Peer Review History

Original SubmissionJuly 4, 2023

Attachments
Attachment
Submitted filename: Response Letter - Review Commons full-revision.docx
Decision Letter - Geraldine Butler, Editor, Kenneth H Wolfe, Editor

Dear Dr Swarbreck,

Thank you very much for submitting your Research Article entitled 'Identification of a Non-Canonical Ciliate Nuclear Genetic Code Where UAA and UAG Code for Different Amino Acids' to PLOS Genetics.

Based on the reviews from Review Commons and your responses, it is likely that I will recommend your manuscript for publication in PLOS Genetics. However, I am asking you to make three small changes and am therefore requesting minor revisions:

1. Figure 5: I agree with Reviewer 1’s request that you should label the internal branches in Figure 5 where genetic code changes probably occurred, and I didn’t find your response to this point satisfactory. The statement (line 350) that you “mapped the genetic code reassignments onto the phylogeny” implies that you identified the branches where the changes happened, so please mark them. You say that you don’t want the figure to be misleading but if you don’t mark the branches where you infer that genetic code changes occurred, the justification for statements such as “the translation of UAR as glutamine has evolved at least 5 times” (line 354) is somewhat unclear and open to misinterpretation by readers. In cases where you can’t determine the order of events, you can show them as happening simultaneously.

2. Your response to Reviewer 3 about the source of the ciliate contains some information that I think should be added to the manuscript’s Methods section (line 379), specifically that it was isolated in April 2021 and that you were unable to find it again.

3. Abstract line 26, please add the word “uncultured”, i.e. change to “a novel uncultured ciliate”.

We therefore ask you to modify the manuscript according to the review recommendations. Your revisions should address the specific points made by each reviewer.

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Yours sincerely,

Kenneth H Wolfe

Guest Editor

PLOS Genetics

Geraldine Butler

Section Editor

PLOS Genetics

Revision 1

Attachments
Attachment
Submitted filename: Response Letter - Review Commons resubmission.docx
Decision Letter - Geraldine Butler, Editor, Kenneth H Wolfe, Editor

Dear Dr Swarbreck,

We are pleased to inform you that your manuscript entitled "Identification of a Non-Canonical Ciliate Nuclear Genetic Code Where UAA and UAG Code for Different Amino Acids" has been editorially accepted for publication in PLOS Genetics. Congratulations!

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Thank you again for supporting open-access publishing; we are looking forward to publishing your work in PLOS Genetics!

Yours sincerely,

Kenneth H Wolfe

Guest Editor

PLOS Genetics

Geraldine Butler

Section Editor

PLOS Genetics

www.plosgenetics.org

Twitter: @PLOSGenetics

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Comments from the reviewers (if applicable):

Dear Dr. Swarbreck,

Thank you for submitting the revision of your manuscript. I am pleased to recommend it for publication without further changes.

yours sincerely,

Ken Wolfe (Guest Editor)

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Data Deposition

If you have submitted a Research Article or Front Matter that has associated data that are not suitable for deposition in a subject-specific public repository (such as GenBank or ArrayExpress), one way to make that data available is to deposit it in the Dryad Digital Repository. As you may recall, we ask all authors to agree to make data available; this is one way to achieve that. A full list of recommended repositories can be found on our website.

The following link will take you to the Dryad record for your article, so you won't have to re‐enter its bibliographic information, and can upload your files directly: 

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Formally Accepted
Acceptance Letter - Geraldine Butler, Editor, Kenneth H Wolfe, Editor

PGENETICS-D-23-00741R1

Identification of a Non-Canonical Ciliate Nuclear Genetic Code Where UAA and UAG Code for Different Amino Acids

Dear Dr Swarbreck,

We are pleased to inform you that your manuscript entitled "Identification of a Non-Canonical Ciliate Nuclear Genetic Code Where UAA and UAG Code for Different Amino Acids" has been formally accepted for publication in PLOS Genetics! Your manuscript is now with our production department and you will be notified of the publication date in due course.

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Soon after your final files are uploaded, unless you have opted out or your manuscript is a front-matter piece, the early version of your manuscript will be published online. The date of the early version will be your article's publication date. The final article will be published to the same URL, and all versions of the paper will be accessible to readers.

Thank you again for supporting PLOS Genetics and open-access publishing. We are looking forward to publishing your work!

With kind regards,

Jazmin Toth

PLOS Genetics

On behalf of:

The PLOS Genetics Team

Carlyle House, Carlyle Road, Cambridge CB4 3DN | United Kingdom

plosgenetics@plos.org | +44 (0) 1223-442823

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