PONE-D-21-01094

Development of the petaloid bracts of a paleoherb species, Saururus chinensis

PLOS ONE

Dear Dr. zhao,

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.

The presentation and languague need serious improvements.

Please submit your revised manuscript by Mar 26 2021 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,

Yun Zheng, Ph.D

Academic Editor

PLOS ONE

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https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0053019

In your revision ensure you cite all your sources (including your own works), and quote or rephrase any duplicated text outside the methods section. Further consideration is dependent on these concerns being addressed.

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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: Yes

Reviewer #2: Yes

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

Reviewer #1: Yes

Reviewer #2: 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

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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: 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: The authors compared the morphologies and physiological indices of petaloid and non-petaloid (green) bracts between the perianthless paleoherb S. chinensis in green and white ones. And compared the transcriptome in these two kinds of bracts, identified and verified some differential expressed genes, also discussed the possibility molecular mechanisms of petal development, which is new to us. However, I have some small questions or some mistakes to figure out in this manuscript in below:

1. In Abstract you mentioned the total differential expression genes(DEGs) were 5978, among them up-regulated DEGs were 1770 and down-regulated were 4770, that total among were 5977, not 5978, may this is a simple mistake by careless?

2. All the figures were not having a good quality, they were too blurred, could provide above 300 dpi pictures?

3. You mentioned the B class genes could be interact with each other, what the significance of these genes interaction with each other? And this work has also demonstrated that A- and B-class gene expression are involved in the development of showy bracts to attract pollinators, however, why don’t you detect the A-and B-class genes’ interaction?

4. You should improve your English more fluently for your manuscript.

Reviewer #2: Zhao et al. studied the development of petaloid bracts in Saururus chinensis. The topic is very interesting, and the results at the anatomy, physiology and gene expression levels support their conclusions. However, several places in result part were confusing, and need be clarified, and some places in Methods were even wrong. Here, I list some:

“RNA-seq abundance analysis identified 43,463 genes that were found to be differentially expressed in S. chinensis bracts. Of these, 5,978 showed strong differential expression, of which 1,770 were up-regulated and 4,207 down-regulated in green compared to white bracts”. That means that 90% genes identified in this study were differentially expressed. What is the criteria to design “differentially expressed gene” and “strong differential expression” used in this study?

“Clean reads from all samples were pooled together, and were further assembled de novo using the Trinity program [23], resulting in 86,532,094 total reads (10,816,511,750 bps) with an average length of 908bp, an N50-value of 1582 bp, andwith 13,821 unigenes (30.71%) longer than 1000 bp (Table 1). Your sequencing method (single end or pair end and length) need be clarified in Material and Methods, “average length of 908bp” is not the length of clean reads.

“22,688 unigenes were assigned to one or more ontologies. 6,727 unigenes were grouped under biological processes, 5,805 unigenes were grouped as cellular components, and 7,445 unigenes were grouped as having a role in molecular functions”. The total unigene number designed to three GO category is less than 22688, even though certain genes can be designed to 2 or 3 GO category.

“Comparing the bract tissues’ transcript profiles with the transcript profiles of developing seedling leaves identified 166 bract DEGs”. In the following sentence, authors showed the up/down regulated DEGs of different development stages compared with seedling leaves, what stage did the 166 DEGs specific to?

In Methods part:

“According to the Illumina manufacturer’s instructions, poly(A)+ RNA was purified from 5 mg of pooled total RNA from petaloid-bract and green-bract cDNA libraries using oligo(dT) magnetic beads”. 5 mg is misspelled or not? How polyA RNA can be isolated from cDNA libraries?

In “Screening of differentially expressed genes” part, “Unigenes that showed different expression levels between the two samples were subjected to GO function analysis and KEGG pathway analysis”, what is the two samples?

“Following amplification, melting curve analyses were performed at 95°C for 10 min, followed by 40 cycles of 95°C for 30 s, 60°C for 30 s, and 72°C for 20 s”, is this for melting curve analysis?

Other issues:

Labelling (A, B….) on figures are not clear.

Sequencing data should be deposited into databases for publicly available.

Authors should pay attention to the grammatical errors, such as “The wild is found mainly in moist sites in southern China from sea level to 1700 m [29]”.

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Reviewer #1: No

Reviewer #2: No

[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.

Attachments

Attachment

Submitted filename: recomendations.docx

PONE-D-21-01094R1

Development of the petaloid bracts of a paleoherb species, Saururus chinensis

PLOS ONE

Dear Dr. zhao,

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.

i) The criteria used in the differential analysis needs to be clarified; ii) The comparisons of different data/results are expected; iii) The presentation should be serious improved.

Please submit your revised manuscript by Jul 17 2021 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. 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,

Yun Zheng, Ph.D

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

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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: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: (No Response)

**********

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

**********

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: 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: This manuscript has been fully satisified my questions about what I am asking, and this manuscript has some new ideas about its topics, so I advise to accept it for publication on this journal.

Reviewer #2: In abstract and result parts, “RNA-seq abundance analysis identified 43,463 genes that were found to be differentially expressed in S. chinensis bracts. Of these, 5,978 showed strong differential expression, of which 1,770 were up-regulated and 4,207 down-regulated in green compared to white bracts”. You claimed “43,463 genes that were found to be differentially expressed in S. chinensis bracts’, then, you claimed “5,978 showed strong differential expression”, what is the criteria to design “differentially expressed gene” and “strong differential expression” used in this study?

Both RNA-Seq and microarray were used in this study, differentially expressed genes (DEGs) were screened with each method, how about the consistence between the DEGs of the two method?

“Scanning Electron Microscopy (SEM) and transmission electron microscope (TEM)” and other subtitles in method are not properly used.

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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: Yang Jun

Reviewer #2: No

[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.

Attachments

Attachment

Submitted filename: renamed_3c372.docx

Development of the petaloid bracts of a paleoherb species, Saururus chinensis

PONE-D-21-01094R2

Dear Dr. zhao,

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.

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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,

Yun Zheng, Ph.D

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

Reviewer #2: 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

Reviewer #2: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: 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

Reviewer #2: 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

Reviewer #2: 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: I have no other comments about this manuscript,I think it could be published in this journal with a little revisement.

Reviewer #2: (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: No

Reviewer #2: No