The Genome-Wide Identification of the R2R3-MYB Gene Family in Chinese Flowering Cabbage and the Characterization of Its Response to Pectobacterium carotovorum Infection
, Guangguang Li 2, Ding Jiang 2, Fanchong Yuan 2, Xianyu Zhou 2, Yansong Zheng 2, Hua Zhang 2,* and Bihao Cao 1,*
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsDear Authors,
Review of the manuscript entited „Genome-wide Identification of the R2R3-MYB Gene Family in Chinese Flowering Cabbage and Characterization of their Response to Pectobacterium carotovorum Infection” written by Shikang Lei, Guangguang Li, Ding Jiang, Fanchong Yuan, Xianyu Zhou, Yansong Zheng, Hua Zhang and Bihao Cao
In the genome of Chinese flowering cabbage 255 R2R3-MYB genes were newly identified. Comprehensive bioinformatics analysis was performed to investigate phylogenetic relationships, chromosomal localization, and collinearity. Phylogenetic analysis suggested that R2R3-MYBs from Chinese flowering cabbage and Arabidopsis thaliana belong to each subgroup, implying that the functions of most R2R3-MYBs are conserved and that genes within a given subgroup share recent common evolutionary origins during evolution. Collinearity analysis revealed the occurrence of genome duplication events in the Chinese flowering cabbage genome. The 254 R2R3-MYB genes were distributed on all 10 chromosomes and that one gene was on the scaffold. RNA-Seq and qPCR analyses suggested that several BcMYB genes respond to Pcc infection. This study provides preliminary evidence that BcMYBs may play important roles in the soft rot stress response in Chinese flowering cabbage.
I can accept this manucript after minor revision. The list of my recommendations/ excuses are presented below.
Abstract is OK. The abstract is within the 200 words frame.
Introduction is OK.
Mat&Methods
line 82: here you should mention that what kind of soil mixture was used (name of the mixture and where did you buy it from)
line 110: „using the ClustalW tool in MEGA7.0.” Here a citation /webpage is necessary to write.
line 116: „Plant RNA Extraction Kit (OMEGA)”.. - you shall have to specify the extraction kit like (e.g. Agilent Technologies Inc., CA, USA).
line 117: „sized with a 1st Strand cDNA Synthesis Kit (Takara)” - - you shall have to specify the Takara, where it is purchased from (names of product, city, state)
lines 118-119: „Quantitative PCR was performed with an ABI 7500 real-time PCR system (Applied Biosystems) using TB Green® qPCR Premix (Takara).” - you shall have to specify theApplied Biosystem and Takara, respectively.
lines 120-121: „The relative expression levels were calculated using the 2-ΔΔCT method based on the mean value of three technical replicates.” Here is a citation is necessary for 2-ΔΔCT method.
lines 127-128:” Transcriptome sequencing was performed on the Illumina HiSeq platform at Sangon Biotech (Shanghai) Co., Ltd.” – from the specification, the state (China) is missing.
line 131: „.HTSeq (v0.6.1) was used to count the read” – specify the HTSeq (v0.6.1), e.g. by webpage
line 136:”analysis was performed via the clusterProfile package”- specify this package.
Results:
lines 142-143:” these genes were named BcMYB1~BcMYB255 according to the sequence ID (Table S1).” The sequence ID can be found in the supplementary Table S2!
line 144: „as shown in Table S1. The number of amino acids …..”. This is the Table S2 which shows the number of amino acids, ect…
line 211: „We next analyzed the DEG sets using the PlantTFDB V5.0 database” Give a webpage here for specification.
lines 245-247: „This section may be divided by subheadings. It should provide a concise and precise description of the experimental results, their interpretation, as well as the experimental conclusions that can be drawn.” What is this? Is this from a previous reviewer?
Discussion:
lines 263-264: „ In previous research on Chinese cabbage (Brassica rapa ssp. pekinensis) Tthe MYB gene family was identified and characterized by Wang et al. and Saha et al.,” Instead of Wang et al. and Saha et al., you shall have to use squarish brackets with numbering of the paper cited and put into References.
lines 287-28:” We found that there were only two tandemly duplicated gene pairs among the BcMYBs, indicating the diversification of their functions (Figure 3, Table S2). It is may be presented in the Table S3….
References
The References shall have to corrected according to the Horticulture Instruction for Authors. References shall have to described as follows:
Journal Articles:
1. Author 1, A.B.; Author 2, C.D. Title of the article. Abbreviated Journal Name Year, Volume, page range.
Namely, the year shall have to write as bold and the Volume in italics, respectively.
Sincerely yours,
Reviewer 1
Author Response
Dear reviewer:
Thank you very much for taking the time to review this manuscript. We have revised the manuscript according to your suggestion and make point-to-point responses to your comments. Please see the attachment.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsDear Authors,
I have an opportunity to review manuscript entitled :” Genome-wide identification of the R2R3-MYB gene family in Chinese flowering cabbage and characterization of its response to Pectobacterium carotovorum infection” submitted to the Horticulturae, MDPI journal.
Authors concentrated on Chinese flowering cabbage response to Pectobacterium carotovorum stress considering the participation of MYB-gene family. Authors identified 255 R2R3-MYB genes in Chinese flowering cabbage genome and classified them into 29 subgroups based on phylogenetic comparison with Arabidopsis thaliana.
In my opinion the most potential results are transcriptomic data analyses, which reported that MYB TF genes are highly enriched in DEG sets. Combined together with phylogenetic and transcriptome analysis. Moreover, Authors identified 12 R2R3-MYB genes that can potentially play a role in the response to soft rot stress.
The introduction is quite sufficient, but I noticed lack of one information, if there are any data about involvement of MYB-TF in response to Pectobacterium or expand information about role to other pathogens, because Authors added mainly information about growth and development.
On the other side, the discussion part is very poor, Authors did not discussed their results deeply.
The first subpart of discussion is very similar to conclusions formed at the end of that work.
Please, erase highlighted changes during correction process in the whole manuscript.
Why analyses of results starting from citation of supplementary material not for figure presented in results?
In my opinion the documentation how plants inoculated looked like, for example in timepoint were plants probe were collected should be added. Especially then Authors presented data associated with resistance reaction;
Figure 2 should be enlarged, because informative data are lots for the reader.
In my opinion Authors have obtained results indicating differentially expressed MYB genes in comparison to reference TUB gene (if I guess properly) in response to Pectobacterium carotovorum inoculation. Nevertheless, Authors did not have any confirmation of defense, for example resistance response to that bacteria. Moreover, all statement underlined defense/ resistance reaction should be corrected. Furthermore, in the title we can find “characterization of its response” – Authors did not characterize the response – they highlighted only one group of genes-TFs like MYB factor. Therefore, in my opinion the manuscript should be re-written.
Please rethink editorial correction especially in abstract and introduction which parts revealed phrases similarities to reference 1and2 [ithentificate correction].
Author Response
Dear reviewer:
Thank you very much for taking the time to review this manuscript. We have revised the manuscript according to your suggestion and make point-to-point responses to your comments. Please see the attachment.
Author Response File: Author Response.pdf
Reviewer 3 Report
Comments and Suggestions for AuthorsThe responses of MYB TFs to abiotic stress in Chinese flowering cabbage have been preferentially studied so far. The article is original and has a high general interest in biotic factors like Pectobacterium carotovorum subsp. carotovorum causing disease in Brassica campestris L. ssp. chinensis. Many functions of the large family of MYB genes (important in regulatory role in plant growth and development) are still unknown in plants. By focusing on R2R3-MYB transcription factors identified in cabbage during bacterial infection, this research enriches our understanding of their role in plant defense mechanisms.
About the content:
The title, abstract, and keywords clearly reflect the paper's content. The introduction concisely delineates the problem. The experimental methods are sufficiently detailed. The discussion and results are well-justified. References are comprehensive and correctly cited.
About Presentation:
Length is commensurate with the paper's content. The manuscript is well written, but some minor points could be improved, in wording and style:
line 50: The gene "chitinase 1" should not be italicized as it is not a sequence name. However, referring to a specific gene like "chit1" with an NCBI accession number such as CA665185 in Triticum aestivum should be italicized. However, I see that the reference by Shan T. et al. (2016) does not adhere to this "italicization" rule.
About Scientific evaluation:
The general scientific approach is well articulated and explained effectively. Identification of the 12 differentially expressed BcMYB transcription factor genes of the R2R3 type under biotic stress conditions is particularly noteworthy. However, some data can be improved:
Line 86: Please mention the origin of the Pcc pathogen (purchased or from a laboratory collection?)
Line 126: Total RNA isolation and transcriptome sequencing were performed only once or at least twice – please clarify
Line 144: The physicochemical properties of the BcMYB proteins were shown in Table S2, not S1
Line 276: Please review the functional divergence data to ensure the correct table reference. Specifically, verify whether the table in question should be Table 2 or Table S3. Kindly cross-reference all supplementary tables mentioned in the manuscript for accuracy.
I recommend publishing the article after making minor corrections.
Author Response
Dear reviewer:
Thank you very much for taking the time to review this manuscript. We have revised the manuscript according to your suggestion and make point-to-point responses to your comments. Please see the attachment.
Author Response File: Author Response.pdf
Round 2
Reviewer 2 Report
Comments and Suggestions for AuthorsI admit that Authors add information to the introduction, discussion was improved. Discussion was slightly changed. Above all taking into account that Authors "softened" their statments conserning immune response I changed my opinion.
Nevertheless, added plants reaction symptoms are insufficient as well as conclusion was almost not changed, despite of it was highlighted as "new text"
