PONE-D-23-05086R1A pilot-scale comparison between single and double-digest RAD markers generated using GBS strategy in sesame (Sesamum indicum L.)PLOS ONE

Dear Dr. Rangan,

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 Jun 18 2023 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,

Tzen-Yuh Chiang

Academic Editor

PLOS ONE

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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 #1: All comments have been addressed

Reviewer #2: (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 #1: Yes

Reviewer #2: Partly

**********

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

Reviewer #1: Yes

Reviewer #2: N/A

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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 #1: Yes

Reviewer #2: Yes

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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 #1: Yes

Reviewer #2: No

**********

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 #1: (No Response)

Reviewer #2: In their manuscript PONE-D-23-05086R1 P. Ruperao and colleagues proposed a revised version of the manuscript entitled "A pilote-scale comparison between single and double-digest markers generated using GBS strategy in sesame (Sesamus indicus)" comparing performances of single and double digest RAD-sequencing to assess the genetic diversity of multiple sesame strains.

First some side comments:

I would like to point that the version with the tracked change does not track all changes in the manuscript, making the review process harder. Please consider for future submission kipping track of all the modifications.

Also, number of lines pointing to changes does not match the actual changes (i.e “The existing genetic information in the sesame were included in the discussion session of the revised manuscript (Lines 283-300)”, changes are in lines 303 and onward.

Major comments:

In their revised version and answer to comments, the authors answered some of my concerns but some caveats remains.

In my previous review, I was pointing that rad-sequencing (sd or dd) is highly dependent on the coverage of each samples, thus impacting the diversity parameters.

I do understand that the authors used defaults parameters in Stacks, but showing as a supplementary material that the coverage / total number of bp sequenced does not corelates with diversity statics could be useful for the reader to trust your results.

I also suggest to the authors to discuss this issue in the discussion.

I pointed in my first review that the authors does not describe the accessions used un this study. Indeed, authors provide in Sup Tab 1 the location of origin of the accession, but the link between them remains elusive to me. I still think the manuscript would benefit of a brief description of the reasons of inclusion of this list of accessions.

I also think that the manuscript contains languages error (grammar, syntax, vocabulary). I suggest the authors takes the time to thoroughly edit the manuscript.

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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 #1: No

Reviewer #2: 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.

A pilot-scale comparison between single and double-digest RAD markers generated using GBS strategy in sesame (Sesamum indicum L.)

PONE-D-23-05086R2

Dear Dr. Rangan,

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,

Tzen-Yuh Chiang

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

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 #1: 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 #1: Yes

**********

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

Reviewer #1: 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 #1: 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 #1: 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 #1: (No Response)

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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 #1: Yes: Engin YOL

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