A comprehensive analysis of transcriptomic data for comparison of plants with different photosynthetic pathways in response to drought stress

Shima Karami; Behrouz Shiran; Rudabeh Ravash; Hossein Fallahi

doi:10.1371/journal.pone.0287761

Peer Review History

Original SubmissionMarch 4, 2023
3 Apr 2023 Decision Letter - Aimin Zhang, Editor PONE-D-23-06353A comprehensive analysis of transcriptomic data for comparison of plants with different photosynthetic pathways in response to drought stressPLOS ONE Dear Dr. Shiran, 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 May 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, Aimin 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. Please include a copy of Table 1 and 2 which you refer to in your text on page 8. [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: 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: No 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: Authors need extensive English editing before reviewing process. I will review it after English editing. Most of the sentences are unusual and more than two meanings. Also, it has grammatical errors. In the current version, I can not reviewed it. Reviewer #2: I suggest to address following two issues to further improve the quality of the manuscript. 1. As mentioned in “Materials and Methods” section, the datasets belonging to five plants wheat, Rice, barley, maize, and sorghum were selected and subjected to RNA-seq analysis including raw reads SRP071248, SRP042233, ERP107297, SRP045409, SRP101470, SRP110211, SRP135093, SRP106756, and SRP057095. The datasets are species limited and indeed not cover detailed growth and development stages challenged by drought. They are also not included for those deposited during past two years. Therefore, the authors should describe the shortages/shortcomings of this research in “Discussion” section. 2. The topics discussed in “Discussion” section need to be concentrated and focused on processes related to photosynthesis, especially on those impacting the behaviors of C3 and C4 plants treated by drought. ****** 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: Aqarab Husnain Gondal Reviewer #2: Yes: Kai Xiao ******** [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.0287761.r001
Revision 1
8 May 2023 Author Response Dear Editor and Reviewers, Thank you for your time and for providing valuable comments to improve our manuscript. Please find the answers to your questions and comments below. All parts that have been changed according to your comments are given in track changes in the revised manuscript. I hope that the revised file satisfies you. Response to Editor 1. Please ensure that your manuscript meets PLOS ONE's style requirements The revised manuscript was prepared based on PLOS ONE's style. 2. Please include a copy of Table 1 and 2 which you refer to in your text on page 8 We inserted Tables 1 and 2 in the revised manuscript. Also a minor revision made in Figure 6 and Table S7-S8 Response to Reviewer #1 1. Extensive English editing before reviewing process. We attempted to edit the entire text of the manuscript in order to make it more understandable. Response to Reviewer #2 Reviewer: I suggest to address following two issues to further improve the quality of the manuscript. 1. The authors should describe the shortages/shortcomings of this research in “Discussion” section. According to the suggestion of the respected reviewer, the limitations of our research were mentioned at the end of the discussion section. 2. The topics discussed in “Discussion” section need to be concentrated and focused on processes related to photosynthesis, especially on those impacting the behaviors of C3 and C4 plants treated by drought. We tried not to limit our study to the main difference between C3 and C4 plants (C3 and C4 cycle) because this leads us to focus only on the effect of drought stress on the activity of C3 and C4 cycle enzymes. Our aim is to obtain comprehensive information about the overall response occurring in the leaves of these plants, which also includes photosynthesis. Because the response of C3 and C4 plants to stress conditions is not only related to photosynthesis but may be related to extensive metabolic pathways. Also, in the energy metabolism section, we tried to explain common and different changes in the expression of genes related to photosynthesis in both groups of plants (Response of light reactions and carbon fixation pathways). Therefore, it seems that it would be better to refer to the photosynthetic pathway in the title of the energy metabolism section, hence this change has been applied in the new version. Furthermore, to complete the photosynthesis section some information has been added. Attachments Attachment Submitted filename: Response to Editor and Reviewers.docx https://doi.org/10.1371/journal.pone.0287761.r002
2 Jun 2023 Decision Letter - Aimin Zhang, Editor PONE-D-23-06353R1A comprehensive analysis of transcriptomic data for comparison of plants with different photosynthetic pathways in response to drought stressPLOS ONE Dear Dr. Shiran, 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 rai============================= Please submit your revised manuscript by Jul 17 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, Aimin Zhang, 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. [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 #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 #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? 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 #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 #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 #2: The authors have well addressed the concerns raised by the reviewers. A suite of minor errors are needed to be corrected before the publish in the journal. Line 57: “CO2” needs to be corrected, in which “2” is lowercased. Line 82 : “The Pots” needs to be corrected by “The pots”. Line 90: “drought stress NCBI Sequence”: a comma needs to added ahead of “NCBI Sequence”. Line 101: “S1 Table” should be “Table S1”. Line 141: cis-regulatory elements: “cis” herein needs to be italic. Line 154: “S2 Table” should be “Table S2”. Same as follow. Line 163: “Fig 1” should be “Fig. 1”. Same as follows.\\ Line 174: “Table 1 and 2” should be “Tables 1 and 2”. Lines 215-221: the capital letters needs to be lowercased. Same as in caption of Fig. 2. Line 256: “Porphyrin” should be “porphyrin”. Line 377: “are participate” should be “arparticipate”. Line 389: “miR-158” should be “miR158”. Line 403: “Mun et al. [27]findings showed” should be “Mun et al. [27 showed”. Line 483: “can also can cause” should be “can also cause”. Line 535: “as an important” should be “an important”. ****** 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 #2: Yes: Kai Xiao ******** [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.0287761.r003
Revision 2
8 Jun 2023 Author Response Dear Editor and Reviewer Thank you for your time and for providing valuable comments to improve our manuscript. We have made modifications to our updated manuscript point by point according to your comments. Our response follows (the comments are in italics). We hope that the revised file satisfies you. Response to Editor 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. Response: We checked all our references, the format of reference number 9 was modified and five references (31-35) were added in the previous revised manuscript (lines 431-437), one of which was forgotten (), and this reference was also added in the new version. The number of references in the text and in the list of references has been updated, which can be traced in the Manuscript with Track Changes. On the other hand, for easier access to the references, the DOI of the articles was added. 9. Babraham Bioinformatics—FastQC A Quality Control tool for High Throughput Sequence Data [Internet]. [cited 2019 Feb 10]. Available from: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ 31. Lin YH, Huang LF, Hase T, Huang HE, Feng TY. Expression of plant ferredoxin-like protein (PFLP) enhances tolerance to heat stress in Arabidopsis thaliana. New biotechnology. 2015; 32(2): 235-242.‏ https://doi.org/10.1016/j.nbt.2014.12.001 32. Lehtimäki N, Lintala M, Allahverdiyeva Y, Aro EM, Mulo P. Drought stress-induced upregulation of components involved in ferredoxin-dependent cyclic electron transfer. J plant physiol. 2010;167(12): 1018-1022.‏ https://doi.org/10.1016/j.jplph.2010.02.006 33. Azzouz-Olden F, Hunt AG, Dinkins R. Transcriptome analysis of drought-tolerant sorghum genotype SC56 in response to water stress reveals an oxidative stress defense strategy. Mol Biol Rep. 2020;47: 3291-3303. https://doi.org/10.1007/s11033-020-05396-5 34. Fracasso A, Trindade LM, Amaducci S. Drought stress tolerance strategies revealed by RNA-Seq in two sorghum genotypes with contrasting WUE. BMC Plant Biol. 2016;16(1): 1-18. https://doi.org/10.1186/s12870-016-0800-x 35. Yang M, Geng M, Shen P, Chen X, Li Y, Wen X. Effect of post-silking drought stress on the expression profiles of genes involved in carbon and nitrogen metabolism during leaf senescence in maize (Zea mays L.). Plant Physiol Biochem. 2019;135: 304-309. https://doi.org/10.1016/j.plaphy.2018.12.025 Response to Reviewer 2 We would like to thank the reviewer for careful and thorough reading of this manuscript and for the thoughtful comments and constructive suggestions, which help to improve the quality of this manuscript. In addition, we appreciate the positive feedback from the reviewer. The responses are as below: Reviewer #2: The authors have well addressed the concerns raised by the reviewers. A suite of minor errors are needed to be corrected before the publish in the journal. Line 57: “CO2” needs to be corrected, in which “2” is lowercased. Response: We have fixed the error. Line 82 : “The Pots” needs to be corrected by “The pots”. Response: We have fixed the error. Line 90: “drought stress NCBI Sequence”: a comma needs to added ahead of “NCBI Sequence”. Response: The correction has been made. Line 101: “S1 Table” should be “Table S1”. Response: We thank the reviewer for pointing this out. According to PLOS ONE's Supporting Information Citations "Format Supporting Information Citations as “S1 Fig”, “S1 Table”, etc.", we have cited this way. Line 141: cis-regulatory elements: “cis” herein needs to be italic. Response: The correction has been made. Line 154: “S2 Table” should be “Table S2”. Same as follow. Response: We thank the reviewer for pointing this out. According to PLOS ONE's Supporting Information Citations "Format Supporting Information Citations as S1 Fig, S1 Table, etc.", we have cited this way. Line 163: “Fig 1” should be “Fig. 1”. Same as follows.\\ Response: We thank the reviewer for pointing this out. According to PLOS ONE's Figure Citations "Cite figures as Fig 1, Fig 2, etc.", we have cited this way. Line 174: “Table 1 and 2” should be “Tables 1 and 2”. Response: The correction has been made. Lines 215-221: the capital letters needs to be lowercased. Same as in caption of Fig. 2. Response: The correction has been made. Line 256: “Porphyrin” should be “porphyrin”. Response: The correction has been made. Line 377: “are participate” should be “arparticipate”. Response: The correction has been made. Line 389: “miR-158” should be “miR158”. Response: We have fixed the error. Line 403: “Mun et al. [27]findings showed” should be “Mun et al. [27 showed”. Response: This observation is correct. We have changed. Line 483: “can also can cause” should be “can also cause”. Response: We have fixed the error. Line 535: “as an important” should be “an important”. Response: The correction has been made. Attachments Attachment Submitted filename: response to veiwers (2).docx https://doi.org/10.1371/journal.pone.0287761.r004
12 Jun 2023 Decision Letter - Aimin Zhang, Editor A comprehensive analysis of transcriptomic data for comparison of plants with different photosynthetic pathways in response to drought stress PONE-D-23-06353R2 Dear Dr. Shiran, 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, Aimin Zhang, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0287761.r005
Formally Accepted
19 Jun 2023 Acceptance Letter - Aimin Zhang, Editor PONE-D-23-06353R2 A comprehensive analysis of transcriptomic data for comparison of plants with different photosynthetic pathways in response to drought stress Dear Dr. Shiran: 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 Prof. Aimin Zhang Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0287761.r006

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