Computational analysis on two putative mitochondrial protein-coding genes from the Emydura subglobosa genome: A functional annotation approach

Megan Yu

doi:10.1371/journal.pone.0268031

Peer Review History

Original SubmissionAugust 17, 2021
10 Mar 2022 Decision Letter - Rakesh Kumar Verma, Editor PONE-D-21-26684Computational analysis on two putative mitochondrial protein-coding genes from the Emydura subglobosa genome: A functional annotation approachPLOS ONE Dear Dr. Yu, 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 Apr 24 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. 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If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.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? 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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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: Thank you for asking me to review this paper and you are free to share my name with the authors if you wish. I recommend this paper for publication, it is highly descriptive and highly detailed and well worthy of publication. A couple of comments below that are in my view minor issues and it should be good. The figures are appropriate and well done. Cheers Scott Scott A Thomson Centro de Estudos dos Quelônios da Amazônia - CEQUA Line 42: Compared to other eukaryotic species, turtles have minimal diversity (360 living species) and over 50% are threatened with extinction [2]. I find this sentence a little awkward and open to interpretation. “other eukaryotic species’ groups” of something similar may be better as it clarifies we you are talking about Orders in this case. Also historically there have been in the past many more species than are alive today there are many hundreds of fossil species, probably comparable with other reptilian orders. In the materials and methods section the writing is as if there were multiple people involved here but there is a sole author. This may read better under the circumstances with some better use of third person writing rather than first person. This is just a suggestion the materials and methods is otherwise thorough. Line 317: when you refer to “other turtle species” are you referring to previously studied taxa you mentioned in the intro? Such as C. n. abingdoni, G. gigantea and C. mydas? Maybe that should be clarified as E. subglobosa is to my knowledge the first Pleurodiran turtle to be studied this way, all others being Cryptodires, as such E. subglobosa being an outgroup or sister to all other studied turtles would be an expected result as at least 165 million years separates them. Addit. Ok I think I get it. It’s the species listed in your tables? you may want to make this clear somewhere early in the manuscript, ie material examined so the reader knows what your comparative material is. ****** 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: Yes:** Scott A. Thomson [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.0268031.r001
Revision 1
18 Apr 2022 Author Response Dear Dr. Rakesh Kumar Verma and Dr. Scott A. Thomson, Thank you for your time and feedback in reviewing my original research article entitled “Computational analysis on two putative mitochondrial protein-coding genes from the Emydura subglobosa genome: A functional annotation approach.” I have addressed the reviewer’s comments and clarified specific phrases that may have been confusing to the reader: Comment #1. Line 42: Compared to other eukaryotic species, turtles have minimal diversity (360 living species) and over 50% are threatened with extinction [2]. I find this sentence a little awkward and open to interpretation. “other eukaryotic species’ groups” of something similar may be better as it clarifies we you are talking about Orders in this case. Also historically there have been in the past many more species than are alive today there are many hundreds of fossil species, probably comparable with other reptilian orders. I agree that talking about individual species may be ambiguous, as I am focusing on Orders in this sentence. I have changed the wording to “other eukaryotic species’ groups” to clarify this. Comment #2. In the materials and methods section the writing is as if there were multiple people involved here but there is a sole author. This may read better under the circumstances with some better use of third person writing rather than first person. This is just a suggestion the materials and methods is otherwise thorough. This point is valid. I am used to writing in first-person, especially since most papers I have worked on have multiple authors. I have removed the first-person language and changed to third person instead. Comment #3. Line 317: when you refer to “other turtle species” are you referring to previously studied taxa you mentioned in the intro? Such as C. n. abingdoni, G. gigantea and C. mydas? Maybe that should be clarified as E. subglobosa is to my knowledge the first Pleurodiran turtle to be studied this way, all others being Cryptodires, as such E. subglobosa being an outgroup or sister to all other studied turtles would be an expected result as at least 165 million years separates them. Addit. Ok I think I get it. It’s the species listed in your tables? you may want to make this clear somewhere early in the manuscript, ie material examined so the reader knows what your comparative material is. I have clarified this point specifically in the Materials and Methods section Lines 289-303. For “other turtle species,” I am referring to the species in the phylogenetic tree, which I obtained from the BLAST results. I expanded out the organism sets in the phylogenetic tree to contain species with lower percent identities in the BLAST results. I clarified “other turtle species” in Line 375-376 to “other turtle species in the phylogenetic tree.” Readers can refer to the Materials and Methods for how this tree was generated. I have also reviewed the journal guidelines and ensured that my manuscript meets PLOS ONE’s style requirements. I confirm that I am affiliated with the University of California, Los Angeles (UCLA) Department of Molecular, Cell & Developmental Biology. I did not update any figures for this revision, and all figures were uploaded to PACE. All references are complete and correct. Please address correspondence to me via email at yumr247@g.ucla.edu. Thank you very much for your time and consideration of this manuscript. I look forward to hearing back from you and PLOS ONE. Sincerely, Megan Yu Attachments Attachment Submitted filename: Rebuttal Letter PLOS.pdf https://doi.org/10.1371/journal.pone.0268031.r002
21 Apr 2022 Decision Letter - Rakesh Kumar Verma, Editor Computational analysis on two putative mitochondrial protein-coding genes from the Emydura subglobosa genome: A functional annotation approach PONE-D-21-26684R1 Dear Dr. Yu, 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, Rakesh Kumar Verma, Ph.D Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0268031.r003
Formally Accepted
10 Aug 2022 Acceptance Letter - Rakesh Kumar Verma, Editor PONE-D-21-26684R1 Computational analysis on two putative mitochondrial protein-coding genes from the Emydura subglobosa genome: A functional annotation approach Dear Dr. Yu: 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. Rakesh Kumar Verma Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0268031.r004

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