PONE-D-21-08015

Genome-wide identification of the MIOX gene family and their expression profile in cotton development and response to abiotic stress

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.

At-least following points should be addressed.

1. An in-depth bioinformatics analysis is suggested to gain insights in the evolution of MIOX genes in cotton.
2. Proper nomenclature should be followed throughout the manuscript to describe the MIOX genes and MIOX proteins.
3. The results should be clearly stated and should be discussed separately in detail.
4. The results of transcriptome analysis should be verified with wet-lab experiments, by quantifying the expression of all the genes by Quantitative Real time PCR under various abiotic and biotic stresses.

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Rana Muhammad Atif

Academic Editor

PLOS ONE

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2. Please amend the manuscript submission data (via Edit Submission) to include author Renhai Peng

Additional Editor Comments (if provided):

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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

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

Reviewer #1: Yes

Reviewer #2: 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

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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: Yes

Reviewer #2: Yes

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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: This manuscript entitled “Genome-wide identification of the MIOX gene family and their expression profile in cotton development and response to abiotic stress” is a routine bioinformatics prediction of MIOX genes, their distribution in different chromosomes, their gene structure, their phylogeny, cis-regulatory elements and insilico expression in cotton species. The most important deficiency of the study is the lack of wet-lab analysis (RT-qPCR) therefore, this manuscript is incomplete. The problems and specific

comments are as follows:

1.Grammar mistakes: Line 48-50, Line 66-69, line 91-95, 2.Line 78: all

of the four diploid species contained 6 MIOX genes? Three diploid species.

3.What is Gossypioides kirkii? Why choose it? The result should be put

in the abstract section.

4.Line 82-86: The authors renamed the MIOX genes. If the renamed MIOX

gene has recognized name, how to deal with it?

5.Line 173: GhMIOX02 and GhMIOX08 should be italic.

6.Line 173-174: It is not obvious from the heat-map that “the expression

of GhMIOX02 and GhMIOX08 showed up-regulation in the early time points

(1h~3h), then down-regulation (3h~6h), and then another up-regulation

(6h~24h).” 7.Line 174-175: The expression pattern was not “While

GhMIOX03 was up-regulated in the early time points (1h~6h), but down

regulated in the late time points (12h~24h) under code stress.”

8.Line 176-178: It is not obvious from the heat-map that“Moreover,

GbMIOX02 showed continuously down-regulation at all of the time points

under salt stress.”

9.Add q-PCR verification for the transcriptome results

10.Line 194-201: This part should be present in the result section even

if there is no none of MIOX gene was amplified by transposable elements.

11.Line 211-216: There is no ka/ks analysis in the result section.

12. The method should be present in detail such as the genome version.

Reviewer #2: This manuscript entitled “Genome-wide identification of the MIOX gene family and their expression profile in cotton development and response to abiotic stress” deals with general bioinformatics prediction of MIOX genes, their distribution in different chromosomes, their gene structure, their phylogeny, cis-regulatory elements and insilico expression in cotton species. Overall, this work presented a regular meta-analysis of MIOX gene family using public available data. The overall logic of the study is relatively clear. However, this manuscript is still lacking in some points. The specific comments are as follows:

Introduction:

1: Grammar mistakes: Line 48-50, “AtMIOX4 over expression can”,

2: Line 66-69, delete “were analyzed”.

Materials and Methods:

3: Cannot see any methodology for multiple sequence alignment.

4: It is suggested to verify the results with we-lab experiments for some genes as q-PCR verification for the transcriptome results that play an important role in stress.

5: The method should be present in detail such as the genome version.

Results:

Generally, the Results are weakly described.

6: Line 78 “all of the four diploid species contained 6 MIOX genes”. Hence there are three diploid species as indicated in abstract too.

7: Further Line 78 has grammatical mistakes. Past and present tenses are in same sentence.

8: Line 91: “protein from” not “protein form”

9: Line 91-95: confusing sentence.

10: Authors should try to annotate the motifs identified through MEME to gain insights in the functions of these motifs.

Discussion:

Very week discussion of the results. Some results are not even discussed in this section.

11: Line238 has a mistake: “using a E value of 1.0E-3” etc. The full manuscript needs to be carefully reviewed and modified.

12: Line 194-204: This part should describe in the result section too even if there is no MIOX gene was amplified by transposable elements.

13: Line 211-216: There is no ka/ks analysis description in results section.

Such weaknesses in the manuscript reduce the readability for general readers and affect the scientific significance of research.

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Reviewer #1: No

Reviewer #2: Yes:

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Genome-wide identification of the MIOX gene family and their expression profile in cotton development and response to abiotic stress

PONE-D-21-08015R1

Dear Dr. Peng,

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,

Rana Muhammad Atif

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

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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

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

**********

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

**********

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

**********

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 Authors have addressed all of the suggestions and have improved the quality and readability of manuscript.

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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: No

Reviewer #2: Yes: Dr. Muhammad Abdul Rehman Rashid