PONE-D-20-28741

An updated census of the maize TIFY family

PLOS ONE

Dear Dr. Yan,

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Heping Cao, PhD

Academic Editor

PLOS ONE

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Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

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Reviewer #1: Yes

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Reviewer #1: N/A

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Reviewer #1: Yes

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Reviewer #1: Review of Manuscript Number: PONE-D-20-28741

An updated census of the maize TIFY family

The authors characterize a family of transcription factor genes and build upon previous studies by Bai et al. 2011, Zhang et al. 2015, and Zhou et al. 2015. This study includes the identification of new genes in this family, includes mapping analyses, analyzes splicing variants, examines conserved domains, examines gene expression, and enhances phylogenic analyses.

This work is well documented and presents important novel information that would be of interest to the readers of PLOS One.

There is one major issue with the classification of this gene family in that is does not build upon the earlier work of the Grassius project (Yilmaz et al. 2009. Plant Physiol 149:171-180; https://doi.org/10.1104/pp.108.128579). This project had identified 36 genes in this “super” family (see: https://grassius.org/family.php?family=ZIM&species=Maize) and used the symbols zim1 - zim36 (ZIM = zinc-finger inflorescence meristem) to describe them. While the authors state that the symbol “ZIM” had more recently been replaced by the symbol “TIFY”, this nomenclature developed in 2009 has precedence, represents the official symbols for these 36 genes and is how they are listed at MaizeGDB.org.

Of these 36 genes, all but 4 overlap with the 43 genes predicted in this manuscript.................

See uploaded complete review

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Reviewer #1: No

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Attachments

Attachment

Submitted filename: Review of Manuscript.docx

PONE-D-20-28741R1

An updated census of the maize TIFY family

PLOS ONE

Dear Dr. Yan,

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 make a minor revision as suggested by the expert.

Please submit your revised manuscript by Mar 04 2021 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,

Heping Cao, PhD

Academic Editor

PLOS ONE

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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

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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

**********

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

Reviewer #1: N/A

**********

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

**********

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

**********

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: All of the comments I made for the previous version have been addressed. However, in the caption of Table 1: "Five TIFY genes have no typical TIFY domain but include Jas motif." This was not modified. Should this now be modified in light of the four additional genes being presented?

Other than this, I do not see any additional issues. This work is well documented and presents important novel information that would be of interest to the readers of PLOS One. The manuscript should be accepted.

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Reviewer #1: 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.

An updated census of the maize TIFY family

PONE-D-20-28741R2

Dear Dr. Yan,

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.

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Kind regards,

Heping Cao, PhD

Academic Editor

PLOS ONE

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