PONE-D-20-29683

Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses

PLOS ONE

Dear Dr. Ling Xu,

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.

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Spellings and English language needs to be checked thoroughly. Overall, drafting of many sentences need to be improved. Tidying up the text is also suggested. I agree with the reviewer that some changes/clarification are needed in Conclusion and M&M section.

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Academic Editor

PLOS ONE

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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: Yes

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: The authors conducted a genome-wide analysis of WRKY gene family in sunflower under drought, salt and weed stresses. The genes were characterized by phylogenetic analysis, gene structure and motif analysis, and expression analysis. Synteny analysis of the genes between sunflower and two other species, rice and Arabidopsis, were also done to understand the evolutionary aspects. The article is well-written. I would recommend publication upon minor revisions as indicated below:

Line 26: add a comma after “WKKY group”; add “the” before “same group”

Line 33: the last sentence could change into ”Those functional genes related to stress tolerance and quality improvement could be applied in marker assisted breeding of the crop”.

Line 86: add a comma after “abiotic constraints”

Line 92: Asteraceae should not be italic, please change into “Asteraceae family”

Line 167-169: the sentence “For biotic stress, common sunflower cultivars TK0409 (susceptible) and JY207 (resistant), and root parasitic weed Orobanche cumana were applied” is not clear. Do you mean: “For biotic stress, root parasitic weed Orobanche cumana were applied to common sunflower cultivars TK0409 (susceptible) and JY207 (resistant)”?

Line 194-203: please also indicate if house-keeping genes were used as reference for the qPCR, and if yes, what genes are used?

Line 332: please change “23” into “Twenty-three”

Line 370: please delete “fortunately”

Line 375: please delete “results” at the end of the line

Conclusion section: please also indicate here what HaWRKY genes (and/or how many) are the most important for each of the biotic or abiotic stresses.

Fig. 4 legend: “On the right side, Different motifs…” please change “Different” into “different”.

Reviewer #2: Comment of Reviewer

In the manuscript “Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses”, Li et al. identified WRKY family genes in sunflower and renamed them according to their locations on 25 chromosomes. They classified them into four main groups including a species-specific WKKY group using phylogenetic analyses, and they provided deep insight to the evolution of HaWRKY genes in sunflower by synteny analyses. Through transcriptomic and qRT-PCR analyses, they displayed distinct expression patterns of HaWRKY genes in different tissues, and under various abiotic and biotic stresses, which provide a foundation for further functional analyses of these genes.

This manuscript provides compelling evidence that HaWRKY family genes are associated with the development of the sunflower, as well as various abiotic and biotic stresses responsive, and provides a foundation for further functional analyses of HaWRKY genes. By using a non-standard genetic model like sunflower, the authors also help diversify studies in plant development. Please find my comments on the manuscript below.

1. Abstract is generally well-written but lacks some important data of the results.

2. Figure 7 and 8: Student’s t-test is fine here, but I suggest using Tukey’s HSD test to test all comparisons. This will help to show if 10% and 20% PEG, as well as 15mM and 30mM NaCl lines are different from each other, rather than just comparing to CK.

3. Line 53 “Functional analyses show that WRKY…” should be “Functional analyses showed that WRKY g…”.

4. In Materials and Methods part, some paragraph should could be more concise such as plant materials, growth conditions and treatments section.

5. The English writing should be substantially improved. Many sentences are illogical and cannot be understandable.

6. Overall: Add test statistics and p-values where significance is mentioned in text.

7. Overall: Italicize gene names.

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Reviewer #1: No

Reviewer #2: No

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Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses

PONE-D-20-29683R1

Dear Dr. Ling XU,

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,

Basharat Ali, Ph.D

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

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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

**********

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: The authors have addressed all my review comments. I would recommend that the current version is ready for publication.

Reviewer #2: (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: Hui Liu

Reviewer #2: No