Peer Review History
| Original SubmissionOctober 29, 2025 |
|---|
|
Dear Dr. Vaghefi, 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 08 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.
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. As the corresponding author, your ORCID iD is verified in the submission system and will appear in the published article. PLOS supports the use of ORCID, and we encourage all coauthors to register for an ORCID iD and use it as well. Please encourage your coauthors to verify their ORCID iD within the submission system before final acceptance, as unverified ORCID iDs will not appear in the published article. Only the individual author can complete the verification step; PLOS staff cannot verify ORCID iDs on behalf of authors. We look forward to receiving your revised manuscript. Kind regards, Karthikeyan Thiyagarajan, PhD 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 stating the following in the Acknowledgments Section of your manuscript: [This research was supported by the University of Melbourne Scholarship and Botanical Resources Australia Pty Ltd. Thanks to Camilla Langlands-Perry for her support during the transformation processes.] We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: [The authors received no specific funding for this work.] Additionally, because some of your funding information pertains to [commercial funding//patents], we ask you to provide an updated Competing Interests statement, declaring all sources of commercial funding. In your Competing Interests statement, please confirm that your commercial funding does not alter your adherence to PLOS ONE Editorial policies and criteria by including the following statement: ""This does not alter our adherence to PLOS ONE policies on sharing data and materials.” as detailed online in our guide for authors http://journals.plos.org/plosone/s/competing-interests. If this statement is not true and your adherence to PLOS policies on sharing data and materials is altered, please explain how. Please include the updated Competing Interests Statement and Funding Statement in your cover letter. We will change the online submission form on your behalf. 3. When completing the data availability statement of the submission form, you indicated that you will make your data available on acceptance. We strongly recommend all authors decide on a data sharing plan before acceptance, as the process can be lengthy and hold up publication timelines. Please note that, though access restrictions are acceptable now, your entire data will need to be made freely accessible if your manuscript is accepted for publication. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If you are unable to adhere to our open data policy, please kindly revise your statement to explain your reasoning and we will seek the editor's input on an exemption. Please be assured that, once you have provided your new statement, the assessment of your exemption will not hold up the peer review process. 4. Please ensure that you include a title page within your main document. You should list the complete name of all authors and all affiliations as per our author instructions and clearly indicate the corresponding author. 5. 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. 6. 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. Additional Editor Comments: Dear Authors, I appreciate your work concerning the Agrobacterium tumefaciens-mediated transformation of two fungal strains with fluorescent protein-encoding genes to elucidate the response on the host. Tanacetum cinerariifolium (pyrethrum) through molecular visualization. Are these fluorescently labeled strains of both D. tanaceti and S. tanaceti natural isolates or registered fungal accessions? Are these transformed strains co-infection shows same virulency as that of wild stains and whether can be used using cryopreservatives and cryoproectants for long term? I have additional suggestions and comments: Please mention the species like this Tanacetum cinerariifolium (Trevis.) Sch.Bip. when you introduce first time in the beginning of the text. Which type of a Agrobacterium tumefaciens strain was used for transformation? in some places the genus species Stagonosporopsis tanaceti was not italicized? Please italicize it. What about the host specificity of these genetically modified strains or wild strains? Are there any naturally resistant lines of Tanacetum cinerariifolium, or does any study show the natural resistance found against any of these fungal pathogens? After sequencing the strains and confirming the T DNA using BLASTN, have you tried to find out the number of integrated copies of the T DNA? If so, how many copies of the T-DNA were found? What kinds of genes were predicted using AUGUSTUS with the Botrytis cinerea reference? Have you predicted the fluorescent-related proteins alone or any more candidate genes and their proteins? If so, could you please list them as a table with candidate gene IDs? In the method section, the Detached Leaves Assay—D. tanaceti transformed strains analysis and the Detached Leaves Assay—S. tanaceti transformed strains analysis. almost follows the same type of analysis; could you please combine them to make it precise? You have mentioned, "Microscopically, no apparent differences in fluorescence intensity were observed among the four S. tanaceti transformant strains." In contrast, slight variations were noted among D. tanaceti transformant strains." Any in planta transformed plant tissues represent the transformation of both these fungi, because you have mentioned co-infection of transformed D. tanaceti and S. tanaceti? Is there any difference between wild and transformed types of fungus in their activity and infection on the host tissues? Please address the comments of reviewers and mine and revise the manuscript very precisely. One of the reviewers has rejected your manuscript; however, based on the revisions and responses, your manuscript may be considered further. 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: Yes Reviewer #2: Partly Reviewer #3: Yes Reviewer #4: Partly Reviewer #5: Yes Reviewer #6: No Reviewer #7: Yes Reviewer #8: Yes Reviewer #9: Partly Reviewer #10: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes Reviewer #4: No Reviewer #5: Yes Reviewer #6: Yes Reviewer #7: Yes Reviewer #8: Yes Reviewer #9: Yes Reviewer #10: Yes ********** 3. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes Reviewer #4: Yes Reviewer #5: Yes Reviewer #6: No Reviewer #7: Yes Reviewer #8: Yes Reviewer #9: Yes Reviewer #10: Yes ********** 4. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes Reviewer #4: Yes Reviewer #5: Yes Reviewer #6: Yes Reviewer #7: Yes Reviewer #8: Yes Reviewer #9: Yes Reviewer #10: Yes ********** Reviewer #1: The following points detail the major concerns and necessary revisions for the manuscript. Addressing these issues is essential for validating the scientific rigor and clarity of the study. 1. Pathogen biomass and colonization dynamics should be validated using more precise techniques such as quantitative PCR (qPCR) or RT-qPCR. This is crucial to provide a definitive quantification of fungal load that complements the qualitative fluorescence data. 2. The authors should use clearer, high-contrast arrows (e.g., bright white or yellow) to ensure visibility against the background. Furthermore, the figure legends must be expanded to provide more descriptive explanations of these markers. 3. Since natural plant autofluorescence can often overlap or be confused with signals from fluorescent proteins, providing these controls is vital to confirm the specificity and accuracy of the pathogen signals. 4. There is a discrepancy in the captioning of Figure 7. While both panels A and B are presented in the figure, the sub-caption/legend only provides an explanation for panel A. 5. For the sake of clarity and scientific consistency, the authors must adopt a single unit of measurement throughout the manuscript. Please, standardize all time points to either HAI or DAI. both "Days After Inoculation" (DAI) and "Hours After Inoculation" (HAI) are used interchangeably (e.g., 24, 48, and 72 hours vs. 1, 2, and 3 days). Reviewer #2: Dear editor, This manuscript presents technically valuable work demonstrating the successful fluorescent transformation of Didymella tanaceti and Stagonosporopsis tanaceti and their visualization within leaf tissues of Tanacetum cinerariifolium. The development of stable fluorescent transformants is an important methodological contribution. However, the current manuscript specially title and abstract overemphasize “pathogen interactions.” The study does not experimentally assess biological interactions between the two fungi beyond demonstrating their simultaneous presence in leaf tissues. In addition, disease biology and infection processes are only partially examined. Therefore, I recommend revising the title, abstract, and discussion to better reflect the main contribution of the study—namely, the successful transformation and in planta tracking of these pathogens—rather than implying that pathogen biology and interactions were elucidated. Minor Comments • Line 74: Revise “isolate UOM ST2 were” to “isolate UOM ST2 was”. • Line 90: Add a comma before “respectively.” • Line 97: Write Agrobacterium in italic format; keep the remaining words in regular font. • Lines 108–111: Please rewrite the sentence for clarity. • Line 128: Write the full genus name at the beginning of the sentence. • Lines 214 and 235: Remove the full stop at the end of the sentence. • Lines 217 and 238: Use either “60%” or “60 percent,” not both. • Line 246: Write the full genus name at the beginning of the sentence. Overall, the study is methodologically sound, but the framing should be aligned more closely with the actual scope and findings. Best regards. Reviewer #3: In general the manuscript was well written and the authors did a credible job in accomplishing their goal and I believe the results will be of interest to the readers. However there are some revisions required. Although details of methodology must be included but if the same procedure was repeated again and again it became cumbersome. Would it be possible to rephrase it as just for instance "as previously described "? On the other hand other details should be included. Why some plates were sealed whereas others were unsealed? What determined when the cultures were incubated in light, user darkness or under light/dark 12 hours duration. I have problem with the measurement of colony diameter. It was stated that it was measured along the same line but where? I assume it was through the center of the plate. Normally, measurements are done along two straight lines perpendicular to each other through the center of the plate to account for any irregularities in the colony outline. However. If the colonies were perfectly smooth and round I suppose one line should be sufficient. Reviewer #4: Comment1 The manuscript « Elucidating pathogen interactions in Tanacetum cinerariifolium (pyrethrum) using fluorescently labelled Didymella tanaceti and Stagonosporopsis tanaceti» describes the creation of fluorescently tagged Didymella tanaceti and Stagonosporopsis tanaceti strains for pyrethrum infection studies. While the technological success of producing these tagged pathogens is impressive, the work has numerous important methodological flaws that restrict its usefulness to plant pathology research. Comment 2 This paper has a mismatch between its declared aims and actual findings. The title presented insights into pathogen interactions in plants, however the data show only co-localization and no evidence of biological interactions, such as competitive assays, antagonistic effects, or quantitative interference analysis (evidence of competitive, synergistic, or antagonistic effects). The work evolved into a techniques validation publication (70% concentrate on transformation protocols) rather than a biological exploration of the two pathogens interaction. I recommend either: 1. Replace the current title with one that accurately reflects the study's main results. 2. Retain the current title but add essential experiments to substantiate the claimed pathogen interactions. A competitive fitness assays comparing single vs. co-infection scenarios with quantitative disease severity measurements is recommended. A resource competition experiments measuring nutrient depletion effects when pathogens occupy the same tissue as well as plant defense response comparisons between single and co-infections using gene expression analysis, must be added. Comment 3 I have several reservations about the organization of the manuscript. Some findings were hidden in the discussion section: Lines 558-567 (epidermal penetration), 570-581 (infection intervals), 583-596 (co-infection observations), and 598-618 (autofluorescence characterisation) include primary data that should be in findings rather than discussion. The discussion section is long and should be reduced or shifted to additional material, particularly thorough technical validation details that do not increase biological knowledge. Comment 4 The manuscript has certain key methodological deficiencies: In terms of statistical analysis and experimental design, Line 155 lacks software specifications, alpha values, and ANOVA assumption testing. Because of the small sample numbers used in detached leaf tests, power analysis must be justified. The paper does not give any information on the replication structure (Biological and technical replicates). Furthermore, the detached leaf test technique is insufficient to validate biological equivalency due to the absence of quantitative disease severity score and no entire plant validation beyond detached leaves especially in the context of pathogens interaction in-planta. Comment 5 There are various limits to genome analysis. The assembly quality measures are lacking, as they lack N50 values and contig counts. If feasible, I would consider comparing the BUSCO data to other Didymellaceae genomes. Genome statistics (lines 322-329) should be tabulated rather than included in the text. Comment 6 Figure 7 does not appropriately display the co-infection data since it only shows microscopic cross-sections without the necessary macroscopic context. The figure should include full leaf pictures (e.g., Figs. 5 and 6) that demonstrate lesion progression, and sampling points where sections were collected. Without this context, we cannot determine if co-infection has synergistic, antagonistic, or additive disease consequences, or how pathogen colonization patterns relate to symptom expression. Comment 7 Given the experimental methodology, the result on direct epidermal penetration (line 558) seems dubious. Within hours, detached leaves lose their stomatal function, which may make epidermal penetration the only viable route. To confirm biological results about natural infection methods, this methodological bias has to be validated using intact plants and functioning stomata. Comment 8 Instead of presenting incomplete interaction studies, this study would be greatly boosted if it were repositioned as the basis for future biological research. Expand the biological characterization with these verified techniques and transfer comprehensive transformation methods to supplemental material. Although the fluorescent strains are useful research tools, they require significant refinement in their biological application before they can be published. Reviewer #5: The article is thorough, well-organized, and clearly presents data on transformation efficiency, fluorescence validation, morphological assessment, molecular characterization, and pathogenicity comparisons. The incorporation of microscopy, quantitative fluorescence analysis (CTCF), genome assembly statistics, BUSCO completeness assessments, and T-DNA insertion mapping effectively supports the study's findings. Nonetheless, certain areas would benefit from clarification, consistency corrections, grammatical improvements, and enhanced data presentation to further strengthen scientific clarity and readability. • Confidence intervals or error bars (SD/SE) should be specified in figure legends. • The p-value range reported for D. tanaceti (p = 0.02 – 0.0002) is unclear. Exact p-values should be reported for each comparison. • You mentioned that 15 ROIs per transformant, need to include the number of biological replicates • Some paragraphs are overly detailed, particularly: T-DNA rearrangements discussion, autofluorescence explanation and literature comparisons. • Improve explanation of findings and discussion • Include proper units and legends • Condense repetitive statements and tighten literature comparison sections. • Briefly reinforce statistical validation if performed. Reviewer #6: The authors wrote this manuscript well for their construction of fluorescent fungal pathogens of pyrethrum and the preliminary observation of the fluorescent images of the derived transformants in planta including single or co-inoculation. The procedures for the construction of fluorescent strains are described in detail and really attain the goal. If the quality of the image can be improved, that will be better or explain the present image quality. Elucidating pathogen interactions in planta by using the resulting fluorescent strains requires more experiments to show their interactions. Symptom caused by co-inoculation of these two fungi was not shown, whether they succeed in causing lesion and the extent of infection were not shown in this study. Line 30: Specify "knowledge gap exists regarding the infection biology of D. tanaceti" in pyrethrum. Line 75: single spore isolation. Lines 129-130: note the reason for using hyphae-tip isolation instead of single spore isolation for S. tanaceti. Line 148: ROI (w=1.96, h=1.96) in hyphae sections. Note that the ROI stand for. Lines 225-234: need rewording for clearer description. Line 256: using Fiji? Omit figure legends in the results section. Line 481: UOM DT5 also has partial T-DNA insertion. This strain has single T-DNA insertion. So, make sure the description is correct or restate the situation. Fig. 6: wrong pictures on (C) and (D), suppose to be exchanged. Reviewer #7: The manuscript is experimentally properly designed. The research is organized straightforwardly to investigate the transformed strains with respect to pathogenicity, morphology, and fluorescence emission. The manuscript is well written, and the statistical analyses meet the purpose of the research. Reviewer #8: The study describes an useful tool/technique to study the fungal pathogens (fungal pathogens Didymella tanaceti and Stagonosporopsis tanaceti) infection of the host Pyrethrum (Tanacetum cinerariifolium) which is an economically important crop for its use as in insecticides. Using the Agrobacterium mediated transformation of these fungi the authors have generated fluorescent label strains that can help gain better insights into the infection process. However, it would have been more convincing to see the gene expression analysis of the genes affected by/flanking the insertions as a result of the T-DNA insertion. Also the results have 3-4% genes missing from analysis. T-DNA transformations can also lead to integration and excision of the T-DNA from sites if it is not stable. In which case it may also cause disruption at these sites which may be regulatory or coding regions. In that light it is not too convincing to have >200 genes missing from the sequencing data analysis. There are minor formatting errors, missed informations, and formatting incongruity in the references and figure legends that can be easily taken care of. My detailed comments are attached with the pdf file of the review manuscripts. At this point I would like the authors to address those concerns and resubmit. Reviewer #9: Dear Authors, This manuscript presents a technically valuable output by developing fluorescently labelled strains of Didymella tanaceti and Stagonosporopsis tanaceti. The successful transformation and characterisation of these strains represent a methodological advance that will benefit the pyrethrum community. However, the manuscript has some major issues regarding the experimental design, data interpretation, and scientific writing that require revision before it meets the requirements for publication. The comment are list in the attached files Reviewer #10: The study is technically sound, well designed, and addresses an important gap in understanding the biology of these pathogens. The combination of Agrobacterium-mediated transformation and whole-genome sequencing to confirm T-DNA insertion sites is a strong aspect of the work. The data support the conclusions and the manuscript is clearly written and logically organized. The microscopy, CTCF quantification, and molecular characterization are well presented, and the infection and co-infection assays provide useful insights into colonisation patterns. I recommend acceptance after minor revision. A few points stated in the attached file could be clarified. Overall, this is a solid and useful contribution to fungal plant pathology, and the fluorescent strains generated here will be valuable tools for future studies. ********** 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: Büşra ALBAYRAK TURGUT Reviewer #2: Yes: Leila Ebrahimi Reviewer #3: No Reviewer #4: Yes: Manel Chaouachi Reviewer #5: No Reviewer #6: No Reviewer #7: Yes: Loukas Kanetis Reviewer #8: No Reviewer #9: No Reviewer #10: 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.
|
| Revision 1 |
|
Dear Dr. Carrillo Portillo 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 Jul 20 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.
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. As the corresponding author, your ORCID iD is verified in the submission system and will appear in the published article. PLOS supports the use of ORCID, and we encourage all coauthors to register for an ORCID iD and use it as well. Please encourage your coauthors to verify their ORCID iD within the submission system before final acceptance, as unverified ORCID iDs will not appear in the published article. Only the individual author can complete the verification step; PLOS staff cannot verify ORCID iDs on behalf of authors. We look forward to receiving your revised manuscript. Kind regards, Karthikeyan Thiyagarajan, PhD Academic Editor PLOS One Journal Requirements: 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. 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. Additional Editor Comments: Dear Authors, I appreciate your revisions and responses; however, there is a need for a minor revision. There are some typos; please check the standard convention for "in planta." Please check the reviewers' comments, respond to them, and revise the manuscript accordingly. Reviewers' comments: Reviewer's Responses to Questions Comments to the Author Reviewer #1: All comments have been addressed Reviewer #3: (No Response) Reviewer #4: All comments have been addressed Reviewer #6: All comments have been addressed ********** 2. Is the manuscript technically sound, and do the data support the conclusions??> Reviewer #1: Yes Reviewer #3: Yes Reviewer #4: Yes Reviewer #6: Partly ********** 3. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: Yes Reviewer #3: Yes Reviewer #4: Yes Reviewer #6: No ********** 4. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #1: Yes Reviewer #3: Yes Reviewer #4: Yes Reviewer #6: No ********** 5. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #3: Yes Reviewer #4: Yes Reviewer #6: No ********** Reviewer #1: I have reviewed the revised manuscript. The author has addressed most of the corrections I suggested, and the manuscript has improved significantly. I recommend that the manuscript be accepted this version. Reviewer #3: In general the manuscript was written prepared and presented. Here are some comments. Line 18 insert a period after losses and start a new sentence with However. Line 60 Insert a period after tissues and start a new sentence with However. Line 100 what was the pore size of the millipore? Express HAI first as Hours after infection. Why were the cultures sometimes incubated under light and sometimes under light/darkness. Line 185 How many plates were measured to get the average colony diameter. Line 502 Appropriate reference should be cited here. You wondered if the pathogen could enter through the stomata did you try to infect the leaves on the lower epidermis where most stomata are located? Reviewer #4: All comments raised by the reviewers have been carefully considered by the authors, and the corresponding corrections and revisions have been fully implemented. Reviewer #6: 1. The quality of figure 2 is quite poor. The resolution should be improved, also check the format required for formal publication. Line 163-166, add the fluorescence quantification method and the information of dichroic filters. The emission filters are long-pass or band-pass ones? 2. Lines 336-339. Why was spore size measurement only for D. tanaceti but not for S. tanaceti? It should be determined if there is statistical difference in spore size between wild-type and transformed strains. Besides, the sporulation speed and amount between wild-type and transformed strains are better to be compared since they often affect fungal virulence. 3. Since the transformed strains are intended to be used in pathological study, the comparable virulence of wild-type and transformed strained strains on hosts is required. The analysis in fungal biomass and plant lesion developments would help. 4. Lacking the medium formulas used in transformant construction. Line 126, Liquid cultures of Agrobacterium strain EHA105 “in LB broth. Add LB medium formula. Line 129, Add the formula of induction medium. ********** 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: Büşra ALBAYRAK TURGUT Reviewer #3: No Reviewer #4: No Reviewer #6: 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. |
| Revision 2 |
|
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 Sep 03 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.
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. As the corresponding author, your ORCID iD is verified in the submission system and will appear in the published article. PLOS supports the use of ORCID, and we encourage all coauthors to register for an ORCID iD and use it as well. Please encourage your coauthors to verify their ORCID iD within the submission system before final acceptance, as unverified ORCID iDs will not appear in the published article. Only the individual author can complete the verification step; PLOS staff cannot verify ORCID iDs on behalf of authors. We look forward to receiving your revised manuscript. Kind regards, Karthikeyan Thiyagarajan, PhD Academic Editor PLOS One Journal Requirements: 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. 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. Additional Editor Comments: Dear Authors, I appreciate your revision and responses, however I suggest to do some minor corrections: Transformant UOMSTC1R2 is mentioned in two ways: UOM STC1R2 and UOMSTC1R2. Please mention the correct one. You have used the k-mer counting software Jellyfish v.2.3.1, and you have also mentioned the following: The estimated genome size for D. tanaceti isolates was 40.7 Mbp using Jellyfish. Here 'Jellyfish' means the software, doesn't it? So, please mention the software with an appropriate version throughout the manuscript. Also in the introduction you have mentioned the following: The green fluorescent protein (GFP), derived from the Aequorea victoria jellyfish, is a highly stable reporter capable of resisting temperatures over 60°C, low pH and proteases. This statement indicates that GFP is derived from jellyfish. Please clearly mention the software and its version, ensuring that it is distinctly different from the GFP derived from jellyfish. Kind regards, Karthikeyan Thiyagarajan PhD Academic Editor, PLOS ONE. ********** [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. |
| Revision 3 |
|
Agrobacterium tumefaciens-mediated transformation and T-DNA insertion characterisation of Didymella tanaceti and Stagonosporopsis tanaceti for infection visualisation in pyrethrum PONE-D-25-58448R3 Dear Dr. Portillo, 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, Karthikeyan Thiyagarajan, PhD Academic Editor PLOS One Additional Editor Comments: Dear Authors, After careful scientific evaluations with peer reviews, I am pleased to confirm the manuscript entitled "Agrobacterium tumefaciens-mediated transformation and T-DNA insertion characterisation of Didymella tanaceti and Stagonosporopsis tanaceti for infection visualisation in pyrethrum" has been accepted for publication in PLOS ONE. Kind regards, Karthikeyan Thiyagarajan PhD Academic Editor, PLOS ONE. Reviewers' comments: |
| Formally Accepted |
|
PONE-D-25-58448R3 PLOS One Dear Dr. Carrillo Portillo, 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. Karthikeyan Thiyagarajan 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 .