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-22-27296Pathogenesis and defense mechanism while Beauveria bassiana JEF-410 infects poultry red mite, Dermanyssus gallinaePLOS ONE

Dear Dr. Kim,

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.

The manuscript is discuss an interesting point but contains some issues as addressed by the reviewers.  

Please submit your revised manuscript by Dec 21 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.

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: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Shawky M Aboelhadid, PhD

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. Thank you for stating the following financial disclosure: 

"This work was supported by the National Research Foundation of Korea(NRF) grant funded by the Korea government(MSIT) (NRF-2018R1A2B6001351)."

Please state what role the funders took in the study.  If the funders had no role, please state: ""The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."" If this statement is not correct you must amend it as needed. 

Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf.

3. Thank you for stating the following in the Acknowledgments Section of your manuscript: 

"This work was supported by the National Research Foundation of Korea(NRF) grant funded by the Korea government(MSIT) (NRF-2018R1A2B6001351)"

We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. 

Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: 

"This work was supported by the National Research Foundation of Korea(NRF) grant funded by the Korea government(MSIT) (NRF-2018R1A2B6001351)."

Please include your amended statements within your cover letter; we will change the online submission form on your behalf.

4. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide.

[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: Partly

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 work is novel and explores the interactions that exist between the entomopathogenic fungus and its host red mites. By elucidating these interactions, it is possible to optimize the insecticidal action of the fungus, either by inducing or overexpressing insecticidal agents or by reducing the insect's defense tools.

However, I have some observations:

1. The introduction adequately contextualizes the red mite pest. However, it does not clearly indicate which are the advances described in the literature about the interactions between entomopathogenic fungus and insect.

1.1. In lines 68-70, a work is cited that studies the transcriptome of two-spotted spider mite, however, this study is about the expression of genes in diapause. Therefore, it does not seem pertinent to cite it without informing that it is in this specific state. Besides, red mites do not go through this stage.

1.2 The pathogenicity mechanisms of the fungus and the defense mechanisms of the insect should be specified in order to provide the reader with guidelines for the work. What factors does the fungus secrete? What are the defense mechanisms of the insect?

2. The methodology is very well explained and the statistical analyses correspond to the type of sample.

However:

2.1. In lines: 97, 98, 120, 127, 203, 203, 204, 205, 209, 210 and 211, separate degrees from the unit celsius (e.g. 20° C).

2.2. On line 166 correct URL: https://bioconductor.org/packages/devel/bioc/html/edgeR.html.

3. The results are well written, just consider these remarks:

3.1 In line 274: add period after 53.0%.

3.2 In Figure 1C, 5 and 6: add meaning of the abbreviation "1R", "2R", "3R".

3.3 In Figure 3: complete the sentences, because it is necessary to specify what each of the evaluated gene groups refers to. The figure should provide all the information by itself.

4. With respect to the results, I consider that some of the conclusions are somewhat hasty. In addition, the information that is taken for granted was not referenced.

4.1. Line 330: The title does not cover what is addressed in the body of the text. If you intend to establish that the mechanism of tryptophan is in the early stages of infection.... What is the range or stages that this encompasses? It should be contextualized as to what "early stage" refers to. Personally, I would not state it as part of the title of the result, since one could not be sure that it is in the early stage. That is mostly a conclusion formulated from the literature, but not from the experiment itself.

4.2. In line 335-335, I would eliminate this sentence, since it is arbitrary. Neither in the introduction or results have they pointed out why tryptophan metabolism is relevant. I consider that eliminating it and starting with the following paragraph is the most appropriate.

4.3. In lines 340-347, add a reference that evidences what has been pointed out.

4.4 In line 380: I would not use "Suggests", since the mechanism of infection is highly evidenced, especially of Beauveria bassiana. So it is a fact that it invades the hemolymph, by penetration of the epicuticle. Use the word "confirms" instead.

4.5 On line 382: Change sentence to "The fungi that invade the cuticle attack the host...".

4.6 On line 452: The conclusion seems unfounded, since one could not speak of promoting. Only that in conjunction with the increase of genes coding for secondary metabolites, it could be established that secondary metabolites are relevant for the infection of the fungus in red mites. The word promote implies temporal order, and neither result accounts for that.

Reviewer #2: In this paper，the pathogenesis of the acaricidal fungus Beauveria bassiana JEF-410 and the

defense mechanisms of red mites were studied by transcriptome analysis. Although the results presented here are intriguing, numerous grave issues still exist.

Major concerns:

1. The strain name needs to be consistently shortened throughout the text. JEF-410 is referred to in lines 25, 28, and 39, but B. bassiana JEF-410 is found in line 29.

2. Lines 68-70, reference 14 should be added at the end of the sentence “suppression of up-regulated genes suggests enhanced insecticidal activity.” However, I couldn’t find the relative information as this paper described in reference 14, please check again.

3. The bar chart's color in figures 2, 3, and 4 is not appealing.

4. Lines 240-249, results regarding the heat map of B. bassiana JEF-410 and red mite (Fig 1C) were inconclusive. Additionally, certain information should be included in the figure1 illustration, such as descriptions of 1R, 2R, and 3R. Why is the B. bassiana JEF-410 control group experiment lacking in 3R data?

5. Line 269, “In the GO analysis of red mite,” should be red mites.

6. Line 340, the author claimed that overexpressed enzymes had no significant effect on pathogenicity, although analysis revealed that synthesizing acetyl-CoA and is involved in various cellular processes required for infection (lines 358-359). Some of the conclusions are in disagreement. Please elaborate.

7. Relevant references should be added to lines 340–344.

8. More detailed information has to be provided because the subject on this page is somewhat broad. Instead of simply discussing their metabolic pathways in general, what are acetyl-CoA and certain energy metabolism-related genes in B. bassiana JEF-410 infecting red mites, and how frequently are they up-regulated or down-regulated?

**********

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: Matias Arias-Aravena

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.

Pathogenesis and defense mechanism while Beauveria bassiana JEF-410 infects poultry red mite, Dermanyssus gallinae

PONE-D-22-27296R1

Dear Dr. Jea Su Kim, 

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,

Shawky M Aboelhadid, PhD

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

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

Reviewer #2: 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

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: 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

Reviewer #2: 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: Yes

Reviewer #2: Yes

**********

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: Dear,

the writing, with the corrections, tells the story much better. Good job!.

The introduction provides relevant background and the conclusions are correct with respect to the work done.

Reviewer #2: (No Response)

**********

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: Yes: Matias Arias-Aravena

Reviewer #2: No

**********

<quillbot-extension-portal></quillbot-extension-portal>