Peer Review History
Original SubmissionJuly 10, 2023 |
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PONE-D-23-21487Transcriptome alterations of peanut reveal the growth-promoting molecular mechanisms of Tsukamurella tyrosinosolvens P9PLOS ONE Dear Dr. Lizhen, 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 03 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:
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, 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 https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and 2. Thank you for submitting the above manuscript to PLOS ONE. During our internal evaluation of the manuscript, we found significant text overlap between your submission and previous work in the [introduction, conclusion, etc.]. We would like to make you aware that copying extracts from previous publications, especially outside the methods section, word-for-word is unacceptable. In addition, the reproduction of text from published reports has implications for the copyright that may apply to the publications. Please revise the manuscript to rephrase the duplicated text, cite your sources, and provide details as to how the current manuscript advances on previous work. Please note that further consideration is dependent on the submission of a manuscript that addresses these concerns about the overlap in text with published work. [If the overlap is with the authors’ own works: Moreover, upon submission, authors must confirm that the manuscript, or any related manuscript, is not currently under consideration or accepted elsewhere. If related work has been submitted to PLOS ONE or elsewhere, authors must include a copy with the submitted article. Reviewers will be asked to comment on the overlap between related submissions (http://journals.plos.org/plosone/s/submission-guidelines#loc-related-manuscripts).] We will carefully review your manuscript upon resubmission and further consideration of the manuscript is dependent on the text overlap being addressed in full. Please ensure that your revision is thorough as failure to address the concerns to our satisfaction may result in your submission not being considered further. 3. Thank you for stating the following financial disclosure: " This work was supported by the the National Natural Science Foundation of China (32060028). In all of authors, Lizhen Han is the corresponding author, Xue Bai and Yujie Han are Lizhen Han’s graduate students. Lizhen Han designed the experiments, Xue Bai investigated this study and wrote the manuscript, the two students performed the experiments." Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. 4. Thank you for stating the following in your Competing Interests section: "No authors have competing interests." Please complete your Competing Interests on the online submission form to state any Competing Interests. If you have no competing interests, please state "The authors have declared that no competing interests exist.", as detailed online in our guide for authors at http://journals.plos.org/plosone/s/submit-now This information should be included in your cover letter; we will change the online submission form on your behalf. 5. We note that you have referenced (unpublished data) on page 23, which has currently not yet been accepted for publication. Please remove this from your References and amend this to state in the body of your manuscript: (ie “Bewick et al. [Unpublished]”) as detailed online in our guide for authors http://journals.plos.org/plosone/s/submission-guidelines#loc-reference-style [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: Partly ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No 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: No 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 have presented good information about the changes in the expression levels of different genes which might help to take Tsukamurella tyrosinosolvens strain P9 to the field level. However, major corrections need to be made to improve the manuscript quality. Differential expression alone cannot reveal any molecular interaction or mechanism. The title must be changed according to the study conducted. This study only explains the changes in the gene expression during the P9 colocalization of peanut roots. No molecular mechanism has been revealed here. Authors are requested to provide the Bioproject ID or GEO ID for the submitted RNAseq data in the data availability statement. A supplementary file containing the list of all the DEGs should be included. Why the authors have used LOC IDs when the full genome sequence of peanuts is available in the database (https://www.peanutbase.org/) is unclear. Line 88- 105: The catalog number of the products can be mentioned here. Mention of the software used for read cleaning and quality filtering, pathway enrichment studies, and GO is required. Line 109-119: Tool used for primer designing needs to be mentioned. As qPCR is a very generic experiment, details of the protocol can be omitted. Mention the citation for 2-∆∆Ct method. Line 97: Mention the table number where the data has been provided. Line 137-138: Selection of two time points needs better justification. At least, the initial phenotyping experiments could have been done in three or more time points (24hrs, 48hrs, 72hrs) to determine the stage at which significant differences are observed. Highly significant differences in the root phenotypic characters may indicate an induction of these changes at an earlier time point. Line 167-175: Please indicate the number of common DEGs due to the addition of P9 strain. Are there any unique genes that are differentially expressed during initial (24hr) and final (72hrs) treatment? Use of a vein diagram rather than a volcano plot might be helpful in this case. Line 220-222, 243-245, 333: Sentence reconstruction required for correct understanding Line 214, 252: citation required Line 303: The authors commented on enhancement in photosynthesis rate. However, no physiological data has been provided. Moreover, the enhancement in chlorophyll content was not significant. Please comment on this. Line 380-383: This part has already been mentioned in Materials and Methods section. The result section should have the interpretation of the data. Fig S1: Statistics required in the bar graph. Suggestion: As a lot of hormonal changes have been observed at the transcript level, a critical analysis of cell division and elongation genes can give better insight. Discussion section could have been written in a better pattern. Mentioning a lot of gene regulations in the first part and connecting them to relevant papers in the later part will confuse the readers. Re-orienting sentences in a connected manner will improve the content. Expanded forms of the abbreviations used for the first time must be included for easy understanding though they are present in the supplementary file. Claims leading to improved accumulation or resistance should be toned down as no evidence for the same has been provided in this study. Mere upregulation or downregulation of genes cannot suggest the final activity in the mature stage of the plant. Suggestion: Volcano plots or PCA analysis figures can be provided in the supplementary files. A heatmap or pictorial representation of the analyzed genes should be presented instead which can provide consolidated information to the readers. A graphical abstract about the important findings of this colocalization study can help the readers too. This manuscript follows the same pattern as the ones published earlier on related topics. This creates redundancy, which must be avoided. The content and pattern of this manuscript are largely inspired by these two papers: Jiang, B., Long, C., Xu, Y., & Han, L. (2023). Molecular mechanism of Tsukamurella tyrosinosolvens strain P9 in response to root exudates of peanut. Archives Of Microbiology, 205(1). doi: 10.1007/s00203-022-03387-7 Han, L., Zhang, H., Bai, X., & Jiang, B. (2023). The peanut root exudate increases the transport and metabolism of nutrients and enhances the plant growth-promoting effects of burkholderia pyrrocinia strain P10. BMC Microbiology, 23(1). doi: 10.1186/s12866-023-02818-9 Reviewer #2: The study titled "Transcriptome Alterations of Peanut Revealing the Growth-Promoting Molecular Mechanisms of Tsukamurella tyrosinosolvens P9," conducted by Lizhen Han and and co-workers established a a co-culture system between Tsukamurella tyrosinosolvens strain-P9 and peanut plants. They performed a transcriptome analysis of peanut roots interacting with strain P9 at two different time points. The primary aim was to investigate how peanut seedlings respond at the molecular level to the influence of strain P9 and to provide direct evidence supporting an in-depth analysis of the growth-promoting mechanisms employed by strain P9 on peanuts. Their previous study reported Tsukamurella tyrosinosolvens P9 exhibits strong phosphate solubilization, indole-3-acetic acid (IAA) secretion, and siderophore production. Which transcripts are directly related to phosphate solubilization and siderophore production? The growth-promoting molecular mechanism of strain P9 is not clear in the present investigation, which which should be addressed in future revisions. Why the authors chose the genome of Arachis hypogaea (assembly arahy.Tifrunner.gnm1.KYV3; GenBank accession number GCA_003086295.2) as a reference guided identification of transcriptome from the RNA-seq data. Silihong, an early maturing, local peanut variety with a dark red seed coat was used as the plant material in the present investigation. Based on the classification of cultivated peanuts, the “Silihong” variety belongs to which group (Spanish bunch type or Verginia runner type), that may be mentioned. Given the published and publicly available genome sequences of these subgroups of the Arachis species [Zhuang, Weijian, et al. Nature genetics 51, no. 5 (2019): 865-876; Bertioli, David J. et al. Nature genetics 51, no. 5 (2019): 877-884; Chen, Xiaoping, Molecular plant 12, no. 7 (2019): 920-934] selecting the appropriate reference genome is crucial for accurate transcriptome analysis. The authors should explicitly define the rationale for selecting only 12 genes for qRT-PCR validation except for the GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses. Moreover, qRT-PCR validation is an important aspect of any transcriptomics study. The data needs to be incorporated in the main text instead of supplementary data. If possible the raw qRT PCR experimental data may be shown in the supplementary file. Additionally, the authors should clarify whether there are any known connections between these 12 genes in the growth-promoting molecular mechanisms of the Tsukamurella tyrosinosolvens P9 strain. A comprehensive analysis of the transcriptome data except for the discussion of log2 fold change data is lacking in the present investigation. While the authors claim that the DEG (differentially expressed gene) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analyses revealed spatiotemporal differences in gene expression in peanut roots in response to strain P9, they have not provided experimental evidence to support this claim. Furthermore, the qRT-PCR validation was conducted only on root transcripts, and the study lacks validation in other tissues to confirm the spatiotemporal distribution of the identified transcripts from the RNA-seq data. The raw RNA-seq data need to be submitted to the data repository and should also be available. Lastly, there are some minor corrections needed in the manuscript, such as using "indices" instead of "indexes" in line numbers 141 and 162, italicizing the scientific name "Tsukamurella tyrosinosolvens" consistently throughout the manuscript, and italicizing gene names. Additionally, "Ca2+" should be written correctly in the whole manuscript. ********** 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: Rajarshi Sanyal 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.
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Revision 1 |
PONE-D-23-21487R1Transcriptional alterations of peanut root during interaction with growth-promoting Tsukamurella tyrosinosolvens strain P9PLOS ONE Dear Dr. Lizhen, 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. Both the reviewers still have some minor suggestions for the improvement of the manuscript. Please submit your revised manuscript by Jan 13 2024 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 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, Anil Kumar Singh, 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 #1: (No Response) 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: Partly ********** 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: No 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 appreciate the effort the authors have put into incorporating the suggested changes. It's evident that the authors have taken the feedback seriously, and the manuscript is progressing well. However, I would like to draw your attention to sentence construction and grammatical errors. 1. There are still some grammatical errors and spelling mistakes throughout the manuscript (for example: Line 58, 182, 185, 192, 188, 205, 250, 332, 333, 364, 367, 377, 420, 466, 499, 505, 549, 558, 561, 634, 651, 656, 658, 665). The use of the phrase, “in regard to” has been used excessively, making the story monotonous. I suggest using a grammar checking software to resolve this. 2. Line 65: Please correct the spelling of peanut type. It should be “Virginia runner” 3. The link given in data availability statement is not working as of 27.11.23. Overall, I believe the manuscript is moving in the right direction, and I appreciate your dedication to refining the content. Reviewer #2: The manuscript has undergone revisions, incorporating a modified title, “Transcriptional alterations of peanut root during interaction with growth-promoting Tsukamurella tyrosinosolvens strain P9”. Numerous comments have been addressed except a few. The primary objective of the study was to explore the molecular response mechanism of peanut seedlings under the influence of strain P9 and to provide direct evidence for an in-depth analysis of the growth-promoting mechanism of strain P9 on peanuts. Their previous study reported that Tsukamurella tyrosinosolvens P9 exhibits strong phosphate solubilization, indole-3-acetic acid (IAA) secretion, and siderophore production. However, the corresponding genes were not extensively discussed except for the role of auxin in the revised manuscript. The root characteristics have a positive correlation with phosphate utilization and the phosphate solubilization also depends on the production of organic acids that helps in maintaining the pH of the environment for phosphate utilization. The modified version of the manuscript could be enhanced by addressing these issues, aligning with the authors' goal of elucidating the growth-promoting molecular mechanism of strain P9. In response to this concern, the authors acknowledge that they did not delve deeply into the genes associated with the growth-promoting molecular mechanisms of Tsukamurella tyrosinosolvens P9. They appreciate the suggestion and express openness to further studying the growth-promoting molecular mechanisms of the P9 strain. However, the query arises about the significance of the present investigation if the molecular mechanism is not thoroughly addressed, considering the title "Transcriptional alterations of peanut root during interaction with growth promoting Tsukamurella tyrosinosolvens strain P9." Moreover, on page 9, line 165, there is a question about the term "multiple metabolisc pathways," with a suggestion that it might be a typographical error, possibly intended to be "metabolic." ********** 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: Rajarshi Sanyal 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.
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Revision 2 |
PONE-D-23-21487R2Transcriptional alterations of peanut root during interaction with growth-promoting Tsukamurella tyrosinosolvens strain P9PLOS ONE Dear Dr. Lizhen, 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. Reviewer 1 has suggested few minor corrections. Please make these corrections and submit the manuscript. Please submit your revised manuscript by Feb 16 2024 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 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, Anil Kumar Singh, 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 #1: (No Response) 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: The modifications made to the manuscript, particularly in response to the previous comments have significantly improved the clarity and precision of the text. The provided link is now functional, addressing a previous issue. Overall, the study presents valuable insights; however, I have some specific comments and suggestions to enhance the clarity and precision of the manuscript. Line 56-59: The statement "….to investigate their interaction" suggests that transcriptome analysis confirms the interaction, which may be misleading. Transcriptome analysis provides an overview resulting from the interaction, if any, but does not confirm it. I recommend modifying the sentence to accurately convey this point. Additionally, the remark, "...aimed to explore the molecular response mechanism," is somewhat ambiguous, as the study did not unveil a molecular mechanism per se. Rather, it focused on elucidating transcriptional alterations in peanut due to Tsukamurella tyrosinosolvens strain P9 inoculation. Therefore, I suggest refining the statements to align more closely with the study's actual findings. Line 162: Please consider removing the word "were" to improve the sentence structure. In my initial review, I mentioned the potential significance of the study's novelty. I would like to emphasize that if the authors can further highlight the significance of their study, which may not be adequately underscored in the current manuscript, it would substantially enhance the paper's potential for publication. Reviewer #2: The manuscript has significantly improved as the authors have addressed the required revisions. The study was conducted on the molecular response mechanism of peanut seedlings to strain P9. They analyzed the transcript alterations to see the growth-promoting effects of strain P9 on peanuts. However, they could have enhanced the manuscript by incorporating a working model that elucidates the molecular mechanisms underlying the growth-promoting effects, providing a more comprehensive understanding of their claims. ********** 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: Rajarshi Sanyal 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 3 |
Transcriptional alterations of peanut root during interaction with growth-promoting Tsukamurella tyrosinosolvens strain P9 PONE-D-23-21487R3 Dear Dr. Lizhen, 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: |
Formally Accepted |
PONE-D-23-21487R3 PLOS ONE Dear Dr. Han, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, 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 customercare@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 |
Open letter on the publication of peer review reports
PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.
We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.
Learn more at ASAPbio .