PONE-D-20-20094

Comparative genomic analysis of three geographical isolates from China reveals high genetic stability of Plutella xylostella granulovirus

PLOS ONE

Dear Dr. Li,

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 Oct 31 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,

Xi Zhou, Ph.D.

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 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.

3. 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.

[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: Zhang et al present a work in which they comparatively analyzed sequences of PlxyGV isolates, providing some valid information about genetic stability and diversity of baculovirus PlxyGV. In addition, they determined the transcription and polyadenylation sites of some PlxyGV ORFs. Specific points were as follows.

1. Line 16. The words "from near" should be corrected using an English statement.

2. Line 19. Change the location of the word "respectively".

3. Line 32-33. Correct to "the transcription and polyadenylation sites of…"

4. Line 49 and 52. Correct "the same".

5. Line 54-58. This is an example to testify "…facilitate the improvement of baculovirus pesticides by mixing different virus genotypes…".

6. Line 59. The abbreviation "PlxyGV" (including others) was written above.

7. Line 60-61. This sentence is confusing and corrected to "…Plutella xylostella, a destructive and widely distributed pest".

8. Line 59-71. This paragraph is redundant and not readable. It is proposed that Plutella xylostella is stated first (destructive, widely distributed, resistance to chemical pesticides, etc.), and then PlxyGV is explained.

9. Line 72-75. The two sentences were corrected to "The complete genome sequence of a PlxyGV isolate (PlxyGV-K1) from Japan was firstly reported in 2000 to consist of 100,999 bp, and encode 120 putative protein-coding ORFs. Subsequently, the genomic sequences of five additional isolates…", to avoid some repeated words.

10. Line 79-80. Remove sentences "PlxyGV-W and PlxyGV-B were isolated in Wuhan and Beijing forty years ago, while PlxyGV-Wn was collected recently in Wuhan". They are stated in section Materials and Methods.

11. Line 91-94. The sentence "PlxyGV-B is from a commercialized biopesticide, that was obtained from the Institute of Zoology, Chinese Academy of Sciences in Beijing and was originally isolated in Beijing in 1980s (Qin, Qi-Lian personal communication)" is confusing.

12. The section 2.1 Virus and insects. Authors explained origin and propagation of PlxyGV, but did not provide some statements about the insects.

13. Line 97-109. Purification of OBs and extraction of DNA (including the following RNA purification and RACE analysis, Bioassays) were common methods in baculovirus field. Authors could cite some references unless there are some modifications.

14. Line 126-127. The sentence is incomplete. In addition, there is a space between 24 and h, etc.

15. In legend of Fig. 1, correct "location" to "locations".

16. Line 235. Correct "correspondent" to "corresponding".

17. Line 250. Change "∨" indicating insertion. Someone may make a mistake to consider it as valine.

18. Line 262, 338, 344, etc. Correct "C-terminal" to "C-terminus".

19. Line 181-282. Correct "and determining LC50 and ST50 in bioassays". Perhaps, they are grammar mistakes.

20. In reviewer’s opinion, the organization of Results could be changed. The results of larvae bioassays could be stated first to make an importance of "facilitate the improvement of baculovirus pesticides by mixing different virus genotypes".

21. Check the References and rewrite them in a uniform format according to PLOS ONE required style.

Reviewer #2: The current study is related to Comparative genomic analysis of three geographical isolates from China reveals high genetic stability of Plutella xylostella granulovirus. They sequenced and comparatively analyzed to investigate genetic stability and diversity of PlxyGV，PlxyGV-W, PlxyGV-B. By alignment of the genome sequences of nine PlxyGV isolates sequenced up to date, the author found that PlxyGV genome is fairly stable in nature.

Some aspects should be addressed to improve this manuscript.

1.PlxyGV-W and PlxyGV-B demonstrate higher insecticidal activity than PlxyGV-Wn for P. xylotella larvae. The LC50 of PlxyGV-Wn is about two times of the ones of the other two virus isolates while there is no significant difference between PlxyGV-W and PlxyGV-B. Could you analyze the reasons for different insecticidal virulence of the three GV isolates from the perspective of insect virus genome?

2.By alignment of the genome sequences of nine PlxyGV isolates sequenced, the author found that PlxyGV genome is fairly stable in nature. What is the enlightenment and significance of your current work for the next step in the development of recombinant viruses or insecticides with higher insecticidal virulence against Plutella xylostella?

**********

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: Zhong-Jian Guo

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 of reviewers.docx

Comparative genomic analysis of three geographical isolates from China reveals high genetic stability of Plutella xylostella granulovirus

PONE-D-20-20094R1

Dear Dr. Li,

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,

Xi Zhou, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: