https://orcid.org/0000-0003-4244-573X
Peer Review History
| Original SubmissionJuly 20, 2021 |
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PONE-D-21-23416Characterization of the chloroplast genome of Lonicera ruprechtiana Regel and comparison with other selected species of CaprifoliaceaePLOS ONE Dear Dr. Weng, 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. ==============================From the Reviewers' reports, it is obviuos that numerous methodological solutions were not properly chosen or at least were not satisfactorily introduced or explained. Please provide a detailed Response to Reviewers stating each of their concerns along with the intervention made in the revised version of the manuscript. Also, be aware of additional remarks provided in the attachment by Reviewer #1.============================== Please submit your revised manuscript by Oct 30 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:
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Šiler, 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 2. Thank you for stating the following financial disclosure: “This study was supported by Provincial Program on Platform and Talent Development of the Department of Science and Technology of Guizhou China under Grant [No. [2019]5655 and [2019]5617], and the Guizhou Provincial Science and Technology Foundation under Grant (No. 2020–1Y096).” Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." 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Currently, your Funding Statement reads as follows: “This study was supported by Provincial Program on Platform and Talent Development of the Department of Science and Technology of Guizhou China under Grant [No. [2019]5655 and [2019]5617], and the Guizhou Provincial Science and Technology Foundation under Grant (No. 2020–1Y096).” Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 4. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. 5. We noticed you have some minor occurrence of overlapping text with the following previous publication, which needs to be addressed: - https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0239823 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 [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: Yes Reviewer #2: Partly ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: No ********** 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: Yes ********** 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: This paper presents the chloroplast genome of Lonicera ruprechtiana and conducts a few comparative genomic analyses between L. rupgrechtiana and other members of Lonicera or Caprifoliaceae. It is short and well done, but it lacks novelty. I have only minor comments about the strutucture of some of the writing and suggested inline edits, which I provide in notes attached. Reviewer #2: The manuscript reports a study that uses methods to thoroughly examine the newly sequenced plastome of Lonicera ruprechtiana in the context of other complete plastomes from Caprifoliaceae family. This is a generally valuable study, like many other complete plastome studies that are currently published. My main concern about the paper is on the assembly stats that are not adequately provided in the results, what was the N50 and the steps involved. Did The authors obtained a single contig with metaspades? I also hadn’t seen the use of the kraker for filtering cp and mt reads. How many reads were used to assembly the cp genome after kraker filtering. The authors really should clarify all of this issue. I also think that PCR should have been done for verifying the junctions followed by Sanger sequencing. This would have helped in justifying the assembly. But, if PCR was not done, I recommend the authors the needs to include a coverage analysis of the assembly to ensure accurate assembly of the chloroplast genome. Please include this important analysis in the paper. In addition, since non-coding region are also powerful for phylogenetic resolution, were these regions tested in this case? If yes, was the result consistent with the one presented in the publication? The authors should also clarify the number of genes used to construct the phylogenetic tree. The figures are also low quality and really should be improved. ********** 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. 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| Revision 1 |
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PONE-D-21-23416R1Characterization of the chloroplast genome of Lonicera ruprechtiana Regel and comparison with other selected species of CaprifoliaceaePLOS ONE Dear Dr. Weng, 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. Additional authors' intervention regarding the phylogenetic analysis is required according to the Reviewer's recommendations. Moreover, the associated text should be considerably improved as it contains numerous inconsistencies. Generally, the whole manuscript should be thoroughly revised regarding proper language usage. Please submit your revised manuscript by Jan 28 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:
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, Branislav T. Šiler, 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 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: No 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: Yes 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: Characterization of the chloroplast genome of Lonicera ruprechtiana Regel and comparison with other selected species of Caprifoliaceae This paper presents the chloroplast genome of Lonicera ruprechtiana and conducts a few comparative genomic analyses (i.e., structure, selection, pairwise alignment) between L. ruprechtiana and other members of Lonicera and Caprifoliaceae, more broadly. The authors provide a valuable genomic resource for future studies of the Caprifoliaceae, particularly repetitive elements that may be used for population genetics. The authors have addressed most of the comments raised by reviewers, but the language is not particularly strong. I therefore have only minor comments about the analyses but provide numerous suggestions to improve the readability of the manuscript. ---------------- General comments ---------------- 1. Phylogenetic analysis. There is still a major issue with the rooting of the phylogeny presented and the way the phylogeny is discussed. Weigela should be the root, as in all other phylogenetic analyses of Caprifoliaceae prior to this study. The members of the Caprifolieae (Lonicera, Triosteum, and Heptacodium) should form a clade sister to the a clade containing Dipelta and Patrinia, with Weigela as the outgroup. The authors should comment on whether or not the phylogeny they present is consistent with previous work. Do the clades recovered make sense in comparison to the numerous plastid phylogenies for the Dipsacales have been published over the past 20 years? The language surrounding phylogenetics is still imprecise. Phylogenies are not generally used to classify clusters of species (although this does occur in pop gen and microbial studies), they represent hypotheses of the relatedness of the samples they contain. In lines 240-242, the author's incorrectly state that L. ruprechtiana is sister to 3 taxa. In fig 3 it is clear that L. ruprechtiana is sister to L. insularis. This needs to be revised. I would caution the authors from placing too much stock into this phylogeny because the sampling is very poor and this is almost certainly not a true sister relationship. I would also suggest moving the long list of genes from lines 132-137 into a table that shows missing data (i.e., which species you were able to gather which sequences from). In one of the comments to the reviewers the authors state that not all loci were recovered for all taxa, but we do not have any estimates of missing data. 2. Selection analysis. More details need to be filled in the Methods and statistics need to be included in the results. What model was used? Did you exclude any codon positions? What window size did you use? Why did you choose the species that you did? They are very closely related and therefore have fewer mutations to consider. A comparison between species with more varying relationships might be more informative. Also, there are no test statistics included here. Because it is very difficult to recover 1 exactly (Ka = Ks), you will always classify genes as under one form or another of selection, when, in reality, the number is not distinguishable from 1. I would like to see test statistics associated with these estimates. The authors state that differences were found when comparing to different species for some genes, due to "evolutionary differences"; what are these difference? Are there reasons we might think these species/genes have ben subject to different selection regimes? 3. Pairwise alignment (Fig. S1). The results shown in Fig S1 should be refered to a pairwise alignment, not covariance, in the text. If I understand the pairwise alignment (synteny) analysis in Fig S1, the genomes mostly preserve synteny, however there is one large inverted repeat that should be noted in the results. Typically in pairwise aligment plots like this, the red line should be broken where the blue lines are. What this plot seems to suggest is an inverted repeat. Is this correct? This should be discussed more in the results. See Fig. 1 of this paper on mammalian microinversions https://www.pnas.org/content/103/52/19824/tab-figures-data ------------------- Line edits/comments ------------------- Abstract - L17-18: "The chloroplast (cp) genome is a powerful tool for resolving genome evolution." This statement is tautological and should be removed. - L27: "IR" needs to be defined before the abbreviation is used - There is a mix throughout the abstract of the present and past tense. This should be resolved so that the results are written in the past tense. Introduction - L39: "The Lonicera genus" to "Lonicera" - L68-69: "Cp sequences have become a useful and powerful tool for revealing plant phylogenies [16]." is redundant with the two preceding sentences and should be removed. - L70: Remove "phylogenomic" - L77: "for the future genetic study" to "for future genetic studies" Materials and Methods - Throughout the M&M you do not need to write "software" after the name of the software - L110: "of the related Lonicera" to "of Lonicera" - L127-128: "between L. ruprechtiana and the other 22 cp genome sequences of the Caprifoliaceae" to "using the de novo L. ruprechtiana cp genome and 22 cp genomes from across the Caprifoliaceae" - L137: "determine the phylogenetic relationship" to "determine phylogenetic relationships" - L143: delete "in the Lonicera genus" - L147: "divergence among the entire cp genome among these related species" to "divergence across entire cp genomes" - I think it would be better to remove the species names from the subtitle "Synonymous and non-synonymous substitution rate calculations of L. ruprechtiana, L. ferdinandi, L. vesicaria, L. maackii, and L. insularis" and instead state the pairwise comparisons done in the body of the paragraph. - L153: "close" to "closely related" Results - It is not important to repeatedly mention that you used an Illumina platform, and I would suggest removing the repeated mentions of it - As in the M&M, you should not write "software" after the name of each program - L158: "identifies" to "identifying" - L159: "in original data by" to "using" - L160: "organelle" to "organellar" and "filtered" to "filtering" - L162-162: "contigs with 1,060,153 bp in length. The N50 value was 6,924 bp." to "contigs totaling 1,060,153 bp in length and with an N50 of 6,924 bp." - L164: What is the reference genome you mention here? - L164-167: This section on comparative genomics should be moved to the subsection below on phylogenetics and comparative genomics. You should also state which program you used to the the pairwise alignment between the two genomes; BLAST+ is the suite of all BLAST-related software, not an actual program iteself. Also see notes above on Fig. S1. - L167-168: Delete "Finally, we successfully construct the complete cp genomes of L. ruprechtiana." - L169: Are the IRA and IRB the repeats shown in Fig S1? If so, it should be referenced. You should also be referencing Fig. 1 when refering to these loci because it shows their positions and orientations. - L177: "double" to "two" - L190 (Table 1 caption): Delete "The detail" - Table 1: "Construction of cp genome" to "Lengths of major regions" - L208: "ranged" to "ranging" - L209: "ranged" to "ranging" - L213: "contributed by" to "contained in" - L214: "intergenic region or partly in the gene spacer region" to "intergenic or spacer regions" - L216 (Table 4 caption): Delete "Detail information of". I don't think Table 4 is important enough to take up so much room in the main text. I would suggest making it supplemental. - L219: "sequences" to "sequences of the" and "produced" to "contained" - L220-221: "Among these, the codon of leucine had the highest usage frequency, at 10.7%, while the usage frequency of cysteine was only 1.1% (S2 Table; Fig 2A)." to "Among these, leucine had the highest usage frequency, at 10.7%, while cysteine was least freuqent, at only 1.1% (S2 Table; Fig 2A)." - L223: "with" to "had" - L224: "in the L. ruprechtiana." to "by L. ruprechtiana" - L225: "were" to "was" - L227-230: The figure caption should be used to explain the figure, not tell results. I suggest simplifying the capture to "Percentage of amino acids of the L. ruprechtiana chloroplast (cp) genome (A) and the ending patterns of biased-usage codons (RSUC>1) (B)." - L234-237: Rephrase "To further understand the phylogenetic relationships of L. ruprechtiana, 68 homologous protein-coding genes of 22 cp genome sequences of the Caprifoliaceae were downloaded from NCBI database to build the phylogenetic tree. The phylogenetic tree was created using MEGA7 [25] with 1,000 bootstrap replicates." to "To further understand the phylogenetic placement of L. ruprechtiana, 68 homologous protein-coding genes of 22 Caprifoliaceae cp genome sequences downloaded from NCBI were used to estimate a phylogeny using MEGA7 [25] with 1,000 bootstrap replicates (Fig. 3)." - Delete lines 237-240 "To show... 2 distinct clusters." The statement that the authors only show a cladogram should be left for the figure caption, and see my notes on clusters above. - L240: Delete "in the Lonicera cluster". Again, Lonicera a clade, not a cluster. The sentence also references Fig. 3 twice, and should only reference it once. - L244-245: Delete "The maximum-likelihood tree shows the two distinct clusters." - L246: Delete "in the figure" - L250: "of five" to "of the five" - L251: "the mVISTA program" to "mVISTA" - L253: "mean" to "show" and "are" to "were" - L254: "are consistent with those of" to "consistent with" - L262: what does "were relatively more highly" mean? More highly what? It seems like something is missing here - L275-276: "were downloaded from GenBank and analyzed" to "are shown" - L277: "negative-strand" to "reverse-strand" - L283-284: "the evolution of genome and selection genes under pressure" to "selection pressure on genes and genomes" - L294: "genes are strong" to "genes are under strong" - L297: "the Illumina" to "an Illumina". There are many Illumina platforms - L298: delete "others" - L298-303 are meandering and repetitive. Possibly rephrase like "The complete cp genome of L. ruprechtiana showed a typical quadripartite cycle of 154,611 bp in length length, comparable to that of published Lonicera species cp genomes (154,513–155,346) (Fig. 1, Tables 1 and S1) [17]." - L303: "variable" to "variation" - 322: "the sequence of ycf2 gene have the highest variable" to "ycf2 is one of the most variable genes" - L338: "the Illumina" to "an Illumina" - L341: delete "information" - L344: "had a close relationship with" to "is closely related to". See my note above; I caution over interpretation of this phylogeny Supplement - L469: "List of the cp genome of 23 species used for phylogenetic analysis." to "List of the 23 cp genomes used for phylogenetic analysis." - L472: "rate" to "rates" Reviewer #2: The authors have addressed all my concerns and therefore I support publication without further changes. ********** 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. |
| Revision 2 |
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Characterization of the chloroplast genome of Lonicera ruprechtiana Regel and comparison with other selected species of Caprifoliaceae PONE-D-21-23416R2 Dear Dr. Weng, 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, Branislav T. Šiler, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: |
| Formally Accepted |
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PONE-D-21-23416R2 Characterization of the chloroplast genome of Lonicera ruprechtiana Regel and comparison with other selected species of Caprifoliaceae Dear Dr. Weng: 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. Branislav T. Šiler Academic Editor PLOS ONE |
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