A new tandem repeat-based genotyping scheme for the global surveillance of Xanthomonas citri pv. mangiferaeindicae, an understudied bacterial pathogen of major importance to mango and cashew production

Karine Boyer; Cyrille Zombre; Laure Payan; Issa Wonni; Olivier Pruvost

doi:10.1371/journal.pone.0336768

Peer Review History

Original SubmissionApril 29, 2025
13 Aug 2025 Decision Letter - Baochuan Lin, Editor Xanthomonas citri pv. mangiferaeindicae Dear Dr. Pruvost, 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 27 2025 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 rebuttal 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'. 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Koebnik for their kind support (MLVAbank database). The European Union (ERDF contract GURDT I2016‐1731‐0006632 and DPP SantéBiodiv project), Conseil Régional de La Réunion and CIRAD provided financial support. The authors greatly acknowledge the Plant Protection Platform (3P, IBiSA). 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. 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[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: Yes Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: Yes Reviewer #2: 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 ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #2: Yes ******** Reviewer #1: Major comments� Xanthomonas citri pv. mangiferaeindicae (Xcm) is the causal agent of bacterial canker, also named bacterial black spot or angular spot, in some species of Anacardiaceae family. With the worldwide introduction and expanded cultivation of certain Anacardiaceae plants with significant economic value, bacterial canker disease has also been continuously spreading and worsening. However, compared to many other xanthomonad pathogens, Xcm has not received sufficient attention. Molecular typing is the basis for population genetics and tracing of the pathogens. The genetic structure of Xcm was primarily dissected by amplified fragment length polymorphism (AFLP), an old typing method with randomness and lacking of sequence information. The development of genomics has provided some new typing methods with more precise, faster, higher in resolution, and easier to operate. In this study, Boyer and her colleagues developed a new tandem repeat-based genotyping scheme targeting 16 TR markers in Xcm, and the MLVA-16 dataset was deposited in a dedicated online database. The MLVA-16 genotyping scheme was only slightly less discriminative than AFLP. Data derived from the two datasets were highly correlated, suggesting a fairly good resolution and phylogenetic signal. This study will further expand our understanding of the genetic diversity of Xcm, and will be helpful for disease diagnosis, early warning, and quarantine of this neglected bacterial pathogen with agricultural risks. The manuscript is well designed and written, and the content is suitable for publication in PLoS ONE. However, there are still some parts that are worth polishing and improving. Questions and suggestions: 1.Tandem repeats are found throughout the genomes, in which the number of repeat units can vary due to slipped-strand mispairing during DNA replication, leading to length polymorphisms. TR typing is manifesting as one kind of genetic fingerprinting of individual organism, indicating that the individual has specific TR markers. It is suggested to construct a pan-MLVA marker library (MLVAbank database) using several representative and high-quality sequenced Xcm strains other than one single Xcm strain. This additional task will not affect the original MLVA-16 genotyping scheme in the manuscript. 2.The manuscript is about the establishing an experimental method or scheme? which needs to have a clear logic and a well-defined technical route. It is recommended to add a technical route map or a research scheme map in the first part of Results. 3.There are only one table and two figures in the main text of this manuscript, seeming somewhat thin and lacking in information. It is better to add a genomic collinear diagram of several representative strains, along with each TR marker in certain genome. 4.Please also pay attentions to the typo errors, including misplaced space and punctuation marks, e.g., Line 30, misplaced space; Line 279, [24]]; Line 148, 2X, 2×; Line 149, 5X, 5×; Line 170, 10X, 10×. Reviewer #2: Thank you for submitting an interesting and useful study. This research highlights the relevance of using MVLA as a tool to study the population diversity of bacterial pathogens. I have some really minor comments: lines 69 and 70 Vietnam not Viet Nam line 78 should be Gram not gram as it is named affer a person Line 79 incomplete sentence, unlike most Xanthomonas species? Line 297 what Rhus species? ******** 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: Dr. Yong-Qiang He Reviewer #2: Yes: Teresa Coutinho ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/ . PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org https://doi.org/10.1371/journal.pone.0336768.r001
Revision 1
27 Sep 2025 Author Response Reviewer #1: Major comments� Xanthomonas citri pv. mangiferaeindicae (Xcm) is the causal agent of bacterial canker, also named bacterial black spot or angular spot, in some species of Anacardiaceae family. With the worldwide introduction and expanded cultivation of certain Anacardiaceae plants with significant economic value, bacterial canker disease has also been continuously spreading and worsening. However, compared to many other xanthomonad pathogens, Xcm has not received sufficient attention. Molecular typing is the basis for population genetics and tracing of the pathogens. The genetic structure of Xcm was primarily dissected by amplified fragment length polymorphism (AFLP), an old typing method with randomness and lacking of sequence information. The development of genomics has provided some new typing methods with more precise, faster, higher in resolution, and easier to operate. In this study, Boyer and her colleagues developed a new tandem repeat-based genotyping scheme targeting 16 TR markers in Xcm, and the MLVA-16 dataset was deposited in a dedicated online database. The MLVA-16 genotyping scheme was only slightly less discriminative than AFLP. Data derived from the two datasets were highly correlated, suggesting a fairly good resolution and phylogenetic signal. This study will further expand our understanding of the genetic diversity of Xcm, and will be helpful for disease diagnosis, early warning, and quarantine of this neglected bacterial pathogen with agricultural risks. The manuscript is well designed and written, and the content is suitable for publication in PLoS ONE. However, there are still some parts that are worth polishing and improving. We thank reviewer#1 for his/her kind comments. Questions and suggestions: 1.Tandem repeats are found throughout the genomes, in which the number of repeat units can vary due to slipped-strand mispairing during DNA replication, leading to length polymorphisms. TR typing is manifesting as one kind of genetic fingerprinting of individual organism, indicating that the individual has specific TR markers. It is suggested to construct a pan-MLVA marker library (MLVAbank database) using several representative and high-quality sequenced Xcm strains other than one single Xcm strain. This additional task will not affect the original MLVA-16 genotyping scheme in the manuscript. Indeed, this was partly achieved in the original submission, as MLVA data from the high-quality genome sequences were already included in the MLVAbank online database. We did not construct a new database in MLVAbank, as suggested, as we believe that it is of limited interest to the readership. Instead, we include in the revised version a table summarizing the total minisatellite content of each sequenced strain for reviewers’ appreciation (including the loci that were not selected for MLVA-16 typing), as determined by Tandem Repeat Finder and the filtering criteria we used. If the editor feels that it is of sufficient interest, it may be included as a supplementary table in the published version of our manuscript. 2.The manuscript is about the establishing an experimental method or scheme? which needs to have a clear logic and a well-defined technical route. It is recommended to add a technical route map or a research scheme map in the first part of Results. In our opinion, the input of the present study is more providing a new genotyping scheme rather than providing an experimental method, as our analytical procedure was really standard, and is highly similar to the one used previously in many molecular epidemiological studies of human, animal or plant bacterial pathogens. Nevertheless, we followed reviewer #1’s recommendation and included at the beginning of the Results section a short paragraph summarizing our technical route. 3.There are only one table and two figures in the main text of this manuscript, seeming somewhat thin and lacking in information. It is better to add a genomic collinear diagram of several representative strains, along with each TR marker in certain genome. A new Fig. 1 was produced as requested. 4.Please also pay attentions to the typo errors, including misplaced space and punctuation marks, e.g., Line 30, misplaced space; Line 279, [24]]; Line 148, 2X, 2×; Line 149, 5X, 5×; Line 170, 10X, 10×. Modified as requested. Reviewer #2: Thank you for submitting an interesting and useful study. This research highlights the relevance of using MVLA as a tool to study the population diversity of bacterial pathogens. I have some really minor comments: lines 69 and 70 Vietnam not Viet Nam line 78 should be Gram not gram as it is named affer a person Line 79 incomplete sentence, unlike most Xanthomonas species? Line 297 what Rhus species? All editorial suggestions placed by reviewer #2 were included in the revised version. The vernacular name of Searsia longipes remains the large-leaved rhus, although its genus name was modified from Rhus to Searsia in 2007 and further validated in Catalog of Life. Attachments Attachment Submitted filename: reviews.docx https://doi.org/10.1371/journal.pone.0336768.r002
30 Oct 2025 Decision Letter - Baochuan Lin, Editor A new tandem repeat-based genotyping scheme for the global surveillance of Xanthomonas citri pv. mangiferaeindicae, an understudied bacterial pathogen of major importance to mango and cashew production PONE-D-25-23106R1 Dear Dr. Pruvost, 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, Baochuan Lin, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author Reviewer #2: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions??> Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #2: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #2: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #2: Yes ****** Reviewer #2: Well written and experimental sound manuscript on an understudied bacterial pathogen. Just out of interest, Xcm was the topic of a DSc thesis in the early 1900s by Ethel M Doidge, a South African plant pathologist and the first woman to receive a doctorate in SA. She later went on to become a leading fungal taxonomist. ****** 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 #2: Yes: Teresa Ann Coutinho ******** https://doi.org/10.1371/journal.pone.0336768.r003
Formally Accepted
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