Peer Review History
| Original SubmissionAugust 22, 2020 |
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PONE-D-20-26347 Identification and characterization of a novel multi-stress responsive gene in Arabidopsis PLOS ONE Dear Dr. Munir, 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 Nov 09 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:
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, Keqiang Wu, 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 2. PLOS ONE now requires that authors provide the original uncropped and unadjusted images underlying all blot or gel results reported in a submission’s figures or Supporting Information files. This policy and the journal’s other requirements for blot/gel reporting and figure preparation are described in detail at https://journals.plos.org/plosone/s/figures#loc-blot-and-gel-reporting-requirements and https://journals.plos.org/plosone/s/figures#loc-preparing-figures-from-image-files. When you submit your revised manuscript, please ensure that your figures adhere fully to these guidelines and provide the original underlying images for all blot or gel data reported in your submission. See the following link for instructions on providing the original image data: https://journals.plos.org/plosone/s/figures#loc-original-images-for-blots-and-gels. In your cover letter, please note whether your blot/gel image data are in Supporting Information or posted at a public data repository, provide the repository URL if relevant, and provide specific details as to which raw blot/gel images, if any, are not available. Email us at plosone@plos.org if you have any questions. 3. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager. Please see the following video for instructions on linking an ORCID iD to your Editorial Manager account: https://www.youtube.com/watch?v=_xcclfuvtxQ 4. Please upload a new copy of Figure S1 as the detail is not clear. Please follow the link for more information: https://blogs.plos.org/plos/2019/06/looking-good-tips-for-creating-your-plos-figures-graphics/ [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: Partly Reviewer #2: No ********** 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: 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: 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: The authors carried out re-analysis of three publically available RNA seq datasets and zeroed in on At4g18280 (here named as GRPL1). The manuscript described the physiological analysis of GRPL1 over expression lines under salt, drought and heat stress. The study does add to knowledge on relatively less explored and functionally uncharacterized protein. However there are several points were this manuscript needs improvements. My observation and comments are as follows. • There is too much of redundancy in introduction section. There are many sentences with similar message or meaning, these needs to be removed. The aim of the study needs to be clearly mentioned. • There is one study on identification and characterization of At4g18280 (here named as GRPL1) ‘Overexpression of a Novel Component Induces HAK5 and Enhances Growth in Arabidopsis’. Adams et al. 2013. The study suggested the role of this gene in pot deficiency and salt stress response. This ref is missing in the whole manuscript. • It would be better to mention the plant /crop to which the SRA data sets belong. The reason or criteria for selecting only these three data sets out of many available for analysis should also be mentioned. • Line 159-160. “leaves of three weeks old were excised to analyse the standardized water content”. What is the meaning of standardized water content?? • Line 187-192: As floral dip method is well known method, instead of detailed description just reference is sufficient to mention the transformation method used. Infact the very ref for floral dip is missing. The details of promoter cloning are also absent. • There is repetition of methods in “Plant Material, Growth Conditions and Stress Treatment” and “Measurement of Physiological and Biochemical Indexes under Salt, Drought and Heat Stress”. These can be combined under one heading. • There is discrepancy in the number of days for drought stress imposition (water with holding) in Line no 156 (20 days), 231 (32 days) and 358 (28 days) . • Result section: • The authors described GO analysis of DEGs and next section started analyzing expression of AT4G18280 (GRPL1) which is too abrupt and requires explanation as to how the authors zeroed in on AT4G18280 (GRPL1). Moreover the first section “Global Gene …..Abiotic Stresses” details can be made shorter. • Again there is redundancy in few lines of section 1 and section 2 of results. • Line no. 277 PEG induces osmotic stress not drought stress. Moreover there is no distinction in the Table (Fig.1a) which is drought and PEG imposed stress. • Line 295: First, the overexpression was analyzed at the… • Fig. 2C should have scale bar for comparison of size. For Fig. 2D data from how many plants was recorded (replicates)? In general no of plants /replicates should be mentioned in all experiments • Instead of “Over-expressed Transgenic Lines”, transgenic lines overexpressing GRPL1 or overexpression lines may be a better term. • In Fig 3 B and C, over expression line 1-4 did not perform better than Wild type. so this should be mentioned instead of generalizing the observation. After how many days the survival % under salt stress was recorded? Should be mentioned in text. • Line 350-353: without understanding of the biological function of GRPL1 , these are too presumptive statements. • Lines 397 -406 these lines should be shifted to section 1 “Global Gene …..Abiotic Stresses” of results. • Lines 410 -459: Discussion of DEGs is not required as these results might have been discussed by the authors of SRA study. Here authors should focus on how many genes they short listed infact a list of genes should have been more appropriate (in results). And then they can discuss validation of their selected gene GRPL1 by qRT-PCR (lines 459-462). • Line 474-476: Authors have discussed propidium iodide staining for recording no of cells however there is no data presented. Similarly Line 528-529 electrolyte leakage observation under salt stress is mentioned however no data is given. • Conclusion can be made more specific and short. Reviewer #2: Reviewer 1 The author identified a gene GRPL1 which was induced by multiple stresses by querying transcriptome results of multiple stresses. The transgenic Arabidopsis was obtained by overexpression of GRPL1. It was proved that GRPL1 can improve the resistance to high salt, drought and heat stress through resistance identification and analysis of various physiological indexes. It is a new idea to identify genes involved in multiple stress resistance processes. However, the quality of the data in this paper is not high, especially the pictures are not standardized. It is difficult to understand that GRPL1 is regulated by ABA2 gene. Therefore, this paper can not be published in the PLOS ONE at present, and we hope to revise it. Suggestions for revision are as follows: 1. Why didn't we use GRPL1 mutants for phenotypic analysis. 2. When analyzing transcriptome data, the reason why GRPL1 gene was chosen is not clear. 3. Paragraph in P303-308 is too short, so it is suggested to combine with other results. 4. The discussion is too long. 5. There are conjectured results in the conclusion part, which are not supported by data, so it is suggested to remove them. 6. Fig2C is lack of scale, the size of pictures is different, and there is no clear picture of salt tolerance. 7. Fig.4A is not clear. 8. The primers of Tables 1 were incomplete and there were no QRT PCR primers. 9. ABA2 gene is alcohol dehydrogenase. It is difficult to understand why ABA2 mutation affects GRPL1 expression, because ABA2 is not a transcription factor. ********** 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: 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. |
| Revision 1 |
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PONE-D-20-26347R1 Identification and characterization of a novel multi-stress responsive gene in Arabidopsis PLOS ONE Dear Dr. Munir, 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 07 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:
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, Keqiang Wu, 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: Line 58 full form of GRPs should be mentioned (when it is mentioned first time) Ilalics for gene names Line 65-67 may be deleted Method of calculation for qRT-PCR should be included in the expression analysis section Mention vector background for overexpression construct, Generation at which the transgenic lines were analysed Line 151 the word dessication should be replaced by dehydration or drought FIG 2C the legend mentions scale bar as 1 cm however the picture does not appear to be in same scale, hence should be otherwise removed Reviewer #2: (No Response) ********** 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 [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. |
| Revision 2 |
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Identification and characterization of a novel multi-stress responsive gene in Arabidopsis PONE-D-20-26347R2 Dear Dr. Munir, 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, Keqiang Wu, Ph.D Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: |
| Formally Accepted |
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PONE-D-20-26347R2 Identification and characterization of a novel multi-stress responsive gene in Arabidopsis Dear Dr. Munir: 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 Professor Keqiang Wu Academic Editor PLOS ONE |
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