Genomic variants from RNA-seq for goats resistant or susceptible to gastrointestinal nematode infection

Hadeer M. Aboshady; Nathalie Mandonnet; Anna M. Johansson; Elisabeth Jonas; Jean-Christophe Bambou

doi:10.1371/journal.pone.0248405

Peer Review History

Original SubmissionFebruary 7, 2020
28 Sep 2020 Decision Letter - Raluca Mateescu, Editor PONE-D-20-03648 Genomic variants from RNA-seq for goats resistant or susceptible to gastrointestinal nematode infection PLOS ONE Dear Dr. Bambou, 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 12 2020 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 We look forward to receiving your revised manuscript. Kind regards, Raluca Mateescu 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 you are reporting an analysis of a microarray, next-generation sequencing, or deep sequencing data set. PLOS requires that authors comply with field-specific standards for preparation, recording, and deposition of data in repositories appropriate to their field. Please upload these data to a stable, public repository (such as ArrayExpress, Gene Expression Omnibus (GEO), DNA Data Bank of Japan (DDBJ), NCBI GenBank, NCBI Sequence Read Archive, or EMBL Nucleotide Sequence Database (ENA)). In your revised cover letter, please provide the relevant accession numbers that may be used to access these data. For a full list of recommended repositories, see http://journals.plos.org/plosone/s/data-availability#loc-omics or http://journals.plos.org/plosone/s/data-availability#loc-sequencing. [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: 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: No 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: This is a clear and interesting manuscript by a highly regarded group. However, some aspects of the methodology are not clear. On line 71 the size of the cohort should be given. Line 121 Groups of six what? Are they replicates from he same animal or were animals pooled? Lines 131-132 The justification for a frequency of over 50% is not clear. Reviewer #2: Article entitled, “Genomic variants from RNA-seq for goats resistant or susceptible to GI nematode infection is not acceptable in the present format and demands thorough revision. Although the content of the article is good enough to publish in PLOS ONE but the MS has been written in a very casual way. I request the authors to take up the challenge to revise the MS thoroughly for improvement. The following points should be taken into consideration: 1. Assignment of resistant and susceptible animals is confusing. The authors are requested to furnish details on this point. 2. In Discussion the meaning of first sentence is not clear. It appears that, they have worked with resistant/susceptible nematodes. 3. In my opinion total reorientation of Discussion is warranted. (a) First paragraph should highlight the novelty of work stating research gap. Subsequently the authors should speak about the importance of the study and its uniqueness compared to other techniques for identification of resistant and susceptible animals. (b) Second paragraph should emphasize “how SNPs have been exploited in caprine for climate adaptations study and other economic trait. Subsequently the authors are requested to mention other genetic studies to identify GIN resistant breeds. To mention a few are: Llie et al., 2018 (study in Romania and Hungary), Alam et al., 2019 published in J Anim Sci Biotechnol and Sharma et al., 2012 published in International J. Anim. Vet. Sci. Apart from these if the authors find few more publications are requested to add in the Discussion. (c) Third paragraph should emphasize the role of T cells for conferring adaptive immunity against GIN. (d) Existing 3rd paragraph sounds good and I feel this should be retained. However, I will be curious to see an elaboration of MAPK signaling pathway with a brief note on the observation in Yichang white goats. Overall Assessment: Worthy to publish in PLOS ONE if the corrections are incorporated. ****** 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: Comments.docx https://doi.org/10.1371/journal.pone.0248405.r001
Revision 1
29 Oct 2020 Author Response Revision Notes Manuscript # PONE-D-20-03648 Dear Editor, First, we would like to thank you for giving us the chance for revision and to respond to the reviewers' comments. We have modified the manuscript according to the reviewers' recommendations and answered their questions in detail. Reviewer #1 1. Reviewer/ This is a clear and interesting manuscript by a highly regarded group. However, some aspects of the methodology are not clear. R/ we made some changes to the methodology to make it more clear according to the raised points from the reviewer 1 and reviewer 2 as mentioned in details subsequently. 2. Reviewer/ On line 71 the size of the cohort should be given. R/ the size of the cohort have been added (n=89) # line 74 3. Reviewer/ Line 121 Groups of six what? Are they replicates from the same animal or were animals pooled? R/ The sentence has been corrected. In the revised version # lines 126-127 “groups of 6 technical replicates” 4. Reviewer/ Lines 131-132 The justification for a frequency of over 50% is not clear. R/ we added justification. In the revised version # lines 137-138. “to ensure the constant of each variant between individuals of the same group (group specific variant)” Reviewer #2 1. Reviewer/ Article entitled, “Genomic variants from RNA-seq for goats resistant or susceptible to GI nematode infection is not acceptable in the present format and demands thorough revision. Although the content of the article is good enough to publish in PLOS ONE but the MS has been written in a very casual way. I request the authors to take up the challenge to revise the MS thoroughly for improvement. The following points should be taken into consideration. R/ we improved the revised manuscript taking into consideration the raised points from the reviewers. 2. Reviewer/ Assignment of resistant and susceptible animals is confusing. The authors are requested to furnish details on this point. R/ we added details on this point. # lines 67-74 and lines 155- 159 3. Reviewer/ In Discussion the meaning of first sentence is not clear. It appears that, they have worked with resistant/susceptible nematodes. R/ we modified the sentence. # lines 273- 275. 4. Reviewer/ In my opinion total reorientation of Discussion is warranted. (a) First paragraph should highlight the novelty of work stating research gap. Subsequently the authors should speak about the importance of the study and its uniqueness compared to other techniques for identification of resistant and susceptible animals. R/ The raised point have been taken into account # lines 240 -255 (b) Second paragraph should emphasize “how SNPs have been exploited in caprine for climate adaptations study and other economic trait. Subsequently the authors are requested to mention other genetic studies to identify GIN resistant breeds. To mention a few are: Llie et al., 2018 (study in Romania and Hungary), Alam et al., 2019 published in J Anim Sci Biotechnol and Sharma et al., 2012 published in International J. Anim. Vet. Sci. Apart from these if the authors find few more publications are requested to add in the Discussion. R/ second paragraph have been rebuilt taking into account the raised point. # lines 256 -277 (c) Third paragraph should emphasize the role of T cells for conferring adaptive immunity against GIN. R/ The raised point have been taken into account # lines 288 -302 (d) Existing 3rd paragraph sounds good and I feel this should be retained. However, I will be curious to see an elaboration of MAPK signaling pathway with a brief note on the observation in Yichang white goats. R/ The raised point have been taken into account # lines 303 -310 Journal Requirements: Raw sequence reads uploaded to a stable, public repository (NCBI BIOPROJECT) http://www.ncbi.nlm.nih.gov/bioproject/667825 Accession: PRJNA667825 ID: 667825 Attachments Attachment Submitted filename: revision note.docx https://doi.org/10.1371/journal.pone.0248405.r002
1 Feb 2021 Decision Letter - Raluca Mateescu, Editor PONE-D-20-03648R1 Genomic variants from RNA-seq for goats resistant or susceptible to gastrointestinal nematode infection PLOS ONE Dear Dr. Bambou, 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 Mar 18 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 We look forward to receiving your revised manuscript. Kind regards, Raluca Mateescu Academic Editor PLOS ONE [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: 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: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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: This is a useful manuscript. I am surprised that there are so many variants within each gene and a definition of how genes were defined would be helpful. Many of the variants occur in the introns and I am surprised that the transcriptome reveals so many introns; perhaps an explanation here would be helpful? There are some minor errors in the English: Line 17 drop 'grazing' Line 60 Ethics Line 77 average Line 78 'distant' to 'separated' Line 89 specify type of plastic Line 157 'The details .... ' to materials and methods Line 159 more information required Line 168 resistant Lines 177 and 221 variants ****** 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 [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.0248405.r003
Revision 2
23 Feb 2021 Author Response Reviewer #1 Reviewer/ This is a useful manuscript. I am surprised that there are so many variants within each gene and a definition of how genes were defined would be helpful. Many of the variants occur in the introns and I am surprised that the transcriptome reveals so many introns; perhaps an explanation here would be helpful? R/ A definition of how genes were defined have been added. In the tracked changes version # lines 144-147 An explanation for the result that the transcriptome reveals so many introns have been added. In the tracked changes version # lines 293-298 Reviewer/ There are some minor errors in the English: Reviewer/ Line 17 drop 'grazing' R/ Corrected. In the tracked changes version # line 17 Reviewer/ Line 60 Ethics R/ Corrected. In the tracked changes version # line 60 Reviewer/ Line 77 average R/ Corrected. In the tracked changes version # line 77 Reviewer/ Line 78 'distant' to 'separated' R/ Corrected. In the tracked changes version # line 78 Reviewer/ Line 89 specify type of plastic R/ The cannula used was made of rubber. In the tracked changes version # line 91 Reviewer/ Line 157 'The details .... ' to materials and methods R/ It has been transferred. In the tracked changes version # line 87-89 Reviewer/ Line 159 more information required R/ More information have been added. In the tracked changes version # line 163-165 Reviewer/ Line 168 resistant R/ Corrected. In the tracked changes version # line 176 Reviewer/ Lines 177 and 221 variants R/ Corrected. In the tracked changes version # line 185 and 229 https://doi.org/10.1371/journal.pone.0248405.r004
26 Feb 2021 Decision Letter - Raluca Mateescu, Editor Genomic variants from RNA-seq for goats resistant or susceptible to gastrointestinal nematode infection PONE-D-20-03648R2 Dear Dr. Bambou, 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, Raluca Mateescu Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0248405.r005
Formally Accepted
4 Mar 2021 Acceptance Letter - Raluca Mateescu, Editor PONE-D-20-03648R2 Genomic variants from RNA-seq for goats resistant or susceptible to gastrointestinal nematode infection Dear Dr. Bambou: 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. Raluca Mateescu Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0248405.r006

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