Insights into tea tree oil-mediated transcriptome modulation in Rosa hybrida

Juliana Lopez-Jimenez; Diego Giraldo; Felipe Cabarcas; Natalia Pabon-Mora; Juan F. Alzate

doi:10.1371/journal.pone.0341809

Peer Review History

Original SubmissionSeptember 22, 2025
12 Dec 2025 Decision Letter - Indu Sharma, Editor Dear Dr. Alzate, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Jan 26 2026 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. A 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 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, Indu Sharma 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 note that PLOS One has specific guidelines on code sharing for submissions in which author-generated code underpins the findings in the manuscript. In these cases, we expect all author-generated code to be made available without restrictions upon publication of the work. Please review our guidelines at https://journals.plos.org/plosone/s/materials-and-software-sharing#loc-sharing-code and ensure that your code is shared in a way that follows best practice and facilitates reproducibility and reuse. 3. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information . 4. If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise. 5. 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. Is the manuscript technically sound, and do the data support the conclusions? Reviewer #1: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: I Don't Know ****** 3. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #1: No ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes ****** Reviewer #1: Lines "Plant tissues were selected based on visual inspection... showing symptoms consistent with Botrytis fungal infection."This reveals a fundamental flaw: all sampled plants were infected, making it impossible to distinguish: Direct TTO effects on plant gene expression Indirect effects mediated through altered disease severity TTO-pathogen interaction effects. Confounding treatment with infection status makes it impossible to determine what drives observed expression changes Absence of disease phenotype data means biological relevance cannot be assessed Insufficient replication (n=3) limits statistical confidence Lack of validation leaves findings preliminary Acknowledge limitations explicitlyi.e insufficient replication, single timepoint, lack of functional validation ****** 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 ensure your figures meet our technical requirements, please review our figure guidelines: https://journals.plos.org/plosone/s/figures You may also use PLOS’s free figure tool, NAAS, to help you prepare publication quality figures: https://journals.plos.org/plosone/s/figures#loc-tools-for-figure-preparation. NAAS will assess whether your figures meet our technical requirements by comparing each figure against our figure specifications. https://doi.org/10.1371/journal.pone.0341809.r001
Revision 1
22 Dec 2025 Author Response PONE-D-25-51544 Insights into Tea Tree Oil-Mediated transcriptome modulation in Rosa hybrida 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 R:/ Manuscript was adjusted following the Journal style recommendations. 2. Please note that PLOS One has specific guidelines on code sharing for submissions in which author-generated code underpins the findings in the manuscript. In these cases, we expect all author-generated code to be made available without restrictions upon publication of the work. Please review our guidelines at https://journals.plos.org/plosone/s/materials-and-software-sharing#loc-sharing-code and ensure that your code is shared in a way that follows best practice and facilitates reproducibility and reuse. R:/ No specific code was generated for this manuscript. Publicly available software was used, as described in the Methods section. 3. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. R:/ Captions for Supplementary tables were added in the revised version of the manuscript. 5. Review Comments to the Author R:/ We thank the reviewers and the editor for the time invested in the review process and for their thoughtful comments, which have helped us improve the quality of the manuscript. The RNA-seq raw data generated for this study have been made publicly available in the NCBI Sequence Read Archive (SRA) under BioProject accession number PRJNA1303024, with the following BioSample accessions: SAMN50491601–SAMN50491612. Reviewer #1: Lines "Plant tissues were selected based on visual inspection... showing symptoms consistent with Botrytis fungal infection."This reveals a fundamental flaw: all sampled plants were infected, making it impossible to distinguish: Direct TTO effects on plant gene expression Indirect effects mediated through altered disease severity TTO-pathogen interaction effects. Confounding treatment with infection status makes it impossible to determine what drives observed expression changes Absence of disease phenotype data means biological relevance cannot be assessed R:/ We appreciate the reviewer’s careful assessment and the opportunity to clarify this point. While Botrytis cinerea is endemic in the commercial production system where the experiment was conducted, disease pressure during the sampling period was very low, and no plants displayed overt or differential disease symptoms. All sampled plants were genetically homogeneous, grown under identical agronomic conditions, and exhibited a similar macroscopic appearance at the time of tissue collection. Importantly, both control and TTO-treated plants were exposed to the same baseline level of natural Botrytis presence, and no plants with advanced or severe symptoms were selected. Therefore, the only experimental variable distinguishing the two groups was the application of the Tea Tree Oil (TTO) formulation, minimizing confounding effects associated with differential disease severity. To further address the possibility of pathogen-driven transcriptomic effects, we quantified Botrytis-derived RNA-seq reads across all samples and tissues. These reads were consistently extremely low and comparable between control and treated plants (ranging from n = 39 to n = 289 RNA-seq reads), indicating minimal and relatively uniform fungal biomass across conditions. While we cannot completely exclude indirect effects associated with pathogen presence, these results suggest that the observed gene expression changes are more likely attributable to the introduction of Tea Tree Oil (TTO) rather than to differences in pathogen load or disease progression. As outlined in the experimental design, our study was not intended to analyze TTO–pathogen interaction mechanisms. We have clarified in the manuscript that pathogen suppression or antifungal efficacy was not part of this work. Furthermore, as noted above, the assessment of Botrytis fungal load revealed very low levels, rendering these RNA-seq data unsuitable for analyzing TTO effects on the fungus. The study was instead designed to evaluate the plant transcriptional response to TTO exposure under realistic field conditions with low disease pressure, reflecting its potential role as a biostimulant or defense-priming agent rather than as a therapeutic antifungal treatment. Insufficient replication (n=3) limits statistical confidence Lack of validation leaves findings preliminary Acknowledge limitations explicitlyi.e insufficient replication, single timepoint, lack of functional validation. R:/ We thank the reviewer for these comments and respectfully note that RNA-seq–based gene expression analysis is now a mature and widely accepted technology that has largely complemented, and in many contexts replaced, traditional qPCR-based approaches for genome-wide expression profiling. RNA-seq is a well-established method for differential gene expression analysis, and multiple studies have shown that three biological replicates per condition generally represent the minimum sufficient replication to detect statistically robust differentially expressed genes (DEGs) when appropriate analytical methods are applied, especially when working with genetically homogenous organisms maintained under controlled crop conditions (Schurch et al., 2016; Conesa et al., 2016). In our study, we applied a stringent false discovery rate threshold (FDR < 0.05) to control for false positives, supporting the reliability of the observed transcriptional changes. While additional replication and functional validation would further strengthen the conclusions, the current data provide a robust overview, particularly for genes showing stronger regulatory changes, of the plant transcriptional response to TTO under realistic field conditions and constitute a valid basis for hypothesis generation and future targeted studies. Attachments Attachment Submitted filename: R1_Response_ReviewersPONE.docx https://doi.org/10.1371/journal.pone.0341809.r002
13 Jan 2026 Decision Letter - Indu Sharma, Editor <p>Insights into Tea Tree Oil-Mediated transcriptome modulation in Rosa hybrida PONE-D-25-51544R1 Dear Dr. Alzate, 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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact billing support . 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, Indu Sharma Academic Editor PLOS One Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0341809.r003
Formally Accepted
Acceptance Letter - Indu Sharma, Editor PONE-D-25-51544R1 PLOS One Dear Dr. Alzate, 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 You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days 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. You will receive an invoice from PLOS for your publication fee after your manuscript has reached the completed accept phase. If you receive an email requesting payment before acceptance or for any other service, this may be a phishing scheme. Learn how to identify phishing emails and protect your accounts at https://explore.plos.org/phishing. 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. Indu Sharma Academic Editor PLOS One https://doi.org/10.1371/journal.pone.0341809.r004

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 .