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Dear Dr. Shu,
Thanks for considering PeerJ. Congratulations, there are two reviewers who recommend accepting your work.
Warm regards
LIN
[# PeerJ Staff Note - this decision was reviewed and approved by Paula Soares, a PeerJ Section Editor covering this Section #]
The manuscript has been improved greatly after the revision, and can be accepted now.
no comment
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The revised manuscript is acceptable
The revised manuscript is acceptable
The revised manuscript is acceptable
The revised manuscript is acceptable
Dear Dr. Su,
Thanks for submitting your work to PeerJ. Based on the comments from the reviewers, I hope to see the new version from you.
Thanks again
LIN
[# PeerJ Staff Note: Please ensure that all review and editorial comments are addressed in a response letter and any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate. #]
[# PeerJ Staff Note: The review process has identified that the English language must be improved. PeerJ can provide language editing services - please contact us at copyediting@peerj.com for pricing (be sure to provide your manuscript number and title) #]
In this study, 145 WRKY genes have been identified in white clover, and the following analysis were performed: gene identification and classification, phylogenetic and motif composition distribution analysis, chromosomal mapping and gene duplication analysis, gene expression analysis, genetic regulation network analysis and Gene Ontology annotation, and quantitative real-time reverse transcription PCR (qRT-PCR) analysis. These findings are likely to be useful for further research on the functions of TrWRKY genes and their role in response to cold stress, which is important to understand molecular mechanism of cold tolerance in white clover, and improve its cold tolerance. But there are still some problems in the manuscript.
1. Line 49-51, “These WRKY TFs can bind to cis-acting element (named as W-box, (T)(T)TGAC(C/T)), and regulate expression of downstream target genes containing W-box in promotors.” Why not do cis-acting element analysis of TrWRKY genes in subsequent analysis? Please explain the reason or add cis-acting element analysis.
2. There were many gene duplication events that have been identified in TrWRKY genes. Moreover, WRKY genes play a variety of important roles in white clover. Why not do selective pressure analysis to see if positive selection occurs, to further explore its evolution. Please explain the reason or add cis-acting element analysis.
These findings are likely to be useful for further research on the functions of TrWRKY genes and their role in response to cold stress, which is important to understand molecular mechanism of cold tolerance in white clover, and improve its cold tolerance. But there are still some problems in the manuscript.
3. Line 54, “Arabidopsis” should be “Arabidopsis thaliana” the species appearing for the first time in the article should be given the Latin name. Please also checked throughout the manuscript.
4. Materials and Methods, please show the versions of softwares used in this study.
5. All gene names appearing in articles and diagrams should be italicized.
6. In the discussion section of the manuscript, a concluding statement should be added at the end of each discussion point.
1Line 121 (Alexa & Rahnenfuhrer 2019), the reference is in the wrong position in the text.
2There is an error in punctuation at the end of line 122.
3In Table 1, the general gene naming is based on the order in which family members appear on chromosomes. First, the genes on chromosome 1 are named according to their positions on chromosomes (such as TrWRKY001-TrWRKY025), and then the genes on chromosome 2 are named (such as TrWRKY026-TrWRKY045). Ask the author to consider whether to change it.
4Line 91 mentions "The WRKY Geneses Were Classified Into Groups Based on Similar WRKY Geneses in Arabia.", and WRKY phylogenetic trees of white clover and Arabidopsis should be provided. When classifying, we should not only refer to Arabidopsis sequences for classification, but also identify each sequence by grouping after mastering the sequence characteristics of classification. And in the later results and analysis, combined with motif analysis, the sequence characteristics of each group groups are expounded.
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