Omics based approaches to decipher the leaf ionome and transcriptome changes in Solanum lycopersicum L. upon Tomato Brown Rugose Fruit Virus (ToBRFV) infection

Aditi Padmakar Thakare; Maria Cristina Della Lucia; Chandana Mulagala; Giovanni Bertoldo; Massimo Cagnin; Piergiorgio Stevanato

doi:10.1371/journal.pone.0313335

Peer Review History

Original SubmissionJuly 8, 2024
7 Aug 2024 Decision Letter - Mojtaba Kordrostami, Editor PONE-D-24-28075Omics based approaches to decipher the leaf ionome and transcriptome changes in Solanum lycopersicum L. crop upon Tomato Brown Rugose Fruit Virus (ToBRFV) infectionPLOS ONE Dear Dr. Stevanato, 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 21 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. 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(Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The manuscript "Omics based approaches to decipher the leaf ionome and transcriptome changes in Solanum lycopersicum L. crop upon Tomato Brown Rugose Fruit Virus (ToBRFV)" where author employed omics-based approaches like leaf ionomics and transcriptomics to decipher the interaction between elemental and nutritional composition and investigated gene expression profile upon the ToBRFV infection in tomatoes. The experiment for transcriptomic data in the manuscript is not well planned. The experimental plant materials are not described. What are the resistant and susceptible cultivars has been used in the study. The introduction is not nicely written and many recent and relevant references for ToBRFV resistance are missing. It is not clear that what plant material has been used for transcriptomic experiment, resistant and susceptible lines or control and infected plants. Line'129': reference is missing for the involvement of these LRR (Solyc02g071860.4.1, Solyc01g111890.3.1) genes in defense response against pathogen recognition. Supplementary data for differential expressed genes with TPM value and annotation is missing. Line '141-151': Not enough data has been provided to support the claim. The author has not provided qPCR data for virus detection. Reviewer #2: The manuscript describes a technically sound piece of scientific research with data that supports the conclusions. Experiments have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions has been drawn appropriately based on the data presented. However, in title technical name of crop should be avoided. Just write tomato inplace of Solanum lycopersicum L. Normally Materials and Methods should appear after Introduction, but here you are mentioning it after Conclusion. Why? Add comma(,) in line 267 after 3'. ****** 6. 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Revision 1
18 Sep 2024 Author Response Thank you for offering us an opportunity to respond to reviewer’s comments. We tried to answer every reviewer's comments independently and to the best of our ability we have addressed all the concerns and have made all necessary changes to the manuscript, which are tracked. We are thankful to the reviewers for such a thorough review, which has been both educational and improved the quality of the manuscript. Sincerely, Piergiorgio Stevanato Journal guidelines and comments that are now revised : ● Manuscript meets the PLOS ONE’s style requirements. ● The funding section has been removed from the manuscript, and has been mentioned only in the online submission form. ● Role of the funders have been disclosed in the online submission form. ● Captions for the ‘Supporting Information’ has been added at the end of the manuscript. Reviewer #1: Q1 :The manuscript "Omics based approaches to decipher the leaf ionome and transcriptome changes in Solanum lycopersicum L. crop upon Tomato Brown Rugose Fruit Virus (ToBRFV)" where author employed omics-based approaches like leaf ionomics and transcriptomics to decipher the interaction between elemental and nutritional composition and investigated gene expression profile upon the ToBRFV infection in tomatoes. The experiment for transcriptomic data in the manuscript is not well planned. The experimental plant materials are not described. What are the resistant and susceptible cultivars has been used in the study ? It is not clear that what plant material has been used for transcriptomic experiment, resistant and susceptible lines or control and infected plants. A1 :We thank the reviewer for this thorough revision and suggestion. The plant material used in this study belongs to a collection of the DAFNAE at the University of Padova, and were grown according to the agricultural and cultivation practice of tomato breeding in Sicily. We used the San Marzano variety of tomatoes that were infected with endemic ToBRFV to monitor changes. Subsequently, 6 control & 8 infected phenotypes of the San Marzano plants were subjected to mRNA sequencing to study differential gene expression patterns. We also evaluated germplasm of 12 lines of tomato with varied genetic backgrounds and different types like (“ciliegino”, “datterino”, and “tondo liscio”) which were grown and exposed to natural infection towards ToBRFV. The resistant & susceptible phenotypic status was assigned to the individual plant material based on the Ct values after performing qPCR. Five of these plants (3 resistant & 2 susceptible) were then subjected to mRNA sequencing, and analysed for variant analysis along with San Marzano samples. The reason to not include the above-mentioned five plants in the differential gene expression analysis, but only in variant analysis is due to the difference in library preparation, sequencing depth and smaller sample size. We have added a note regarding the plant materials in the updated Figure 6, and have also rephrased the sentences in the ‘Selection of plant material and sampling’ section of Materials and Methods. Q2 : The introduction is not nicely written and many recent and relevant references for ToBRFV resistance are missing. A2 : We have now added more parts to the introduction section. The added sections emphasize on the recent findings done by (i) Wang et.al (https://www.mdpi.com/1422-0067/25/7/4012) on tomato plant response to ToBRFV infection; (ii) the role of ionomics in understanding plant nutrition dynamics, and (iii) pathways involved in plant immunity and defence responses. All these additions are highlighted as tracked changes. Q3 : Line'129': reference is missing for the involvement of these LRR (Solyc02g071860.4.1, Solyc01g111890.3.1) genes in defence response against pathogen recognition. A3 : We have added the reference of Padmanabhan et. al, (https://onlinelibrary.wiley.com/doi/10.1111/j.1462-5822.2008.01260.x). The line numbers will be changed in both the tracked (line no. 147) & clean untracked version (line no. 215) of the manuscript. Q4 : Supplementary data for differential expressed genes with TPM value and annotation is missing. A4 : The data for the TPM values is now provided in Supplementary Table 5. Q5 : Line '141-151': Not enough data has been provided to support the claim. A5 : These mutations were obtained using variant analysis performed by 'bcftools' suite & annotated using 'SnpEff'. The details of the SNP position, amino acid change, mutation type etc. are provided in the supplementary table 2. Q6 : The author has not provided qPCR data for virus detection. A6 : The Ct values for the qPCR performed on all the leaf samples is now provided in supplementary table 4. Reviewer #2: The manuscript describes a technically sound piece of scientific research with data that supports the conclusions. Experiments have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions has been drawn appropriately based on the data presented. Q7 : However, the technical name of the crop should be avoided. Just write tomato in place of Solanum lycopersicum L. A7 : We thank the reviewer for this suggestion. We have now removed the word “crop” from the title. To avoid using the word "tomato" repeatedly next to each other, all the authors would like to retain the name 'Solanum lycopersicum L.' in the title. Q8 : Normally Materials and Methods should appear after Introduction, but here you are mentioning it after Conclusion. Why? A8 : We apologise for misunderstanding the structure. We have now adhered to the PLOS guidelines for the manuscript organisation in the clean, untracked version of the manuscript titled 'Manuscript_Untracked17Sept2024'. Q9 : Add comma(,) in line 267 after 3'. A9 : We have added the “,” after 3’. The line number will be changed in the revised version (line no. 299) and in the clean untracked version (line no. 147) of the manuscripts. Attachments Attachment Submitted filename: ResponseToReviewers.pdf https://doi.org/10.1371/journal.pone.0313335.r002
23 Oct 2024 Decision Letter - Mojtaba Kordrostami, Editor Omics based approaches to decipher the leaf ionome and transcriptome changes in Solanum lycopersicum L. upon Tomato Brown Rugose Fruit Virus (ToBRFV) infection PONE-D-24-28075R1 Dear Dr. Stevanato, 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. If you have any questions relating to publication charges, 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, Mojtaba Kordrostami, Ph.D. 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 #3: (No Response) ******** 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 #3: (No Response) ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #3: (No Response) ****** 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 #3: (No Response) ****** 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 #3: (No Response) ****** 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 #3: The authors have implemented the desired changes to a satisfactory degree, and the responses they have received are deemed appropriate. ****** 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 #3: No ******** https://doi.org/10.1371/journal.pone.0313335.r003
Formally Accepted
29 Oct 2024 Acceptance Letter - Mojtaba Kordrostami, Editor PONE-D-24-28075R1 PLOS ONE Dear Dr. Stevanato, 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. Mojtaba Kordrostami Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0313335.r004

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