Investigation of Astyanax mexicanus (Characiformes, Characidae) chromosome 1 structure reveals unmapped sequences and suggests conserved evolution

Maelin Silva; Duílio Mazzoni Zerbinato Andrade Silva; Jonathan Pena Castro; Alex I. Makunin; Felipe Faix Barby; Edivaldo Herculano Correa de Oliveira; Thomas Liehr; Marcelo Bello Cioffi; Fábio Porto-Foresti; Fausto Foresti; Roberto Ferreira Artoni

doi:10.1371/journal.pone.0313896

Peer Review History

Original SubmissionAugust 20, 2024
8 Oct 2024 Decision Letter - Maykon Passos Cristiano, Editor Transfer Alert This paper was transferred from another journal. As a result, its full editorial history (including decision letters, peer reviews and author responses) may not be present. PONE-D-24-35999Investigation of Astyanax mexicanus (Characiformes, Characidae) chromosome 1 structure reveals unmapped sequences and suggests conserved evolutionPLOS ONE Dear Dr. Mazzoni Zerbinato A Silva, 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 Nov 22 2024 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. 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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 2. To comply with PLOS ONE submissions requirements, in your Methods section, please provide additional information regarding the experiments involving animals and ensure you have included details on (1) methods of sacrifice, (2) methods of anesthesia and/or analgesia, and (3) efforts to alleviate suffering. 3. Please include your full ethics statement in the ‘Methods’ section of your manuscript file. In your statement, please include the full name of the IRB or ethics committee who approved or waived your study, as well as whether or not you obtained informed written or verbal consent. If consent was waived for your study, please include this information in your statement as well. 4. We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data. Additional Editor Comments: The present study addresses the use of classical and molecular cytogenetics to understand the evolutionary relationship of the fish Astyanax mexicanus and its congeners. The authors attempt to establish a relationship between the conserved chromosome 1 among the species A. mexicanus, A. altiparanae, Psalidodon bifasciatus, and P. scabripinnis. In this study, microdissection of chromosome 1 from A. mexicanus was used to develop a probe, which was then applied to the target species and its congeners. The manuscript is well written, clear, and objective. The reviewers suggest a minor revision; however, I will recommend a more thorough revision of the manuscript before accepting it for publication. I have some suggestions for improving the text, as well as for the presentation of some figures. Please find my comments below. Introduction In my opinion, the objective of the study is not clearly stated at the end of the introduction. I suggest that the authors clarify the objective of the study clearer (Page 05). Page 07, lines 140-153. I think the presentation of Figure 2 is confusing. In the text, it is referred to as Fig. 2a or Fig. 2b, but in Figure 2, there are no "a" or "b" labels, for example. I understand that it refers to SatA and SatB, but for better reader comprehension, it would be important to improve the information in Figure 2. The organization of Figure 2 is a bit confusing. Please improve it by indicating each image as "A," "B," "C," and so on. The information SatE_mex, for example, could be placed in parentheses below the figure. The authors may consider developing another way to indicate each image in Figure 2. Page 08, lines 170-171. As this sentence is written, I believe it may create some confusion regarding which figure the authors are referring to. In this regard, I suggest that the authors improve the wording of this sentence. Captions In all the figure captions, a "tiff" is shown after the figure number. Please check if it is indeed meant to be in the figure caption for the manuscript and remove it if necessary. Line 117 – “Fig 1.tiff.” Line 155 - “Fig 2.tiff.” Line 173 - “Fig 3.tiff.” Reviewers Please address the suggestions made by the reviewers and note that Reviewer 1 included an attached file with their suggestions. The authors are welcome to contact me if they feel the need for any clarification or additional information. [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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: N/A Reviewer #2: N/A ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy 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: Dear Dr. Silva, I have carefully read your manuscript entitled "Investigation of Astyanax mexicanus (Characiformes, Characidae) chromosome 1 structure reveals unmapped sequences and suggests conserved evolution". I believe it contains important information on the structure and location of various DNA sequences of chromosome 1 of A. mexicanus and related species. The study is very well-performed and written in good English, and I therefore suggest this paper to be published in PLOS ONE. However, I have a few technical corrections to the text (please see the attached file). Reviewer #2: Dear editor, This study presents classical and molecular cytogenetic patterns Astyanax mexicanus. The papaer "The Investigation of Astyanax mexicanus (Characiformes, Characidae) chromosome 1 structure reveals unmapped sequences and suggests conserved evolution" is a useful and very informative paper, discussing important information about the group's chromosomal Evolution. Some points need to be clarified and revised before the manuscript can be considered for publication. Dear authors, I point some doubts: • Where were the specimens collected? Were the specimens collected in a single location? I suggest adding the geographic coordinates. • How many specimens were collected? • Were the individuals deposited in an ichthyological collection? If so, I suggest indicating the collection number. • I suggest review the chromosome classification of pairs 24 and 25 in Figure 1A. • Were the specimens reviewed by a taxonomist? ****** 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. Attachments Attachment Submitted filename: PONE-D-24-35999-revised.docx https://doi.org/10.1371/journal.pone.0313896.r001
Revision 1
28 Oct 2024 Author Response Response to reviewers We thank the reviewers for the careful proofreading of our manuscript. Below, we address all their concerns, as well as the editor’s suggestions. 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 Answer: The manuscript has been revised to ensure it meets PLOS ONE's style requirements, including file naming conventions. We have used the style templates provided at the provided links. 2. To comply with PLOS ONE submissions requirements, in your Methods section, please provide additional information regarding the experiments involving animals and ensure you have included details on (1) methods of sacrifice, (2) methods of anesthesia and/or analgesia, and (3) efforts to alleviate suffering. Answer: A section has been added in the Materials and Methods to include this information. 3. Please include your full ethics statement in the ‘Methods’ section of your manuscript file. In your statement, please include the full name of the IRB or ethics committee who approved or waived your study, as well as whether or not you obtained informed written or verbal consent. If consent was waived for your study, please include this information in your statement as well. Answer: A section has been added in the Materials and Methods to include this information. 4. We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data. Answer: After careful consideration, we have decided to remove the phrase “data not shown” from our manuscript, as the data in question are not a core part of the research being presented in our study. Additional Editor Comments: The present study addresses the use of classical and molecular cytogenetics to understand the evolutionary relationship of the fish Astyanax mexicanus and its congeners. The authors attempt to establish a relationship between the conserved chromosome 1 among the species A. mexicanus, A. altiparanae, Psalidodon bifasciatus, and P. scabripinnis. In this study, microdissection of chromosome 1 from A. mexicanus was used to develop a probe, which was then applied to the target species and its congeners. The manuscript is well written, clear, and objective. The reviewers suggest a minor revision; however, I will recommend a more thorough revision of the manuscript before accepting it for publication. I have some suggestions for improving the text, as well as for the presentation of some figures. Please find my comments below. Introduction In my opinion, the objective of the study is not clearly stated at the end of the introduction. I suggest that the authors clarify the objective of the study clearer (Page 05). Answer: We have carefully reviewed your suggestion and have made the necessary changes to clarify the objective of the study, particularly at the end of the introduction. Page 07, lines 140-153. I think the presentation of Figure 2 is confusing. In the text, it is referred to as Fig. 2a or Fig. 2b, but in Figure 2, there are no "a" or "b" labels, for example. I understand that it refers to SatA and SatB, but for better reader comprehension, it would be important to improve the information in Figure 2. The organization of Figure 2 is a bit confusing. Please improve it by indicating each image as "A," "B," "C," and so on. The information SatE_mex, for example, could be placed in parentheses below the figure. The authors may consider developing another way to indicate each image in Figure 2. Answer: Thank you for your valuable feedback on the presentation and organization of Figure 2. We have addressed the issues as follows: 1.We have added labels "A," "B," "C," etc., to each image in Figure 2 for clarity. 2.The information previously labeled as SatA, SatB, etc., has been placed in parentheses below each image to improve readability and comprehension. We believe these changes will help enhance the clarity and organization of the figure. Page 08, lines 170-171. As this sentence is written, I believe it may create some confusion regarding which figure the authors are referring to. In this regard, I suggest that the authors improve the wording of this sentence. Answer: Thank you for pointing out the potential confusion in the sentence. We have revised the wording for clarity. Captions In all the figure captions, a "tiff" is shown after the figure number. Please check if it is indeed meant to be in the figure caption for the manuscript and remove it if necessary. Line 117 – “Fig 1.tiff.” Line 155 - “Fig 2.tiff.” Line 173 - “Fig 3.tiff.” Answer: Thank you, you are correct. We have removed the "tiff" from the captions. Reviewers Reviewer #1: Dear Dr. Silva, I have carefully read your manuscript entitled "Investigation of Astyanax mexicanus (Characiformes, Characidae) chromosome 1 structure reveals unmapped sequences and suggests conserved evolution". I believe it contains important information on the structure and location of various DNA sequences of chromosome 1 of A. mexicanus and related species. The study is very well-performed and written in good English, and I therefore suggest this paper to be published in PLOS ONE. However, I have a few technical corrections to the text (please see the attached file). Answer: All the suggested corrections in the text have been accepted and implemented. Reviewer #2: Dear editor, This study presents classical and molecular cytogenetic patterns Astyanax mexicanus. The papaer "The Investigation of Astyanax mexicanus (Characiformes, Characidae) chromosome 1 structure reveals unmapped sequences and suggests conserved evolution" is a useful and very informative paper, discussing important information about the group's chromosomal Evolution. Some points need to be clarified and revised before the manuscript can be considered for publication. Dear authors, I point some doubts: • Where were the specimens collected? Were the specimens collected in a single location? I suggest adding the geographic coordinates. • How many specimens were collected? • Were the individuals deposited in an ichthyological collection? If so, I suggest indicating the collection number. Answer: A section has been added in the Materials and Methods to include this information. • I suggest review the chromosome classification of pairs 24 and 25 in Figure 1A. Answer: We reviewed the figure and increased the resolution of the original photo and the resolution of the plate for better observation. • Were the specimens reviewed by a taxonomist? Answer: Yes, a section has been added in the Materials and Methods to include information for the study subjects. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0313896.r002
4 Nov 2024 Decision Letter - Maykon Passos Cristiano, Editor Investigation of Astyanax mexicanus (Characiformes, Characidae) chromosome 1 structure reveals unmapped sequences and suggests conserved evolution PONE-D-24-35999R1 Dear Dr. Mazzoni Zerbinato A Silva, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Maykon Passos Cristiano, D. Sc. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0313896.r003
Formally Accepted
7 Nov 2024 Acceptance Letter - Maykon Passos Cristiano, Editor PONE-D-24-35999R1 PLOS ONE Dear Dr. Mazzoni Zerbinato A Silva, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Mr. Maykon Passos Cristiano Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0313896.r004

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