The plastome sequence of Bactris gasipaes and evolutionary analysis in tribe Cocoseae (Arecaceae)

Raquel Santos da Silva; Charles Roland Clement; Eduardo Balsanelli; Valter Antonio de Baura; Emanuel Maltempi de Souza; Hugo Pacheco de Freitas Fraga; Leila do Nascimento Vieira

doi:10.1371/journal.pone.0256373

Peer Review History

Original SubmissionApril 9, 2021
17 Jun 2021 Decision Letter - Berthold Heinze, Editor PONE-D-21-11791 The plastome sequence of Bactris gasipaes and evolutionary analysis in tribe Cocoseae (Arecaceae) PLOS ONE Dear Dr. do Nascimento Vieira, 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. Considering the reports of three reviewers, and my own assessment, I think a minor revision, which nevertheless answers to the suggestions in the reviews carefully, is the appropriate thing to do. Please check the details further below! Please submit your revised manuscript by Aug 01 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. 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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 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 If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references.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 If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. Additional Editor Comments (if provided): We have received three reviews for this manuscript. All authors emphasize that the study is straightforward and mostly well done. Normally, I am reluctant to recommend accepting manuscript which describes chloroplast sequencing, because this has become routine work, really (but be aware to rely too heavily on refernce-guided assembly! Have a look at a book chapter where I rather recommend to publish such data as "data reports": https://doi.org/10.1007/978-1-0716-0997-2_5). So my recommendation is to include a Phoenix species, as some reviewers have done, and mention and discuss the study recommended (with the 100 primers for monocotyledon chloroplasts). [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: Yes Reviewer #3: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: N/A Reviewer #3: 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: No Reviewer #3: 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 Reviewer #3: 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 is a straightforward but sound description of the newly sequenced plastome of the economically important palm, Bactris gasipaes. The properties of the plastome are analysed in a simple phylogenetic framework including seven other species from tribe Cocoseae plus a small outgroup. The analysis is fine, the manuscript is well written and the discussion makes sense. My only comment is that the authors have overlooked a paper on phylogenetically informative plastid regions in palms: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019954 I think the discussion would benefit from a comparison of the variable regions identified here to those of Scarcelli et al. Reviewer #2: In this paper, authors sequenced and characterized the plastome of Bactris gasipaes (Bactridinae) and compared it with eight species from the three Cocoseae sub-tribes to perform comparative analysis and to identify hypervariable regions. Reviewer #3: The main study objective is the use of the plastidial regions and the nuclear markers PRK and RPB2 for a suitable approach for phylogenetic inferences and produces phylogenetic trees with well-resolved and the expected topologies in tribe Cocoseae. Without using another subfamily far from the Cocoseae subtribe, e.g. P dactylifera, the conclusion cannot be drawn with confidence. ****** 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: Yes: M. Kamran Azim Reviewer #3: Yes:** Ibrahim Al-Mssallem [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. Attachments Attachment Submitted filename: The plastome sequence of Bactris gasipaes and evolutionary analysis in tribe 24052021.docx https://doi.org/10.1371/journal.pone.0256373.r001
Revision 1
31 Jul 2021 Author Response Curitiba, July 31, 2021 Dear Dr. Berthold Heinze Academic Editor of PLOS ONE Manuscript ID: PONE-D-21-11791 Manuscript resubmission Requirement We received the results of evaluation of the refereed MS. We thank the corrections and recommendations, which improved the MS overall quality. All the queries, recommendations and suggestions were considered, as follow: Academic editor We have received three reviews for this manuscript. All authors emphasize that the study is straightforward and mostly well done. Normally, I am reluctant to recommend accepting manuscript which describes chloroplast sequencing, because this has become routine work, really (but be aware to rely too heavily on reference-guided assembly! Have a look at a book chapter where I rather recommend to publish such data as "data reports": https://doi.org/10.1007/978-1-0716-0997-2_5). So my recommendation is to include a Phoenix species, as some reviewers have done, and mention and discuss the study recommended (with the 100 primers for monocotyledon chloroplasts). R: Thank you for the positively evaluation and the constructive comments. We assembled the plastome using a de novo strategy. The reference-guided strategy was only used to order the contigs. The final assemble was verified by read mapping to ensure no contigs were mistakenly united. We have one species from subfamily Coryphoideae (the same subfamily of Phoenix) in the phylogenetic analysis. Also, Archontophoenix alexandrae (F.Muell.) H.Wendl. & Drude from subfamily Arecoideae, but Areceae subtribe. We included the recommended study (Scarcelli et al. 2011) in the discussion. #Reviewer 1 This is a straightforward but sound description of the newly sequenced plastome of the economically important palm, Bactris gasipaes. The properties of the plastome are analysed in a simple phylogenetic framework including seven other species from tribe Cocoseae plus a small outgroup. The analysis is fine, the manuscript is well written and the discussion makes sense. My only comment is that the authors have overlooked a paper on phylogenetically informative plastid regions in palms: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019954 I think the discussion would benefit from a comparison of the variable regions identified here to those of Scarcelli et al. R: Thank you for the positively evaluation and the constructive comments. The discussion were improved and the following sentences were included: “Also, Scarcelli et al. [51] reported 100 primers for phylogeny in monocots. However, four of the hypervariable regions reported in our study were not contemplated (e.g., psaC-ndhE, petN-psbM, accD-psaI, trnS-trnG). Among them. trnS-trnG and accD-psaI primers designed by Scarcelli et al . [51] showed no amplification in Arecaceae, and petN-psbM and psaC-ndhE were not mentioned, probably due to gene rearrangements in monocots plastomes. This reinforces that the highly variable regions vary between clades, and their identification may be necessary for distinct taxonomic levels.”. #Reviewer 2 In this paper, authors sequenced and characterized the plastome of Bactris gasipaes (Bactridinae) and compared it with eight species from the three Cocoseae sub-tribes to perform comparative analysis and to identify hypervariable regions. R: Thank you for the positively evaluation. #Reviewer 3 The main study objective is the use of the plastidial regions and the nuclear markers PRK and RPB2 for a suitable approach for phylogenetic inferences and produces phylogenetic trees with well-resolved and the expected topologies in tribe Cocoseae. Without using another subfamily far from the Cocoseae subtribe, e.g. P dactylifera, the conclusion cannot be drawn with confidence. R: In the phylogenetic analysis, we included Brahea brandegeei (Purpus) H. E. Moore from the subfamily Coryphoideae (the same subfamily of Phoenix) and Archontophoenix alexandrae (F.Muell.) H.Wendl. & Drude from subfamily Arecoideae, but Areceae subtribe. These species as outgroup contemplates the suggestion. Also, we included the average depth of coverage of 67.64 (SD = 24.32). Best regards, Leila do Nascimento Vieira leilavieira@ufpr.br Corresponding author Attachments Attachment Submitted filename: Response to Reviewers.doc https://doi.org/10.1371/journal.pone.0256373.r002
5 Aug 2021 Decision Letter - Berthold Heinze, Editor The plastome sequence of Bactris gasipaes and evolutionary analysis in tribe Cocoseae (Arecaceae) PONE-D-21-11791R1 Dear Dr. do Nascimento Vieira, 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, Berthold Heinze Section Editor PLOS ONE Additional Editor Comments (optional): Many thanks for submitting the revision. I see that all comments and recommendations were either followed up, or sufficiently discussed, in the letter and/or the manuscript itself. Also from a copyediting view, the manuscript seems ready for print. Reviewers' comments: https://doi.org/10.1371/journal.pone.0256373.r003
Formally Accepted
9 Aug 2021 Acceptance Letter - Berthold Heinze, Editor PONE-D-21-11791R1 The plastome sequence of Bactris gasipaes and evolutionary analysis in tribe Cocoseae (Arecaceae) Dear Dr. do Nascimento Vieira: 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. Berthold Heinze Section Editor PLOS ONE https://doi.org/10.1371/journal.pone.0256373.r004

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