PONE-D-19-34855

Genome-wide identification and functional analysis of ARF transcription factors in Brassica juncea var. tumida

PLOS ONE

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Academic Editor

PLOS ONE

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

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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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Reviewer #1: Yes

Reviewer #2: Yes

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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 addressed to clarify the members of ARF genes in tumorous stem mustard, a popular vegetable in China, and their possible function based on the in silico analysis and experiments. The topic is interesting and the results obtained are useful for futher understanding the roles of ARF gene family in plants. The experiments were well designed, the data were presented in solid, and the manucript was well written. I think this manuscript is at a good shap and can be accepted to publish in PLoS ONE.

Reviewer #2: This manuscript describes detailed characterization of sequences and expression profiles of Auxin response factor (ARF) genes in Brassica juncea var tumida. The presentation of the data in this paper seems to follow authors’ previous paper “Genome-wide identification and characterization, phylogenetic comparison and expression profiles of SPL transcription factor family in B. juncea (Cruciferae)”. This manuscript uses the same original data and similar bioinformatics methods to the previous paper. However, targeted genes (SPLs or ARFs) for the analysis are different; Both SPLs and ARFs are transcriptional factor but there is no functional or structural relationship between them. I feel the present work has been written independently and present original results.

Although characterizing ARF family genes has been already done in many plant species, this work is still valuable for some scientists who are interested in evolution in Brassica species and also who need detailed information about ARF gene family.

I feel two major problems are in this manuscript;

First, the discussion part is largely filled by repeating the result section. The authors should explore their present data by comparing the data in their previous publication or other related articles. For example, authors may be able to discuss about difference and similarity between ARFs and SPLs in regard to the phylogenetic relationships in B. juncea, A. thaliana, and B. napus. Also it may be interesting to discuss how extent miR160/167c-mediated post-transcriptional regulation is conserved in plant species.

The second problem is that explanation for specialized words is insufficient. The manuscript is not very clear for a person who is not familiar with this plants, B. juncea as well as ARFs. For example, there is no explanation what is ARF. Also it is hard to understand what tumor stem is.

(other minor points)

L 52, a typo; “genes –.”

L151-153,　For reader without knowledge for this plant, it may be good to show illustrations or photos for seedling stage (SS), mature stage (MS), and flower stage (FS) with approximate developmental date. Or cite an appropriate reference if you just followed previous work.

What is YA1, 2, and 3? Are they just different individuals or name of cultivar? Please indicate clearly in the manuscript.

L165, For the IAA treatment, it is not clear how did you spray IAA to plants; keep to spray IAA for 8 hours, or sprayed IAA then keep 8 hours?

L188, explain here what is Auxin-resp domain.

Please be consistent with the terms used in the document, “a”uxin_resp domain or “A”uxin_resp domain.

L223-227,　In the text, it sounds that the subgroup is independent from group III. However, in figure 2 the subgroup is belong to Group III.

L 234, a typo; “in B .juncea” should be “in B. juncea”

L 270, colored boxs numbered 1 to 9 are NOT at the bottom.

L 295, no explanation for fig 5. What do the numbers as well as values of x-axis mean?

L 300, the authors should explain why they focused on these miRNA at the beginning of this section or in the introduction.

L 302, what is sub-group II? There is no sub-group II in figure 1. It maybe group II.

L 304, what is BjmiR160a-c? Is it same meaning to BjmiR160?

L310-303 Fig6 A and B. Labels seem to be wrong.

L328, explain why you used three different materials, YA1 (yonganxiaoye1), YA2 (yonganxiaoye2), and YA3.

L338, the authors should provide more information about developmental stage of this plants so that readers can image them (e.g. stem nodule of vegetal period (VP), flower period (FP) and etc).

L404. Although the authors mention that B.napa was more closely related to B juncea in evolution, it sounds totally obvious to require any analyses shown in this manuscript. More explanation of the implications of this findings should be provided.

L410, a typo, “showed that revealed that”

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Reviewer #1: Yes: Kun-Ming Chen

Reviewer #2: No

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Genome-wide identification and functional analysis of ARF transcription factors in Brassica juncea var. tumida

PONE-D-19-34855R1

Dear Dr. Gao,

We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements. Please note that I put two very minor comments below. 

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With kind regards,

Yutaka Oono

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

L21-23：　The sentence does't seem grammatically correct. Do you mean "In this study, 65 B. juncea genes that encode ARF proteins were identified in the B. juncea whole-genome, classified into three phylogenetical groups and found....., "?

L305-306:　Please separate title and explanation. Only title should be written in bold.