Responses of Manila Grass (Zoysia matrella) to chilling stress: From transcriptomics to physiology

Sixin Long; Fengying Yan; Lin Yang; Zhenyuan Sun; Shanjun Wei

doi:10.1371/journal.pone.0235972

Peer Review History

Original SubmissionJanuary 11, 2020
31 Mar 2020 Decision Letter - Anil Kumar Singh, Editor PONE-D-20-00949 Responses of Manila Grass (Zoysia matrella) to cold stress: from transcriptomics to physiology PLOS ONE Dear Dr Wei, 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. We would appreciate receiving your revised manuscript by May 15 2020 11:59PM. When you are 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. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols 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). This letter should be uploaded as separate file and labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out. We look forward to receiving your revised manuscript. Kind regards, Anil Kumar Singh, 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 http://www.plosone.org/attachments/PLOSOne_formatting_sample_main_body.pdf and http://www.plosone.org/attachments/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. We noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed: https://www.ncbi.nlm.nih.gov/pubmed/26115186 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0050785 https://www.tandfonline.com/doi/abs/10.1080/07352689.2014.870411?journalCode=bpts20 https://onlinelibrary.wiley.com/doi/full/10.1111/j.1365-313X.2007.03100.x http://www.plantphysiol.org/content/143/2/639.full 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. [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: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 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: Yes ****** 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 ****** 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: Study by Long et al on transcriptomic profiling of Manila grass under cold stress presents alteration in transcripts in response to cold stress and related physiological traits presented as markers of stress. Authors have presented a huge set of information in terms changes in transcript levels involve in various metabolic pathways and physiological process. Although the information presented is useful and can be utilized in related future studies, here in this study the conclusions made by authors are mostly speculative and not interconnected. I agree that 'omics' data is always huge and it is difficult to perform a directional analysis and reach to logical conclusions. A cold stress exposure would certainly change every physiological trait and metabolic pathway in the plant. The necessary part is the analysis of the data, which is entirely missing in this study. Almost everything is covered which has made the things even more complex to understand. Physiological data is very generalized and adds nothing new in the study. I would highly recommend author to focus the manuscript in a way that can be connected to cold susceptibility or tolerance and exclude rest of the data which is not really serving the purpose. Avoid speculative conclusions as they may be misleading unless validated. Authors are also suggested to reduce the overall length of manuscript with a proper rationale, brief introduction and a more focussed discussion of findings. Reviewer #2: In the manuscript entitled "Responses of Manila Grass (Zoysia matrella) to cold stress: from transcriptomics to physiology", authored by Long et al., done a good piece of work, but few comments are to be answered: 1- Do manila grass wilts in the winter or it completes its life cycle? 2- Plant material and treatment: why this temperature was chosen? 3- day night hours not mentioned. 4- Too long discussion. 5- Why only leaves not roots were taken for study? ****** 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: RAJEEV NAYAN BAHUGUNA 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 to be viewed.] 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 us at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0235972.r001
Revision 1
15 May 2020 Author Response Dear reviewers and editor, Thank you for giving us the chance to modify the manuscript. Wei learned a lot during the modifying process. The following are the details. 1. To academic editor （1）Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. We have downloaded two FDF files: “PLOSOne_formatting_sample_main_body” and “PLOSOne_formatting_sample_title_authors_affiliations”. Our manuscript has been arranged under the guide of the two files. （2） We noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed。 We have revised the manuscript carefully and tried our best to rewrite the overlapping text. 2、To Reviewer #1 Study by Long et al on transcriptomic profiling of Manila grass under cold stress presents alteration in transcripts in response to cold stress and related physiological traits presented as markers of stress. Authors have presented a huge set of information in terms changes in transcript levels involve in various metabolic pathways and physiological process. Although the information presented is useful and can be utilized in related future studies, here in this study the conclusions made by authors are mostly speculative and not interconnected. I agree that 'omics' data is always huge and it is difficult to perform a directional analysis and reach to logical conclusions. A cold stress exposure would certainly change every physiological trait and metabolic pathway in the plant. The necessary part is the analysis of the data, which is entirely missing in this study. Almost everything is covered which has made the things even more complex to understand. Physiological data is very generalized and adds nothing new in the study. I would highly recommend author to focus the manuscript in a way that can be connected to cold susceptibility or tolerance and exclude rest of the data which is not really serving the purpose. Avoid speculative conclusions as they may be misleading unless validated. Authors are also suggested to reduce the overall length of manuscript with a proper rationale, brief introduction and a more focussed discussion of findings. Response: Since the transcriptome data is huge and complex. Many clues can be available, but it is not easy to draw firm conclusions, unless corresponding physiological data are also available. In this study, five physiological characters were detected to assist the analysis of the transcriptome data. Among the five physiological parameters, the desecration stress and low bioactive GA level induced by cold are first reported in Manila grass, although they have been reported in other species. Because of the character of transcriptome data, only the direct results were provided in the section of results, most of analysis is arranged in the discussion section. Basing on our transcriptome data as well as the physiology data of our own and of documents, the cold-responding characters in Manila grass were discussed from five aspects: cold sensing and signaling, changes on system and photosynthesis activity, effect on nitrogen metabolism and carbohydrates, metabolism and signaling of plant hormones, and stresses coupled with cold. According to the comment, we read over the manuscript seriously and revised it carefully, especially in the discussion section. In details, in the first aspect, words that interpret the calcium pathway and transcription factors have been reduced; In the second aspect, the activity of mitochondria on photosynthesis has been deleted and the remained content has been reorganized; In the aspect of nitrogen metabolism, words that interpret the transport of nitrate and the assimilation process haves been reduced; in the aspect of plant hormones, only content of GA and CK that could come clear conclusions were remained; In the aspect of multiple stresses, the first paragraph as well the content related to karrikins have been deleted. The revised discussion seems more readable, though there are still many deficiencies need to improve on academic aspect. 3. To Reviewer #2 (1) Do manila grass wilts in the winter or it completes its life cycle? Response: Manila grass is a type of perennial turfgrass. In winter, the shoots wilts and the stolons are dormant. But if it is freezing severely, the dormant stolons will also die off. The word “perennial” has been supplemented in the introduction as following: For instance, Manila grass (Zoysia matrella Merr.), a popular warm season perennial turfgrass, shows excellent tolerance to drought and high temperature stresses, but is sensitive to low temperature. The turf it builds always exhibits a long yellow period in temperate zones or even dies off during winter freezes, which compromises its ornamental value and usage greatly. (2) Plant material and treatment: why this temperature was chosen? Response: 4℃-cold is often used to treat plant for cold-responding study. So we also used the condition to investigate the cold response in Manila grass. (3)day night hours not mentioned. Response: The day/night hours are 14h/10h. In the method section, we say: For cold treatment, plants were transferred to a growth chamber set to a 14h-photoperiod. (4)Too long discussion. Response:The discussion section has been reduced, as described in the response to reviewer #1. (5)Why only leaves not roots were taken for study? Response: Since leaves are sensitive to low temperature. When the atmospheric temperature drops to 10℃ or lower, leaves turn yellow and wilt gradually. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0235972.r002
18 Jun 2020 Decision Letter - Anil Kumar Singh, Editor PONE-D-20-00949R1 Responses of Manila Grass (Zoysia matrella) to cold stress: from transcriptomics to physiology PLOS ONE Dear Dr. Wei, 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. Authors are advised to clarify the concern raised by the reviewer 2 and make the necessary changes accordingly. Please submit your revised manuscript by Aug 02 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, Anil Kumar Singh, Ph.D. Academic Editor PLOS ONE [Note: HTML markup is below. Please do not edit.] 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 ******** 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: (No Response) Reviewer #2: One point is that there is quite difference in cold stress, chilling stress and frost stress. Please check which one fits in your criteria as in grass species all three affects differentially, and change the title accordingly. ****** 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: RAJEEV NAYAN BAHUGUNA 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. https://doi.org/10.1371/journal.pone.0235972.r003
Revision 2
24 Jun 2020 Author Response Cold stress includes chilling stress (0 - 20 °C) and freezing stress (< 0 °C) (Chinnusamy et al., 2007). Strictly speaking, we should use chilling stress instead of cold stress. Therefore, we has changed the tile to “Responses of Manila Grass (Zoysia matrella) to chilling stress: from transcriptomics to physiology”. Chinnusamy, V., Zhu, J., & Zhu, J.-K. (2007). Cold stress regulation of gene expression in plants. Trends in Plant Science, 12(10), 444–451. doi:10.1016/j.tplants.2007.07.002 Attachments Attachment Submitted filename: Response to reviewers.docx https://doi.org/10.1371/journal.pone.0235972.r004
26 Jun 2020 Decision Letter - Anil Kumar Singh, Editor Responses of Manila Grass (Zoysia matrella) to chilling stress: from transcriptomics to physiology PONE-D-20-00949R2 Dear Dr. Wei, 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, Anil Kumar Singh, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0235972.r005
Formally Accepted
6 Jul 2020 Acceptance Letter - Anil Kumar Singh, Editor PONE-D-20-00949R2 Responses of Manila Grass (Zoysia matrella) to chilling stress: from transcriptomics to physiology Dear Dr. Wei: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. 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. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Anil Kumar Singh Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0235972.r006

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