Genome Identification and Characterization of WRKY Transcription Factor Gene Family in Mandarin (Citrus reticulata)

Round 1

Reviewer 1 Report

Dear Editor of the journal agriculture,

The article titled with "Genome-wide identification and characterization of WRKY transcription factor gene family in Citrus reticulate" is written in good manner and also planed very well. The manuscript is kind off bioinformatics article which deals with data mining and analysis which existed in data base. The Idea is good and I encourage these scientists to do more but the manuscript could be improved if authors add the following suggestions to it;

1: Title should be changed into:  "Genome identification and characterization of WRKY transcription factor gene family in Citrus species"

2-The structure of WRKY genes studied in this study and how could the structure of specific genes among the studied citrus species?

3-The effects of the number of WRKY genes in the specific allele and a combined this with the environmental changes. i.e. the origin of the studied plants and the environmental conditions in their countries.

4-Abstract is too long and should be summarized; also the importance of mandarin should be added in the beginning of the abstract.

5-Disscussion is too long and should be summarized more.

6-The authors study many items and forget to study the repetitive DNA among the studied genes.

7-The authors studied the Cis-elemet and did not mentioned anything about the Trans-element.

8-Does the WRKY genes have combined roles with the transposon elements.

Author Response

Reviewer 1

Dear Editor of the journal agriculture,

The article titled "Genome-wide identification and characterization of WRKY transcription factor gene family in Citrus reticulate" is written in a good manner and also planned very well. The manuscript is a kind of bioinformatics article which deals with data mining and analysis which existed in databases. The idea is good and I encourage these scientists to do more but the manuscript could be improved if the authors add the following suggestions to it;

1: Title should be changed into:  "Genome identification and characterization of WRKY transcription factor gene family in Citrus species"

Response by the Authors: Thanks for the valuable comment. The study was conducted to identify and characterize the WRKY transcription factors in the genome of Mandarin (Citrus reticulata). In total, 46 WRKY genes were identified in the specie, while 76 WRKY genes had already been reported in C. sinensis, and their number may vary in different species of Citrus. Hence, this study cannot generalize the WRKY genes in the whole genus, and the specie name, i.e., Citrus reticulata, must be mentioned in the title.   

2-The structure of WRKY genes studied in this study and how could the structure of specific genes among the studied citrus species?

Response by the Authors: The results of this study provide new insight into the regulatory function of WRKY genes under abiotic and biotic stresses in citrus species. The structure of the specific genes identified in the current study provides a robust platform for comparative genomics targeting the Citrus species.

3-The effects of the number of WRKY genes in the specific allele and a combined this with the environmental changes. i.e. the origin of the studied plants and the environmental conditions in their countries.

Response by the Authors: Several studies demonstrate that WRKY genes are involved in plant responses to biotic stress,such as wound, and abiotic stresses, such as light, low temperature, heat, drought, and salinity. And some WRKYgenes regulate various hormones (such as MeJARE (MeJA-responsive element), ABRE (abscisic acid-responsive element), SARE (salicylic acid-responsive element), ethylene-responsive elements (ERE) and Gibbereline response elements (GARE)). The origin of the studied plants was China. It is known that China is more likely to be influenced by biotic and abiotic factors mentioned above due to their agro-climatic conditions in the citrus growing region, where the studied plants were grown.

4-Abstract is too long and should be summarized; also the importance of mandarin should be added in the beginning of the abstract.

Response by the Authors: Thanks for your constructive comment. The authors made the changes accordingly.

5-Disscussion is too long and should be summarized more.

Response by the Authors: Thanks for your constructive comment. The discussion has been summarized.

6-The authors study many items and forget to study the repetitive DNA among the studied genes.

7-The authors studied the Cis-elements and did not mention anything about the Trans-element.

Response by the Authors: Thanks for your constructive comment. The authors would like to respond to Questions # 6 and 7 collectively. The study was conducted in silico analyses on existing data available online in the databases. Cis-regulatory elements analysis was done on the 1000bp promoter region sequences of CrWRKY genes via the PlantCARE database (https://bioinformatics.psb.ugent.be/webtools/plantcare/html/). There is no such database for identifying trans-acting elements in the author’s knowledge yet. Therefore, Trans-element analysis was not conducted in the current study.

8-Does the WRKY genes have combined roles with the transposon elements?

Response by the Authors: Thanks for your constructive comment. We acknowledge the best suggestion, but that is out of the scope of the current study. The authors are working on this aspect and will publish separately. However, a detailed response is below for two-way communication purposes.

WRKY genes and transposon elements have distinct roles; sometimes, they can interact or have combined effects. It has been observed that transposons can insert themselves within or near WRKY genes, potentially affecting their expression or function. The insertion of transposons can lead to gene silencing or activation depending on their location and the presence of regulatory elements. In some cases, transposon insertions near WRKY genes have been associated with altered gene expression patterns and the evolution of new regulatory networks (Babu, Iyer, Balaji, & Aravind, 2006).

Additionally, evidence suggests that WRKY genes can regulate transposon activity. Some WRKY transcription factors have been shown to interact with transposons and control their expression directly. By binding to specific sequences within transposon elements, WRKY proteins can regulate the activity of transposons and prevent their harmful effects on the genome (Kuang et al., 2009).

While WRKY genes and transposon elements have distinct roles, they can interact and influence each other's activity in certain situations. Their interaction's precise nature and extent may vary depending on the specific context and the organisms being studied.

 

 

Babu, M. M., Iyer, L. M., Balaji, S., & Aravind, L. (2006). The natural history of the WRKY–GCM1 zinc fingers and the relationship between transcription factors and transposons. Nucleic Acids Res, 34(22), 6505-6520.

Kuang, H., Padmanabhan, C., Li, F., Kamei, A., Bhaskar, P. B., Ouyang, S., . . . Baker, B. (2009). Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: new functional implications for MITEs. Genome research, 19(1), 42-56.

 

Reviewer 2 Report

Paper is very good. Reading I only focused on lingustic error. My congratulatin of very valuable work.

Comments for author File: Comments.pdf

I do not have any essential comments.

Author Response

Reviewer 2

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Sformatowano: Polski              Irrelevent reference was removed

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Reviewer 3 Report

Although the article highlights the authors' impressive work, it contains several significant issues. Firstly, the authors have not provided any information about the materials used, such as their variety and processing. This could cause confusion and errors among readers and the scientific community, particularly since it is common practice to frequently cite the bibliography. Even minor mistakes could have serious consequences over time.

 

Secondly, the references in the article are not properly adapted to the journal's format, which may affect the clarity and consistency of the article.

 

Thirdly, "Citrus reticulata" and/or "C. reticulata" appear in the text without the appropriate italics, violating standard scientific writing conventions.

 

Finally, the text contains formatting and grammatical errors, which should be corrected to enhance the clarity and professionalism of the article.

A thorough revision of the text's grammar and spelling is necessary.

Author Response

Reviewer 3

Although the article highlights the authors' impressive work, it contains several significant issues. Firstly, the authors have not provided any information about the materials used, such as their variety and processing. This could cause confusion and errors among readers and the scientific community, particularly since it is common practice to frequently cite the bibliography. Even minor mistakes could have serious consequences over time.

 Response by the Authors:  The study was conducted in silico analyses in C. reticulata genome on data already existing in the databases i.e., the Citrus Genome Database (CGD) (https://www.citrusgenomedb.org/).

Secondly, the references in the article need to be properly adapted to the journal's format, which may affect the clarity and consistency of the article.

 

Thirdly, "Citrus reticulata" and/or "C. reticulata" appear in the text without the appropriate italics, violating standard scientific writing conventions.

 Response by the Authors:  The scientific names have been italicized.

Finally, the text contains formatting and grammatical errors, which should be corrected to enhance the clarity and professionalism of the article.

Response by the Authors: The grammatical errors have been dealt with and the text quality has been improved.

 

Comments on the Quality of English Language

Response by the Authors: A thorough revision of the text's grammar and spelling is necessary.

Round 2

Reviewer 3 Report

The authors made all the requested modifications and improved the work. The manuscript is ready for publication.

The authors reviewed and corrected the text appropriately.