Draft genome of the bluefin tuna blood fluke, Cardicola forsteri

Lachlan Coff; Andrew J. Guy; Bronwyn E. Campbell; Barbara F. Nowak; Paul A. Ramsland; Nathan J. Bott

doi:10.1371/journal.pone.0276287

Peer Review History

Original SubmissionJuly 19, 2022
19 Sep 2022 Decision Letter - Hudson Alves Pinto, Editor PONE-D-22-18941Draft genome of the bluefin tuna blood fluke, CardicolaforsteriPLOS ONE Dear Dr. Bott, 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 03 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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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 If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.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: I congratulate the authors for this interesting and relevant contribution for field of ichtyoparasitology. [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: Yes Reviewer #2: 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: 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: The article by Coff et al. presents a high-quality genome of Cardicola fosteri, a much needed genomic resource for an important parasite of aquacultured fish. The authors highlight the value of this resource through their identification and characterisation of known proteins associated with host:parasite interactions or that have been identified as promising drug targets or vaccine candidates. The only limitation of this study was a lack of transcriptomic evidence of species-specific genes that may have reduced the number of overall genes predicted from the genome. Overall, I thought he article was excellent and aligns with the scope of this journal. I had some minor comments or suggestions for consideration below. Lines 29 to 32. I suggest a simplified outline of co-infecting Cardicola spp. and their importance in the introduction before focussing on fosteri. Lines 45 to 54 could be further summarised. Or removed. FOcus on Cardicola and importance of a genomic resource is fine. seven autosomes? and the sex chromosomes? Lines 62 to 66. Suggest better integration of knowledge gaps that could be addressed with genomic data. The glycome section seems out of place in an introduction (but great for discussion). Abbreaviate species names upon first use throughout Lines 86 to 89. Fine to just state that you had ethics approval without stating that it was not required. Line 168. given the wealth of proteomic data for Platyhelminthes, why was ProtHint only provided with S. mansoni? This is of particular importance considering the lack of transcriptomic data for C. fosteri Line 187, Please specify the substitution model used. Line 192. WIll the data for specimen 1 be made public? Raw data and/or assembly? Line 221. It is okay to refer to the "hybrid contigs" as scaffolds as long as the DNA was from the same species. Hybrid makes it sound like you used a different species. Perhaps add a clear definition of hybrid? Line 225.A comparison of completeness when compared to other flatworms is important. No flatworm will have 100% as many genes appear to be absent or lack sequence homology for BUSCO Detection compared to other metazoans. I think you are underselling the completeness of your genome here. Line 280. It would be possible to use PloipY or SmudgePlot with your GenomeScope results to estimate ploidy. As this is an important discussion point, it is worth considering this additional analysis. Lack of transcriptomic data limits the conclusions from the proteins characterised herein (e.g. important to know in which stage of the parasite they are being expressed) Lines 423 to 427. Would have been nice to hear something about the other Cardicola species and the future directions in the concluding Reviewer #2: I consider that the manuscript is suitable for publication in this journal, mainly because it is complete, very well written, and because of the importance it provides for parasitology. This type of work is a significant advance in the parasitology applied to fish, mainly due to the impact that the species of the parasite under study can have on the economy of the fishing area. I believe that its justification and the possible application of the results obtained for the management and control of Cardicola fosteri in the future are very convenient. ****** 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. https://doi.org/10.1371/journal.pone.0276287.r001
Revision 1
27 Sep 2022 Author Response Reviewer #1: The article by Coff et al. presents a high-quality genome of Cardicola fosteri, a much needed genomic resource for an important parasite of aquacultured fish. The authors highlight the value of this resource through their identification and characterisation of known proteins associated with host:parasite interactions or that have been identified as promising drug targets or vaccine candidates. The only limitation of this study was a lack of transcriptomic evidence of species-specific genes that may have reduced the number of overall genes predicted from the genome. Overall, I thought he article was excellent and aligns with the scope of this journal. I had some minor comments or suggestions for consideration below. Lines 29 to 32. I suggest a simplified outline of co-infecting Cardicola spp. and their importance in the introduction before focussing on fosteri. Response: We believe this outline is important for establishing the distinctions between the co-infecting Cardicola spp., Thunnus spp., and blood fluke infections of bluefin tuna in different parts of the world. The focus on C. forsteri is justified by it being the dominant species infecting bluefin tuna. Lines 45 to 54 could be further summarised. Or removed. FOcus on Cardicola and importance of a genomic resource is fine. seven autosomes? and the sex chromosomes? Response: ‘Seven chromosomes’ has been corrected to ‘seven autosomes and two sex chromosomes’ on p. 4, ln. 56–57 of the revised manuscript, in accordance with the reviewer’s comment. Lines 62 to 66. Suggest better integration of knowledge gaps that could be addressed with genomic data. The glycome section seems out of place in an introduction (but great for discussion). Response: Glycomics has been removed from this section of the Introduction, in accordance with the reviewer’s comment. Abbreaviate species names upon first use throughout Response: Species names have been abbreviated after their first appearance throughout the manuscript, with the exception of headings and legends, in accordance with the reviewer’s comment. Lines 86 to 89. Fine to just state that you had ethics approval without stating that it was not required. Response: The ethics statement has been amended on p. 5, ln. 84–86 of the revised manuscript, in accordance with the reviewer’s comment. Line 168. given the wealth of proteomic data for Platyhelminthes, why was ProtHint only provided with S. mansoni? This is of particular importance considering the lack of transcriptomic data for C. fosteri Response: The S. mansoni proteome was selected as the protein database for ProtHint because it is the closest relative of C. forsteri with a published genome annotation, which has been carefully curated for over ten years. Other proteomes from platyhelminths could have been included as a reference, but we decided against this for two reasons. The first was to reduce the size of this protein database to optimize computational efficiency. The second was to reduce bias in the annotation from lower-quality reference annotations. Brůna et al. 2021 showed that the accuracy of their BRAKER2 gene prediction pipeline improved when ProtHint was provided with proteomes of closer evolutionary distance. They refer to this approach as ‘BRAKER2 with proteins of short evolutionary distance’, which is what we employed for this manuscript. They also showed that a larger database of proteins could compensate for evolutionary distance, but only outside of the Family. It is therefore not expected that the accuracy of gene prediction would substantially increase with the addition of reference proteins from more evolutionarily distant platyhelminths, although this could be tested for future assemblies. Line 187, Please specify the substitution model used. Response: The substitution model has been specified as ‘the WAG amino acid substitution model’ on p. 9, ln. 189–190 of the revised manuscript, in accordance with the reviewer’s comment. Line 192. WIll the data for specimen 1 be made public? Raw data and/or assembly? Response: The raw sequence data for Specimen 1 will be made public upon publication of this manuscript, having been submitted to the NCBI’s Sequence Read Archive. Line 221. It is okay to refer to the "hybrid contigs" as scaffolds as long as the DNA was from the same species. Hybrid makes it sound like you used a different species. Perhaps add a clear definition of hybrid? Response: ‘Hybrid’ has been defined as ‘assembled from short and long reads’ as per Di Genova et al. 2021 on page 11, ln. 225–226 of the revised manuscript, in accordance with the reviewer’s comment. Line 225.A comparison of completeness when compared to other flatworms is important. No flatworm will have 100% as many genes appear to be absent or lack sequence homology for BUSCO Detection compared to other metazoans. I think you are underselling the completeness of your genome here. Response: Comparisons to the BUSCO analyses of Fasciola hepatica and Schistosoma mansoni have been added to p. 11, ln. 230–232 of the revised manuscript, in accordance with the reviewer’s comment. Line 280. It would be possible to use PloipY or SmudgePlot with your GenomeScope results to estimate ploidy. As this is an important discussion point, it is worth considering this additional analysis. Response: A Smudgeplot analysis was conducted, which proposed C. forsteri to be diploid in its adult life cycle stage. This result was included in the revised manuscript, in accordance with the reviewer’s comment. Lack of transcriptomic data limits the conclusions from the proteins characterised herein (e.g. important to know in which stage of the parasite they are being expressed) Response: This is a point for further investigation discussed on p. 15, ln 315–317 of the revised manuscript. This study was limited by collection of sufficient quantities of the parasite from the field, and it would be difficult to collect different stages of the parasite in such a manner. Therefore, a study of this kind would need to be funded and carefully planned in coordination with industry beforehand. Lines 423 to 427. Would have been nice to hear something about the other Cardicola species and the future directions in the concluding Response: A brief statement outlining the impact of this study for other Cardicola spp. has been added to the concluding remarks of the Discussion on p. 20, ln. 432–434 of the revised manuscript, in accordance with the reviewer’s comment. Reviewer #2: I consider that the manuscript is suitable for publication in this journal, mainly because it is complete, very well written, and because of the importance it provides for parasitology. This type of work is a significant advance in the parasitology applied to fish, mainly due to the impact that the species of the parasite under study can have on the economy of the fishing area. I believe that its justification and the possible application of the results obtained for the management and control of Cardicola fosteri in the future are very convenient. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0276287.r002
4 Oct 2022 Decision Letter - Hudson Alves Pinto, Editor Draft genome of the bluefin tuna blood fluke, Cardicola forsteri PONE-D-22-18941R1 Dear Dr. Bott, 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, Hudson Alves Pinto, Ph.D Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0276287.r003
Formally Accepted
6 Oct 2022 Acceptance Letter - Hudson Alves Pinto, Editor PONE-D-22-18941R1 Draft genome of the bluefin tuna blood fluke, Cardicola forsteri Dear Dr. Bott: 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. Hudson Alves Pinto Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0276287.r004

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