PONE-D-24-02626Lineage-specific gene duplication and expansion of DUF1216 gene family in BrassicaceaePLOS ONE

Dear Dr. Zhang,

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I agree with all the reviewers who suggested that experimental validation would be helpful. You can use qRT-PCR to validate some of your results.

I have verified that the reviewer's name is not the author of any of the papers they have suggested for citations. Please make sure they are relevant if you want to add any of them.

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Additional Editor Comments:

I agree with all the reviewers who suggested that experimental validation would be helpful. You can use qRT-PCR to validate some of your results.

I have verified that the reviewer's name is not the author of any of the papers they have suggested for citations. Please make sure they are relevant if you want to add any of them.

The paper needs to be proofread thoroughly.

[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

Reviewer #3: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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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

Reviewer #3: Yes

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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: No

Reviewer #2: Yes

Reviewer #3: No

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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: I suggest authors to check the English by a native English speaker. More comments have been upload in the online system.

• I suggest authors to check the English by a native English speaker

• Italicize the word “Brassicaceae” througout the manuscript

• Avoid starting senetence with a mathematical figure (see line 36)

• Check for space (see lin3 36)

• All scientific names should be italicized for an example see line 74.

• The section of introduction is underdeveloped. Also, it misses out on several important references like authors gene duplication is the main way to produce new gene in Brassica, such statements need to be cited. The authors must mention about other gene families (at least two) which experienced gene duplication events.

• How do DUF1216 modulate gene duplication?

• To analyze phylogeny, on what basis different listed plants were selected.

• In the methodology section, references are not cited for some context for the protocols used for experimentation by the author. Please cite appropriate references along with the text to acknowledge the contribution of other researchers and to justify the authenticity of the protocols used. For example, cite for HMMER, IQ-TREE.

• There is tense inconsistency in methodology. Kindly check and rectify as it a grammatical error which must be rectified for uniform reading of manuscript.

• Authors must add more clarity about the Ka/Ks related results obtained. What can be deduced if a gene family experience purifying selection pressure.

• It is suggested that qRT-PCR will add more meaning in your expression experiment work.

• What is the contribution of this research in field of science and to the society?

You can add citation from these articles just to add general importance of brassica.

• Farooq, O., Ali, M., Sarwar, N., Mazhar Iqbal, M., Naz, T., Asghar, M., & Ehsan, F. (2021). Foliar applied brassica water extract improves the seedling development of wheat and chickpea. Asian Journal of Agriculture and Biology, 1.

• Ahmad, N., Fazli Ahad, R., Iqbal, T., Khan, N., Nauman, M., & Hameed, F. (2020). Genetic analysis of biochemical traits in F3 populations of rapeseed (Brassica napus L.). Asian Journal of Agriculture and Biology, 8(4).

Following reference should be cited to add more information about gene family duplication events in brassica.

• Lv, X., Wei, F., Lian, B., Yin, G., Sun, M., Chen, P., ... & Wei, H. (2022). A Comprehensive Analysis of the DUF4228 Gene Family in Gossypium Reveals the Role of GhDUF4228-67 in Salt Tolerance. International Journal of Molecular Sciences, 23(21), 13542.

Reviewer #2: The article entitled "Lineage-specific gene duplication and expansion of DUF1216 gene family in Brassicaceae" is well-compiled manuscript, and the authors performed comprehensive genome-wide analyses on the phylogenetic relationships, gene structures and expressing patterns of DUF1216 members, highlighting its crucial role in flower development of Brassicaceae. In general, the insufficient results are innovative, significant and useful for the research of DUF1216 gene family in Brassicaceae, while many technical issues must be put forward first.

(1)The writing of the manuscript needs improvement, and some grammatical and spelling errors still exist. Suggest to invite someone native to help with the polish.

(2)Normally, numbers should be presented with capitalized word rather than Arabic numerals when being as Subject. Also, Latin names or gene names should be italic, while the authors were not strict with the rules.

(3)The references were not the latest and uniform, as some ones lack the issue number, and some ones use the full names of the cited journal, while some not.

(4)Plenty of gene members were chosen in this study to perform conjoint analyses, while the figures were not big or precise enough to present the results, and suggest to select the specific ones to show in the manuscript.

(5)Only the evolutionary analyses were conducted, while no experimental verification was not supplied in this manuscript.

Reviewer #3: the manuscript reported DUF domain containing gene family in few selected species of family brassicaceae. the manuscript required revision before reaching conclusion. required extensive english editing. moreover, the manuscript lacking functional validation of selected genes.

for instance,

1. the introduction is not related to the topic but random selection of literature. there are plenty of publications reported DUF domain genes author should cite some relative studies here.

2. in last paragraph of introduction, summarize few significant findings as well.

3. line 1226 what are other species? enlist those here.

4. line 133-134 molecular weight should be in KDa.

5. remove discussion from results line 259-287.

6. why expression analysis is done using RNA-seq data from mutants, as in line 393-395.

7. author should characterize few genes for functional validation ?

8. is there any gene with evolutionary importance?

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

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Attachments

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Submitted filename: Pone-D-24-02626 Review file.docx

Lineage-specific gene duplication and expansion of DUF1216 gene family in Brassicaceae

PONE-D-24-02626R1

Dear Dr. Zhang,

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.

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Kind regards,

Achraf El Allali, 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

Reviewer #3: 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

Reviewer #2: Yes

Reviewer #3: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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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

Reviewer #3: Yes

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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

Reviewer #3: Yes

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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: (No Response)

Reviewer #2: The article entitled "Lineage-specific gene duplication and expansion of DUF1216 gene family in Brassicaceae" is well-compiled manuscript, and the authors performed comprehensive genome-wide analyses on the phylogenetic relationships, gene structures and expressing patterns of DUF1216 members, highlighting its crucial role in

flower development of Brassicaceae. In general, the insufficient results are innovative, significant and useful for the research of DUF1216 gene family in Brassicaceae, and all the incorrect portions have been revised.

Reviewer #3: (No Response)

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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: Shoaib Ur Rehman

Reviewer #2: No

Reviewer #3: Yes: MUHAMMAD WASEEM

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