PONE-D-20-22960

Integration of Small RNA, Degradome and Proteome Sequencing in Oryza sativa Reveals a Delayed Senescence Network in Tetraploid Rice Seed

PLOS ONE

Dear Dr. He,

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 ensure that your decision is justified on PLOS ONE’s publication criteria and not, for example, on novelty or perceived impact.

==============================

Please submit your revised manuscript by Oct 26 2020 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: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

We look forward to receiving your revised manuscript.

Kind regards,

Baohong Zhang, Ph.D

Academic Editor

PLOS ONE

Journal Requirements:

When submitting your revision, we need you to address these additional requirements.

1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at

https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and

https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

2.We suggest you thoroughly copyedit your manuscript for language usage, spelling, and grammar. If you do not know anyone who can help you do this, you may wish to consider employing a professional scientific editing service.  

Whilst you may use any professional scientific editing service of your choice, PLOS has partnered with both American Journal Experts (AJE) and Editage to provide discounted services to PLOS authors. Both organizations have experience helping authors meet PLOS guidelines and can provide language editing, translation, manuscript formatting, and figure formatting to ensure your manuscript meets our submission guidelines. To take advantage of our partnership with AJE, visit the AJE website (http://learn.aje.com/plos/) for a 15% discount off AJE services. To take advantage of our partnership with Editage, visit the Editage website (www.editage.com) and enter referral code PLOSEDIT for a 15% discount off Editage services.  If the PLOS editorial team finds any language issues in text that either AJE or Editage has edited, the service provider will re-edit the text for free.

Upon resubmission, please provide the following:

• The name of the colleague or the details of the professional service that edited your manuscript
• A copy of your manuscript showing your changes by either highlighting them or using track changes (uploaded as a *supporting information* file)
• A clean copy of the edited manuscript (uploaded as the new *manuscript* file)

3. Thank you for stating the following in the Financial Disclosure section:

[This project was supported by the Chinese National Natural Science Foundation (Grant Nos.31960068，31270356, 31271690, and 31571639),  2017 Hubei Science and Technology Department Innovation Team (2017CFA023), 2016 Wuhan Yellow Crane Talents (science) Foundation.].   

We note that one or more of the authors are employed by a commercial company: Wuhan Polyploid Biology Technology Co. Ltd,

1. Please provide an amended Funding Statement declaring this commercial affiliation, as well as a statement regarding the Role of Funders in your study. If the funding organization did not play a role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript and only provided financial support in the form of authors' salaries and/or research materials, please review your statements relating to the author contributions, and ensure you have specifically and accurately indicated the role(s) that these authors had in your study. You can update author roles in the Author Contributions section of the online submission form.

Please also include the following statement within your amended Funding Statement.

“The funder provided support in the form of salaries for authors [insert relevant initials], but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.”

If your commercial affiliation did play a role in your study, please state and explain this role within your updated Funding Statement.

2. Please also provide an updated Competing Interests Statement declaring this commercial affiliation along with any other relevant declarations relating to employment, consultancy, patents, products in development, or marketed products, etc.  

Within your Competing Interests Statement, please confirm that this commercial affiliation does not alter your adherence to all PLOS ONE policies on sharing data and materials by including the following statement: "This does not alter our adherence to  PLOS ONE policies on sharing data and materials.” (as detailed online in our guide for authors http://journals.plos.org/plosone/s/competing-interests) . If this adherence statement is not accurate and  there are restrictions on sharing of data and/or materials, please state these. Please note that we cannot proceed with consideration of your article until this information has been declared.

Please include both an updated Funding Statement and Competing Interests Statement in your cover letter. We will change the online submission form on your behalf.

Please know it is PLOS ONE policy for corresponding authors to declare, on behalf of all authors, all potential competing interests for the purposes of transparency. PLOS defines a competing interest as anything that interferes with, or could reasonably be perceived as interfering with, the full and objective presentation, peer review, editorial decision-making, or publication of research or non-research articles submitted to one of the journals. Competing interests can be financial or non-financial, professional, or personal. Competing interests can arise in relationship to an organization or another person. Please follow this link to our website for more details on competing interests: http://journals.plos.org/plosone/s/competing-interests

[Note: HTML markup is below. Please do not edit.]

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: Yes

Reviewer #2: No

**********

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

Reviewer #1: Yes

Reviewer #2: No

**********

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

**********

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

**********

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: The manuscript describes a technically sound scientific study with data to support the findings. Experiments were performed with appropriate controls, repetitions and sample sizes. Conclusions are duly drawn from the data presented. The statistical analysis been performed appropriately. The authors have made fully available all the data underlying the conclusions in their manuscript. The manuscript presented in an intelligible fashion and written in standard English

Reviewer #2: This manuscript described a comprehensive comparison between tetraploid and diploid rice accessions via miRNA-seq together with Degradome and proteome sequencing analyses. The authors provide preliminary data showing that miR164d and some other small RNAs may play roles in regulation of the activity of antioxidant enzymes, leading to determining of seed senescence and seed longevity. However, I did not found any degradome and proteome data to support the claims throughout the manuscript. Besides, I have the following concerns to argue the publishable of this manuscript.

There are many confusing or unclear sentences, I listed some below.

Lines 42-64, the two sentences here are confusing.

Lines 84-90, the long sentence here is confusing.

Lines 97-98, the mean of the sentence “With…decline” is unclear.

Line 121, “identifying” is not a correct word here, how can “mechanisms” be identified? I suggest to use “understanding” instead.

Lines 343-344 and Fig 6, the gene IDs for SOD, CAT and POD are not clear. I suggest that the authors use either RAP locus (for example, Os02g0672200) or MSU locus (LOC_Os02g45070), so that the readers can see what genes are been talking about.

Lines 364-368 and Table 3, I cannot understand what the protein accession numbers are used. Are the numbers from the database of LC-MS/MS or from any public databases? If these numbers are from the database of LC-MS/MS, please change to numbers corresponding to those of a public database. If the numbers are from a public database, please point out what database is used.

Other concerns:

Lines 53-54 and throughout the manuscript, delete the “-” between “miR” and the “number”. The name of miRNAs should follow the previous reports.

Lines 103-111, I suggest to move “MicroRNAs…process” into a new paragraph.

Lines 110-111, the statement of the sentence “Previous studies…” seems not consistent with the context and the cited reference (33) is incorrect.

Lines 118-119, I cannot understand how proteomics can be used to verify the miRNA and degradome sequencing results. RNA sequencing data should be verified by RT-PCR.

Lines 70-74 and 125-128, the authors reasoned that PMeS rice lines have advantages, I am suspicious that the polyploidy 9311-4x is with high seed setting. I suggest that the authors show the panicle images to display this trait.

Line 136, “6000lx” should be “6000 lx”.

Line 137, “20 seeds for” should be “Twenty seeds were used for”

Lines 221-223, antioxidant enzyme activity assays should cite references or give a brief description of the method.

Line 291, here should cite previous published papers because of the claim “consistent with previous studies in O. sativa”.

Lines 305-306 and table 1, I do not think that miR164d targets a gene encoding Cu-Zn superoxide. I suggest that the authors double check and cite a reference for this claim. I also suggest that the authors double check the fold change (FC) value in table 1 and clarify whether they are log2FC.

Line 326, there is not Supplement Table S3.

Lines 329-332 and 356-358, I did not find the data in Fig 5 or any other place to support the claims here. I suggest that the authors present the degradome data in a supplemental data set.

Lines 394-396, the authors should be aware that the expression of OsNCED3 and OxABA80x2 is far from ABA biosynthesis or degradation. I suggest that the authors revision the claims here. Besides, what is OxABA80x2? Please give the gene ID.

Lines 448-456, superoxide dismutase genes are not the target of miR164, instead, they are the target of miR398. The target of miR164 are members of NAC transcription factor gene family.

**********

6. 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: Professor Anatoliy Ivashchenko

Reviewer #2: Yes: Wen-Ming Wang

[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.

Integration of Small RNA, Degradome and Proteome Sequencing in Oryza sativa Reveals a Delayed Senescence Network in Tetraploid Rice Seed

PONE-D-20-22960R1

Dear Dr. He,

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,

Baohong Zhang, Ph.D

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: