Phylogenetic investigation and mitochondrial genome description of ten species in nine genera of Cicadellinae from China (Hemiptera: Cicadellidae)

Likun Zhong; Yan Jiang; Xiaofei Yu; Bin Yan; Renhuai Dai; Maofa Yang

doi:10.1371/journal.pone.0329906

Peer Review History

Original SubmissionMarch 15, 2024
7 May 2024 Decision Letter - James Crainey, Editor Dear Dr. Yang, 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 Jun 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. 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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We look forward to receiving your revised manuscript. Kind regards, James Lee Crainey, Ph.D. 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. We noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed: 10.7717/peerj.14026 In your revision ensure you cite all your sources (including your own works), and quote or rephrase any duplicated text outside the methods section. Further consideration is dependent on these concerns being addressed. 3. 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To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager. Please see the following video for instructions on linking an ORCID iD to your Editorial Manager account: https://www.youtube.com/watch?v=_xcclfuvtxQ 5. We notice that your supplementary figures are uploaded with the file type 'Figure'. Please amend the file type to 'Supporting Information'. Please ensure that each Supporting Information file has a legend listed in the manuscript after the references list. 6. 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: Yes Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: N/A Reviewer #2: N/A ****** 3. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #1: No 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: The manuscript entitled "Phylogenetic investigation and mitochondrial genome description of ten species in nine genera of Cicadellinae from China (Hemiptera: Cicadellidae) " reports the sequencing, assembly, annotation, and phylogenetic analysis of ten mitochondrial genomes from nine genera of Cicadellinae. This work provides a valuable genetic resource for this subfamily. Key results include the identification of gene features across different species, variations in transfer and ribosomal RNA genes, and insights regarding the phylogeny within the Cicadellinae subfamily. Overall, the MS demonstrates a scientifically sound approach to studying the mitochondrial genomes and phylogenetic relationships of Cicadellinae species. The methodology applied to assemble and analyze the genomes was well described. However, there are some issues regarding methods and discussion, as commented below. 1. The authors may provide a supplementary table with summary statistics of the sequenced species, for example, number of sequenced raw reads, number of clean reads, number of reads used to assemble the mitochondrial genomes, mapping information, such as coverage and depth of the assembled genomes. 2. The raw reads must be deposited to a public repository (for example, SRA) and made available. 3. There is limited explanation of the methodology used for phylogenetic analyses. On Materials and Methods, section 2.3 Phylogenetic analyses, the authors stated that “the best partitioning scheme and evolutionary models for 13 predefined partitions were selected using PartitionFinder2”, however the IQ-TREE (ML analysis) was used on ‘Auto’ mode for model selection. If IQ-TREE automatically selected the model, it is unclear why the best partition scheme and model were selected with PartitionFinder2? 4. The authors claimed that all ten species of Cicadellinae had their whole mitochondrial genomes assembled, however on Fig. 2 there is no annotation of ‘Control Region’ for two species (Anagonalia emeiesis and Seasogonia rosea). Please correct the figure or provide clarification on the annotation process. 5. The authors stated at the introduction that the “leafhoppers are effective vectors of plant pathogens such as phytoplasmas, as well as other bacteria and viruses that cause illness in a variety of plants”. The MS lacks detailed discussion on the implications of the findings for broader evolutionary and ecological contexts. In the conclusion section, there is a lot of repeated information from the results. Minor: • The authors should improve figure captions with more detailed information about the figures themselves and methods employed to generate them. For example, what represents the inner circles of Fig. 1? • The authors should revise the language. For example, “topological topologies”. Reviewer #2: The results presented in this work are robust and well-described. However, to ensure the reproducibility of the study, it is crucial to include detailed information about the library preparation kits and sequencing method used, as well as the sequencing depth (number of sequenced reads) for each sample. I recommend that this information be provided as supplementary material, which will significantly enhance the contribution of your article to the scientific community. ****** 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: Daniel A. Moreira Reviewer #2: 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.] 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.0329906.r001
Revision 1
23 Jan 2025 Author Response Dear Reviewer, Greetings from all authors! We express our gratitude for your meticulous perusal, helpful comments, and constructive suggestions, which have substantially enhanced the exposition of our manuscript. We have carefully considered all comments and revised our manuscript accordingly, which includes writing polish, data availability, etc. For more details about our revised work, kindly refer to the response provided below. Query: The authors may provide a supplementary table with summary statistics of the sequenced species, for example, number of sequenced raw reads, number of clean reads, number of reads used to assemble the mitochondrial genomes, mapping information, such as coverage and depth of the assembled genomes. Response: Thanks for your suggestions. Table has been supplemented (Table S2). Q: The raw reads must be deposited to a public repository (for example, SRA) and made available. Response: Regards for your recommendations. Raw data has been uploaded to the Sequence Read Archive (Table S3). Q: There is limited explanation of the methodology used for phylogenetic analyses. On Materials and Methods, section 2.3 Phylogenetic analyses, the authors stated that “the best partitioning scheme and evolutionary models for 13 predefined partitions were selected using PartitionFinder2”, however the IQ-TREE (ML analysis) was used on ‘Auto’ mode for model selection. If IQ-TREE automatically selected the model, it is unclear why the best partition scheme and model were selected with PartitionFinder2? Response: Thank for your comment. IQ-TREE (ML analysis) was used on 'Auto' mode for model selection in order to identify PartitionFinder2 selected partitions and models automatically (Table S8). The description in the text has been changed (Line number: 120). Q: The authors claimed that all ten species of Cicadellinae had their whole mitochondrial genomes assembled, however on Fig. 2 there is no annotation of ‘Control Region’ for two species (Anagonalia emeiesis and Seasogonia rosea). Please correct the figure or provide clarification on the annotation process. Response: Thank you for your comments, (Anagonalia emeiesis and Seasogonia rosea) the control area is incomplete and we have used Geneious for mapping and have never been able to complete the identification of the full control area, but its completeness does not affect the phylogenetic study, and the terminology has now been changed for the 10 species of COMPLETE (Line number: 145, 259). Q: The authors stated at the introduction that the “leafhoppers are effective vectors of plant pathogens such as phytoplasmas, as well as other bacteria and viruses that cause illness in a variety of plants”. The MS lacks detailed discussion on the implications of the findings for broader evolutionary and ecological contexts. In the conclusion section, there is a lot of repeated information from the results. Response: Thank you for your valuable comments. Leafhoppers cause direct feeding damage to plants and transmit plant pathogens. Some leafhopper species are agricultural pests, but this was not the focus of the Cicadelliane phylogenetic study in this paper, so they are not discussed in their ecological context. Duplicate information in the conclusion has been changed. Q: The authors should improve figure captions with more detailed information about the figures themselves and methods employed to generate them. For example, what represents the inner circles of Fig. 1? Response: Thanks for your comments. Genes are depicted as blocks of different colors. Genes on the J-strand are indicated by color blocks outside the circle; genes on the N-strand are indicated by color blocks inside the circle. Each circle is coloured in a different way to represent different information within the mitochondrial genome, such as the location and orientation of genes, the amount of GC, etc. . For example, the inner circle of Figure 1 represents the size range of the mitochondrial genome (Line number: 147). Reviewer 2 Query: The results presented in this work are robust and well-described. However, to ensure the reproducibility of the study, it is crucial to include detailed information about the library preparation kits and sequencing method used, as well as the sequencing depth (number of sequenced reads) for each sample. I recommend that this information be provided as supplementary material, which will significantly enhance the contribution of your article to the scientific community. Response: Thanks for your suggestions. The library preparation kits and sequencing methods used are described in Materials and Methods, and the kits were used according to the instructions, as well as the depth of sequencing (number of sequencing reads) for each sample, which is provided as Supplementary Material (Table S2). Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0329906.r002
11 Feb 2025 Decision Letter - James Crainey, Editor Dear Dr. Yang, 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 Mar 28 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'. 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, James Lee Crainey, Ph.D. Academic Editor PLOS ONE Journal Requirements: 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 Reviewer #1: All comments have been addressed Reviewer #2: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions??> Reviewer #1: Yes Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: N/A Reviewer #2: N/A ****** 4. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #1: Yes Reviewer #2: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #2: Yes ****** Reviewer #1: (No Response) Reviewer #2: The authors should clarify the discrepancy regarding the sequencing platform. In the manuscript, they report using the Illumina NovaSeq 6000, whereas in the NCBI/SRA submission, the sequencing platform is listed as the Illumina HiSeq 2000. This inconsistency should be addressed to ensure data accuracy and reproducibility. ****** 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: Daniel Andrade Moreira Reviewer #2: 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.] 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.0329906.r003
Revision 2
26 Mar 2025 Author Response Dear Reviewer, We express our gratitude for your meticulous perusal, helpful comments, and constructive suggestions, which have substantially enhanced the exposition of our manuscript. Query: The authors should clarify the discrepancy regarding the sequencing platform. In the manuscript, they report using the Illumina NovaSeq 6000, whereas in the NCBI/SRA submission, the sequencing platform is listed as the Illumina HiSeq 2000. This inconsistency should be addressed to ensure data accuracy and reproducibility. Response: We sincerely appreciate the reviewer’s attention to detail. The inconsistency between the manuscript and the NCBI/SRA submission arose due to an inadvertent error during metadata entry in the SRA submission portal. To resolve this: Clarification of Sequencing Platform: The sequencing was performed using the Illumina NovaSeq 6000 platform, as stated in the manuscript. The reference to the HiSeq 2000 in the SRA metadata was incorrect and has now been updated in the NCBI/SRA records (BioProject ID: [PRJNA1200972, PRJNA1211036]). We regret this oversight and thank the reviewer for highlighting it. All analyses and conclusions remain unaffected, as the sequencing platform does not alter the downstream bioinformatics workflows employed. Sincerely, Maofa Yang Attachments Attachment Submitted filename: Response_to_Reviewers_auresp_2.docx https://doi.org/10.1371/journal.pone.0329906.r004
23 Jul 2025 Decision Letter - James Crainey, Editor Phylogenetic investigation and mitochondrial genome description of ten species in nine genera of Cicadellinae from China (Hemiptera: Cicadellidae) PONE-D-24-10527R2 Dear Dr. Yang, 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, James Lee Crainey, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0329906.r005
Formally Accepted
Acceptance Letter - James Crainey, Editor PONE-D-24-10527R2 PLOS ONE Dear Dr. Yang, 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. James Lee Crainey Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0329906.r006

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