The chloroplast genome sequence and phylogenetic analysis of Apocynum venetum L.

Xiaonong Guo; Zhuanxia Wang; Deyu Cai; Lei Song; Jialin Bai

doi:10.1371/journal.pone.0261710

Peer Review History

Original SubmissionJune 27, 2021
25 Aug 2021 Decision Letter - Maoteng Li, Editor PONE-D-21-20974 The chloroplast genome sequence and phylogenetic analysis of Apocynum venetum L. PLOS ONE Dear Dr. Wang, 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 Oct 08 2021 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. Please include the following items when submitting your revised manuscript: 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 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: http://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, Maoteng Li 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 note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section. 3. Thank you for stating the following in the Funding Section of your manuscript: “The National Natural Science Foundation of China (Grant No. 31760242), Gansu Provincial Natural Science Foundation (Grant No. 20JR10RA120), Gansu Provincial Natural Science Foundation the Ministry of Education of China for an Innovative Research Team in University (IRT 17R88), and the Fundamental Research Funds for the Central Universities (Grant No. 31920190021)”. 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 Funding 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 funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript”. Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 4. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. 5. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. 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. 6. Please amend the manuscript submission data (via Edit Submission) to include author Xiaonong Guo. 7. Thank you for submitting the above manuscript to PLOS ONE. During our internal evaluation of the manuscript, we found significant text overlap between your submission and the following previously published works, some of which you are an author. https://www.researchgate.net/publication/322729499_Complete_Chloroplast_Genome_Sequence_and_Phylogenetic_Analysis_of_Paeonia_ostii https://www.mdpi.com/1422-0067/19/8/2443/htm We would like to make you aware that copying extracts from previous publications, especially outside the methods section, word-for-word is unacceptable. In addition, the reproduction of text from published reports has implications for the copyright that may apply to the publications. Please revise the manuscript to rephrase the duplicated text, cite your sources, and provide details as to how the current manuscript advances on previous work. Please note that further consideration is dependent on the submission of a manuscript that addresses these concerns about the overlap in text with published work. We will carefully review your manuscript upon resubmission, so please ensure that your revision is thorough. [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? 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 #1: Partly Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: N/A Reviewer #2: Yes ****** 3. 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 #1: Yes Reviewer #2: Yes ****** 4. 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 #1: Yes Reviewer #2: No ****** 5. 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 #1: In this manuscript, the authors reported a chloroplast genome sequence Apocynum venetum and performed phylogenetic analysis of this species with other land plants. However, I do have some concerns before its final acceptance. 1. While the study appears to be sound, the language is unclear, making it difficult to follow. I advise the authors work with a writing coach or copyeditor to improve the flow and readability of the text. 2. The authors should carefully read and follow the PLOS ONE guidelines. There is no line number in the manuscript. Figures should be cited “Fig 1”, “Fig 2”, etc. References with more than six authors should list the first six author names, followed by “et al.” 3. The authors should give more details for chloroplast genome assembly. How they defined the chloroplast-like reads? Please check the version of NOVOPlasty. 4. In Results, there are no results description in “Comparative Analysis of Genomic Structure” and “Phylogenetic Analysis”. 5. In Discussion, authors should avoid the first paragraph, they are part of the Introduction. And, authors need to emphasize the novel insights obtained from their study. 6. The authors said “used 13 chloroplast genome sequences for phylogenetic analysis” in Page 5, but there are 21 complete chloroplast genome sequences in Page 10 and Figure 3. Please check and correct it. 7. Which software was used to draw the phylogenetic tree? The authors said “used MEGA7.0 to analyze and draw a phylogenetic tree with ML (maximum likelihood)” in method. However, in Discussion was “the Bayesian Inference (BI) method based on RAxML was used to construct a phylogenetic tree”. Please carefully check. 8. The reviewer suggested the authors to remove the Table 2. 9. In page 12, the authors mentioned the reference 74 in “Previous studies have reported that ycf3 is necessary for the stable accumulation of photosystem I complexes [42, 74]”, but missed it in References. Reviewer #2: This manuscript “The chloroplast genome sequence of Apocynum venetum L.” reported the chloroplast genome sequence of Apocynum venetum, and provided some basic information about this genome, such as GC contents, LSC, SSC and coding gene information, which will be helpful for the studies in plant evolution. However, the written is very poor, and it is very descriptive that missing some very important information. For example, the author claim that the A. venetum chloroplast genome encodes 131 genes, including 86 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. Is there any novel genes? How about this gene expression pattern, especially when plants meet the stress? The author could also compare the protein amount of chloroplast genes in some relative plant species and try to explain why Apocynum venetum could grow in such dry condition. ****** 6. 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 #1: No 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. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0261710.r001
Revision 1
9 Oct 2021 Author Response Dear Editors and Reviewers: Thank you for your advice and for the reviewers’ comments concerning our manuscript entitled “The chloroplast genome sequence and phylogenetic analysis of Apocynum venetum L”. Those comments are all valuable and very helpful for revising and improving our paper, in addition to their important guiding significance for our research. We have studied the comments carefully and have made corrections, which we hope will meet with approval. The revised portions are marked in red in the paper. The main corrections in the paper and the responses to the editor’s and reviewers’ comments are as follows: Responses to the editor’s comments: 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. Response: Thank you very much for your comments, which helped to improve our manuscript. We have revised the manuscript accordingly. 2. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section. Response: Thank you very much for your comments. We have revised the mistakes. 3. Thank you for stating the following in the Funding Section of your manuscript: “The National Natural Science Foundation of China (Grant No. 31760242), Gansu Provincial Natural Science Foundation (Grant No. 20JR10RA120), Gansu Provincial Natural Science Foundation the Ministry of Education of China for an Innovative Research Team in University (IRT 17R88), and the Fundamental Research Funds for the Central Universities (Grant No. 31920190021)”. 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 Funding 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 funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript”. Response: We are thankful for this suggestion. We apologize for our mistake, and we have deleted the funding information in the manuscript. 4. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. Response: We are thankful for your suggestion. No changes were required. 5. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. 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. Response: Thank you for your positive response to our work and the kind advice. We have linked an ORCID iD to the Editorial Manager. 6. Please amend the manuscript submission data (via Edit Submission) to include author Xiaonong Guo. Response: Thank you very much for these comments. We have amended the manuscript submission data. 7. Thank you for submitting the above manuscript to PLOS ONE. During our internal evaluation of the manuscript, we found significant text overlap between your submission and the following previously published works, some of which you are an author. https://www.researchgate.net/publication/322729499_Complete_Chloroplast_Genome_Sequence_and_Phylogenetic_Analysis_of_Paeonia_ostii https://www.mdpi.com/1422-0067/19/8/2443/htm We would like to make you aware that copying extracts from previous publications, especially outside the methods section, word-for-word is unacceptable. In addition, the reproduction of text from published reports has implications for the copyright that may apply to the publications. Please revise the manuscript to rephrase the duplicated text, cite your sources, and provide details as to how the current manuscript advances on previous work. Please note that further consideration is dependent on the submission of a manuscript that addresses these concerns about the overlap in text with published work. We will carefully review your manuscript upon resubmission, so please ensure that your revision is thorough. Response: We apologize for our negligence and mistakes. We have checked throughout the text and corrected similar format issues. On the basis of the methods, we have reedited the contents and deleted the repetitive statements. Please see lines 111–134. Responds to the reviewer’s comments: Reviewer #1: 1. While the study appears to be sound, the language is unclear, making it difficult to follow. I advise the authors work with a writing coach or copyeditor to improve the flow and readability of the text. Response: We have improved both the language and readability and sent our manuscript to LetPub for additional improvement of language and grammar. 2. The authors should carefully read and follow the PLOS ONE guidelines. There is no line number in the manuscript. Figures should be cited “Fig 1”, “Fig 2”, etc. References with more than six authors should list the first six author names, followed by “et al.” Response: We apologize for our negligence and mistakes. We have checked throughout the text and corrected similar format issues. We added the line number in the revised manuscript. Thank you for pointing out this mistake in the figures. It has now been corrected. The reference format has also been corrected. Please see lines 387–388, 395–396, 519–522. 3. The authors should give more details for chloroplast genome assembly. How they defined the chloroplast-like reads? Please check the version of NOVOPlasty. Response: According to your suggestion, we have described this method with more detail in the revised text. Please see lines 103–107. We have checked and corrected the version of NOVOPlasty. Please see line 99. 4. In Results, there are no results description in “Comparative Analysis of Genomic Structure” and “Phylogenetic Analysis”. Response: Thank you for pointing this out. The mistake has now been corrected and this information has been added. Please see lines 185–196 and 206–219. 5. In Discussion, authors should avoid the first paragraph, they are part of the Introduction. And, authors need to emphasize the novel insights obtained from their study. Response: Thank you for your advice. We modified the text according to your suggestion. 6. The authors said “used 13 chloroplast genome sequences for phylogenetic analysis” in Page 5, but there are 21 complete chloroplast genome sequences in Page 10 and Figure 3. Please check and correct it. Response: We apologize for our negligence and mistakes. You are absolutely right about the number of chloroplast genome sequences for phylogenetic analysis, and we thank you for pointing out this mistake, which we have corrected. Please see line 136. 7. Which software was used to draw the phylogenetic tree? The authors said “used MEGA7.0 to analyze and draw a phylogenetic tree with ML (maximum likelihood)” in method. However, in Discussion was “the Bayesian Inference (BI) method based on RAxML was used to construct a phylogenetic tree”. Please carefully check. Response: Thank you for pointing this out. We only used MEGA7.0 to analyze and draw a phylogenetic tree with ML (maximum likelihood). We have fixed the mistake at lines 274–278. 8. The reviewer suggested the authors to remove the Table 2. Response: Thank you for your advice. We have removed it from our revised manuscript. Please see line 161. 9. In page 12, the authors mentioned the reference 74 in “Previous studies have reported that ycf3 is necessary for the stable accumulation of photosystem I complexes [42, 74]”, but missed it in References. Response: Thank you for pointing out this mistake about the reference. According to the reviewer’s suggestion, we have added the mentioned literature in the reference section. Please see lines 544–546. Reviewer #2: This manuscript “The chloroplast genome sequence of Apocynum venetum L.” reported the chloroplast genome sequence of Apocynum venetum, and provided some basic information about this genome, such as GC contents, LSC, SSC and coding gene information, which will be helpful for the studies in plant evolution. However, the written is very poor, and it is very descriptive that missing some very important information. For example, the author claim that the A. venetum chloroplast genome encodes 131 genes, including 86 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. Is there any novel genes? How about this gene expression pattern, especially when plants meet the stress? The author could also compare the protein amount of chloroplast genes in some relative plant species and try to explain why Apocynum venetum could grow in such dry condition. Response: Thank you very much for this insightful comment. The article has been polished by a professional editing company. At present, we could not detect novel genes in the chloroplast genome sequence of Apocynum venetum. In the future, we will excavate the stress-resistant genes and study their stress-resistance mechanisms in combination with transcriptome and physiological experiments. Attachments Attachment Submitted filename: rebuttal letter2021.10.9.docx https://doi.org/10.1371/journal.pone.0261710.r002
17 Nov 2021 Decision Letter - Maoteng Li, Editor PONE-D-21-20974R1The chloroplast genome sequence and phylogenetic analysis of Apocynum venetum L.PLOS ONE Dear Dr. Guo, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Jan 01 2022 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. Please include the following items when submitting your revised manuscript: 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 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. We look forward to receiving your revised manuscript. Kind regards, Maoteng Li 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 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 #1: (No Response) Reviewer #2: All comments have been addressed ******** 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 #1: Partly Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 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 #1: No Reviewer #2: Yes ****** 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 #1: No Reviewer #2: Yes ****** 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 #1: The new version of the manuscript has revised most of the comments and concerns that I rose in my previous review. However, there are many English language errors throughout the article. The author doesn't write seriously，there are many errors need to be corrected. Many references listed in the manuscript are not quoted accurately. For example, the references 50-53 and 54-56 in lines 129 and 131 respectively, these citations does not appear to have any context to the text. Moreover, the references are not numbered in the order in which they appear in the text. The cp genome sequence of A. venetum (MT568765) was not found in GenBank. Reviewer #2: The authors have addressed all questions that I concerned. I recommend to accept this manuscript in this version. ****** 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 #1: No 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. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0261710.r003
Revision 2
3 Dec 2021 Author Response Dear Editors and Reviewers: Thank you for your letter and comments on our manuscript. These comments helped us improve our manuscript, and provided important guidance for future research. We have addressed the editor’s and reviewers’ comments to the best of our abilities, and revised text to meet PLOS ONE style requirements. We hope this meets requirements for a publication. The revised portions are marked in red in the manuscript. The main comments and our specific responses are detailed below: Responses to the editor’s comments: 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. Response: Thank you very much for your comments, we carefully checked the format of references and improved references 2-4, 24 and 27, which are in lines 272-277 and 348-358 respectively; It was further verified that references 13 and 22 were adjusted interchangeably according to the citation, in lines 305-310 and 338-343, respectively, and reference 42 replaced a more appropriate reference. The details are in lines 400-405. Please include the following items when submitting your revised manuscript: • 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'. Response: The above three documents are named as required Reviewer #1: The new version of the manuscript has revised most of the comments and concerns that I rose in my previous review. However, there are many English language errors throughout the article. The author doesn't write seriously，there are many errors need to be corrected. Response: Thanks for the constructive suggestions to improve our manuscript. We commissioned letpub, a professional editing agency, to edit the full text of the article, and attach the letpub editing certificate. Many references listed in the manuscript are not quoted accurately. For example, the references 50-53 and 54-56 in lines 129 and 131 respectively, these citations does not appear to have any context to the text. Moreover, the references are not numbered in the order in which they appear in the text. Response: We are very sorry that some references were cited inappropriately due to our negligence. For 50-56 references, we selected the appropriate ones and replaced them one by one. See lines 427-462for details. secondly, we carefully checked the format of references and improved references 2-4, 24 and 27, which are in lines 272-277 and 348-358 respectively; It was further verified that references 13 and 22 were adjusted interchangeably according to the citation, in lines 305-310 and 338-343, respectively, and reference 42 replaced a more appropriate reference. The details are in lines 400-405. The cp genome sequence of A. venetum (MT568765) was not found in GenBank. Response: Since our article has not been published yet and the data has not been released yet, it cannot be searched on GenBank. This article is currently under minor revision. The data we communicate with ncbi will be released on December 6th. Reviewer #2: The authors have addressed all questions that I concerned. I recommend to accept this manuscript in this version. Response: Thank you very much for your comments. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0261710.r004
9 Dec 2021 Decision Letter - Maoteng Li, Editor The chloroplast genome sequence and phylogenetic analysis of Apocynum venetum L. PONE-D-21-20974R2 Dear Dr. Guo, 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 for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, 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, Maoteng Li Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0261710.r005
Formally Accepted
1 Mar 2022 Acceptance Letter - Maoteng Li, Editor PONE-D-21-20974R2 The chloroplast genome sequence and phylogenetic analysis of Apocynum venetum L. Dear Dr. Guo: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. 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 plosone@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. Maoteng Li Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0261710.r006

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 .