Concomitant phytonutrient and transcriptome analysis of mature fruit and leaf tissues of tomato (Solanum lycopersicum L. cv. Oregon Spring) grown using organic and conventional fertilizer

Richard M. Sharpe; Luke Gustafson; Seanna Hewitt; Benjamin Kilian; James Crabb; Christopher Hendrickson; Derick Jiwan; Preston Andrews; Amit Dhingra

doi:10.1371/journal.pone.0227429

Peer Review History

Original SubmissionSeptember 10, 2019
27 Sep 2019 Decision Letter - Yuan Huang, Editor PONE-D-19-25332 Concomitant phytonutrient and transcriptome analysis of mature fruit and leaf tissues of tomato (Solanum lycopersicum L. cv. Oregon Spring) grown using organic and conventional fertilizer PLOS ONE Dear Professor Dhingra, 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 Nov 11 2019 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, Yuan Huang Academic Editor PLOS ONE Journal Requirements: When submitting your revision, we need you to address these additional requirements. 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.journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and http://www.journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 1. We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data. [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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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: This manuscript presenting some valuable information and has sufficient level of novelty, this may be published after necessary revision. Page 7: “In this study, less than a 9% difference in the transcriptional abundance of GPP1 between the fruit tissues was observed” Normally differential expression is mentioned based on Log2 fold change, you have calculated the difference of expression in percentages, apparently 9% seems an obvious change however if you calculate based on log2 fold change the difference might not be so obvious, please check correct accordingly. Please represent the changes (up-regulation and down-regulation) in gene expressions/transcripts based on log2 fold change rather fold change or percentages (throughout the document). Page 5: Please replace “fertility treatments” with “fertilizer treatment” The manuscript seems overly long, please make it comparatively shorter. Another observation is that throughout the manuscript reader has focused to highlight or show the up-regulated genes however the information or description of down-regulated genes has not got due attention. Conclusion section is also long, this must not be more than 150-200 words. Probably the raw data of transcriptome has not been uploaded to any publicly available platform such as NCBI or any other, please upload raw data and mention accession number in the manuscript. This article may be cited in the discussion as this is closely related with the current study "19. Muhammad Azher Nawaz, Chen Chen, Fareeha Shireen, Zuhua Zheng, Hamza Sohail, Muhammad Afzal, Muhammad Amjad Ali, Bie Zhilong, Yuan Huang. 2018. Genome-wide expression profiling of leaves and root of watermelon in response to low nitrogen. BMC Genomics. 19: 456 " https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-018-4856-x ****** 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: Muhammad Azher Nawaz [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.0227429.r001
Revision 1
27 Oct 2019 Author Response Dear Editor, The authors are thankful to the reviewers for their critical and supportive comments. We have considered each comment and have made revisions to the manuscript along with responding to the comments. A point-by-point response to the reviewer’s comments is provided below. The suggested revisions have improved the manuscript and we hope that the manuscript will now be acceptable for publication in PLOS One. Editorial Comment: We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data. Response: The phrase “data not shown” was an oversight in the original submission. All data are included in the main body or in the supplementary section of the revised submission. Comment #1: This manuscript presenting some valuable information and has sufficient level of novelty, this may be published after necessary revision. Response: Authors appreciate the reviewer’s overall support. Comment #2: Page 7: “In this study, less than a 9% difference in the transcriptional abundance of GPP1 between the fruit tissues was observed” Normally differential expression is mentioned based on Log2 fold change, you have calculated the difference of expression in percentages, apparently 9% seems an obvious change however if you calculate based on log2 fold change the difference might not be so obvious, please check correct accordingly. Please represent the changes (up-regulation and down-regulation) in gene expressions/transcripts based on log2 fold change rather fold change or percentages (throughout the document). Response: The authors agree with the reviewer that normally differential expression is mentioned based on log2 fold-change. The focus of this study, as stated in the hypothesis, was that the genes involved in pathways that corresponded to the phytonutrient differences (Lycopene and Ascorbate pathways), would be differentially expressed. However, we didn’t find support for the hypothesis, perhaps due to the fact that we analyzed only the mature leaf and fruit tissues. When we performed GO (gene ontology) enrichment, we observed the terms that were differentially enriched between ORG vs CONV. In the ontologies that showed significant enrichment according to the Fisher’s Exact Test, we identified the associated genes and their RPKM values. Thereafter, we analyzed the changes in RPKM values of the said genes in the context of the pathways they participate in. This methodology is detailed in the methods section. We refrained from stating that any of these genes were significantly differentially expressed unless the RPKM values were doubled from one treatment to the other, which then would be considered to be differentially expressed using the log2 fold-change parameter. We used this approach to understand the relationships between the pathway enzymes. Therefore, the data are represented as percentage based on RPKM values. However, if the editor considers we should represent the data in terms of significant changes only, we will be happy to make the necessary edits. Comment #3: Page 5: Please replace “fertility treatments” with “fertilizer treatment” Response: The manuscript has been edited as advised. Comment #4: The manuscript seems overly long, please make it comparatively shorter. Response: The authors chose to submit the manuscript to PLOS One as there are no strict limits to the length of the article. The authors contend that a study and analysis as complex as the one presented in this study warrants addressing the key pathways known to be impacted by the conditions of the study. We appreciate the reviewer’s comment, however, in the absence of specific feedback, we are unsure which sections to move to supplementary section. Comment #5: Another observation is that throughout the manuscript reader has focused to highlight or show the up-regulated genes however the information or description of down-regulated genes has not got due attention. Response: This is indeed an astute observation, something the authors had noticed during the preparation of the manuscript. The focus on upregulation of genes stems from the specific hypotheses that were evaluated in the context of ORG treatment over CONV. Comment #6: Conclusion section is also long, this must not be more than 150-200 words. Response: As per the instructions to authors, there is no word limit for the conclusion section. The only requirement is that the language should be clear and concise. In the absence of any specific suggestions, the authors feel that the conclusion as written appropriately sums up all the aspects of the study clearly and concisely. Comment #7: Probably the raw data of transcriptome has not been uploaded to any publicly available platform such as NCBI or any other, please upload raw data and mention accession number in the manuscript. Response: In the material and methods section, under the subsection Illumina Sequencing the raw data has been described as being uploaded to the NCBI SRA and the accession numbers were included. Comment #8: This article may be cited in the discussion as this is closely related with the current study "19. Muhammad Azher Nawaz, Chen Chen, Fareeha Shireen, Zuhua Zheng, Hamza Sohail, Muhammad Afzal, Muhammad Amjad Ali, Bie Zhilong, Yuan Huang. 2018. Genome-wide expression profiling of leaves and root of watermelon in response to low nitrogen. BMC Genomics. 19: 456 " https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-018-4856-x Response: Thank you for the suggestion. The published article is pertinent to this work and has been cited in the discussion. Attachments Attachment Submitted filename: ReviewerCommentsAndResponses PLOS ONE_10272019.docx https://doi.org/10.1371/journal.pone.0227429.r002
1 Nov 2019 Decision Letter - Yuan Huang, Editor PONE-D-19-25332R1 Concomitant phytonutrient and transcriptome analysis of mature fruit and leaf tissues of tomato (Solanum lycopersicum L. cv. Oregon Spring) grown using organic and conventional fertilizer PLOS ONE Dear Professor Dhingra, 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 Dec 16 2019 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, Yuan Huang 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 ******** 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 ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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: You have not followed the suggestions, and merely changed a few words in the revised version. We understand there is no page limit for PLOSONE articles, but it dose not means authors should write an article of 50 or 70 or 80 pages. Please reduce the length of the document, as for as conclusion section is concerned that should look like a "Conclusion". Reduce it to nearly 150-200 words written in a single paragraph. Please see some previously published articles to understand what does "conclusion" means? Represent genes expression data in Log2fold change form ****** 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 [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.0227429.r003
Revision 2
7 Dec 2019 Author Response December 7, 2019 Dear Editor, The authors would like to thank the reviewer for their critical, and very helpful comments. We have incorporated major revisions to reduce the size of the manuscript and have also incorporated the log2fold-change data for gene expression. All the edits are visible in the manuscript with track changes. It is our hope that the manuscript will be acceptable for publication in its revised form. As advised, we have provided a point-by-point response to the reviewers’ comments. The author’s responses to reviewers’ comments are as follows. Reviewer Comment #1: You have not followed the suggestions, and merely changed a few words in the revised version. We understand there is no page limit for PLOSONE articles, but it dose not means authors should write an article of 50 or 70 or 80 pages. Please reduce the length of the document, as for as conclusion section is concerned that should look like a "Conclusion". Reduce it to nearly 150-200 words written in a single paragraph. Please see some previously published articles to understand what does "conclusion" means? Author’s Response: The manuscript has been substantially shortened in length. The conclusion section is now 195 words long, and presented as a single paragraph. Reviewer Comment #2: Represent genes expression data in Log2fold change form. Author’s Response: The gene expression data has now been presented in Log2Fold-change form both in the text as well as in the tables accompanying the revised figures in the main manuscript as well as in the supplementary tables and figures. Attachments Attachment Submitted filename: Response to Reviewer_Sharpe et al 12052019.docx https://doi.org/10.1371/journal.pone.0227429.r004
19 Dec 2019 Decision Letter - Yuan Huang, Editor Concomitant phytonutrient and transcriptome analysis of mature fruit and leaf tissues of tomato (Solanum lycopersicum L. cv. Oregon Spring) grown using organic and conventional fertilizer PONE-D-19-25332R2 Dear Dr. Dhingra, We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements. Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication. Shortly after the formal acceptance letter is sent, an invoice for payment will follow. To ensure an efficient production and billing process, please log into Editorial Manager at https://www.editorialmanager.com/pone/, click the "Update My Information" link at the top of the page, and update your user information. 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 enable them to help maximize its impact. If they will be preparing press materials for this manuscript, you must inform our press team as soon as possible and 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. With kind regards, Yuan Huang Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #1: All comments have been addressed ******** 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 ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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) ****** 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: Muhammad Azher Nawaz https://doi.org/10.1371/journal.pone.0227429.r005
Formally Accepted
23 Dec 2019 Acceptance Letter - Yuan Huang, Editor PONE-D-19-25332R2 Concomitant phytonutrient and transcriptome analysis of mature fruit and leaf tissues of tomato (Solanum lycopersicum L. cv. Oregon Spring) grown using organic and conventional fertilizer Dear Dr. Dhingra: I am 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 notify them about your upcoming paper at this point, to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, 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. For any other questions or concerns, please email plosone@plos.org. Thank you for submitting your work to PLOS ONE. With kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Yuan Huang Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0227429.r006

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