The small RNA locus map for Chlamydomonas reinhardtii

Sebastian Y. Müller; Nicholas E. Matthews; Adrian A. Valli; David C. Baulcombe

doi:10.1371/journal.pone.0242516

Peer Review History

Original SubmissionSeptember 24, 2020
24 Sep 2020 Author Response 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. Attachments Attachment Submitted filename: 108108_1_rebuttal_1845878_qfpwww.pdf https://doi.org/10.1371/journal.pone.0242516.r001
19 Oct 2020 Decision Letter - Miguel A Blázquez, Editor PONE-D-20-30089 Annotating the algal epigenome: The small RNA locus map for Chlamydomonas reinhardtii PLOS ONE Dear Dr. Matthews, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit and it is acceptable pending a minor revision addressing the points raised during the review process. In particular, the reviewer suggests to remove "epigenome" from the title, but of course you may argue against it in your response if you wish to advocate for small RNAs as part of the epigenome. The reviewer also points out a couple of mistakes that can be easily corrected, and perhaps reducing the number of figures in the main text. Please submit your revised manuscript by Dec 03 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. 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PLOS defines a competing interest as anything that interferes with, or could reasonably be perceived as interfering with, the full and objective presentation, peer review, editorial decision-making, or publication of research or non-research articles submitted to one of the journals. Competing interests can be financial or non-financial, professional, or personal. Competing interests can arise in relationship to an organization or another person. Please follow this link to our website for more details on competing interests: http://journals.plos.org/plosone/s/competing-interests [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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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: In this work, mostly computational, the authors annotate the sRNA loci in the genome of the unicellular green alga Chlamydomonas reinhardtii. The generated small RNA locus map of C. reinhardtii should facilitate the study of the evolution of small RNA pathways, and their mechanistic diversification compared to those from higher plants. I think the manuscript, although mostly descriptive, is well written and conceived, applies appropriate computational methods (some of them previously published in a previous work of the same lab in Arabidopsis thaliana) and presents a good discussion of the results. The manuscript has already been thoroughly revised in Review Commons, and I have only a few minor comments detailed next. -I do not think the title should include the word “epigenome”, as the reader may think the paper is about C. reinhardtii epigenome, that is the universe of compounds and proteins that can attach to DNA to turn on or off gene expression, and this is not the main topic of the paper. Therefore, I suggest replacing the title by just the second part of it, which is more realistic: “The small RNA locus map for Chlamydomonas reinhardtii”. -What is the reason to look for a phasing score if, in theory, no phasiRNAs exist in C. reinhardtii due to the lack of RDRs? -In Figure 2, labels of the different axes include text of different sizes. Correct and keep labelling consistent across all graphs of the manuscript. -In Figure 7, there is an orange box with no label. What does it represent? -The Results section is relatively short in terms of text but contains 9 figures. To have a more balance text/figures ratio I suggest moving at least 1 but preferentially 2 or 3 figures to supplemental. Maybe Figure 7 and/or Figure 8 and/or Figure 9? ****** 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:** Alberto Carbonell [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. 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Revision 1
2 Nov 2020 Author Response We broadly agree with the comments of the reviewer (Alberto Carbonell) and greatly appreciate their taking the time to review the manuscript. Comment #1: “I do not think the title should include the word “epigenome”, as the reader may think the paper is about C. reinhardtii epigenome, that is the universe of compounds and proteins that can attach to DNA to turn on or off gene expression, and this is not the main topic of the paper. Therefore, I suggest replacing the title by just the second part of it, which is more realistic: “The small RNA locus map for Chlamydomonas reinhardtii”.” • Response: On reflection, we are happy to accept the reviewer’s suggestion. It is important that our title clearly communicates the content of the article and the reviewer makes a valid observation concerning the breadth of what can be considered the “epigenome”. Comment #2: “What is the reason to look for a phasing score if, in theory, no phasiRNAs exist in C. reinhardtii due to the lack of RDRs?” • Response: This is an important observation. There are indeed no conserved RDR in the Chlamydomonas genome which might suggest a lack of phasiRNAs in Chlamydomonas. However, there could be a non-canonical RDR. Additionally, phasing has in-fact been previously reported in Chlamydomonas (see this study), although we hadn’t cited this in the present manuscript. As this was an exploratory study, we thought it best to keep an open-mind to the potential presence of some form of phasiRNAs and corresponding phasing. We recognise that we could have made these arguments explicitly in the manuscript and have therefore added text into the introduction to highlight the phasiRNAs have been previously identified (lines 31-34) and a brief discussion of the possible implications of this (line 363-369). Comment #3: “In Figure 2, labels of the different axes include text of different sizes. Correct and keep labelling consistent across all graphs of the manuscript.” • Response: Thank you for pointing this out, we have now tidied up the figure labels on this figure. Comment #4: “In Figure 7, there is an orange box with no label. What does it represent?” • Response: Good spot. We’ve now added a label to the orange box. Comment #5: “The Results section is relatively short in terms of text but contains 9 figures. To have a more balance text/figures ratio I suggest moving at least 1 but preferentially 2 or 3 figures to supplemental. Maybe Figure 7 and/or Figure 8 and/or Figure 9?” • Response: Thanks for this helpful piece of feedback. We agree that moving some figures to the supplemental would tidy up the flow. As for which, we thought it best to move the plots which were more focussed on validation or “diagnostics” rather than core results. We therefore decided to move figures 2, 4 and 6 to the supplementary. https://doi.org/10.1371/journal.pone.0242516.r003
4 Nov 2020 Decision Letter - Miguel A Blázquez, Editor The small RNA locus map for Chlamydomonas reinhardtii PONE-D-20-30089R1 Dear Dr. Matthews, 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, Miguel A Blázquez Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0242516.r004
Formally Accepted
11 Nov 2020 Acceptance Letter - Miguel A Blázquez, Editor PONE-D-20-30089R1 The small RNA locus map for Chlamydomonas reinhardtii Dear Dr. Matthews: 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. Miguel A Blázquez Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0242516.r005

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