Genome-Wide Identification and Expression Analyses of the PP2C Gene Family in Paulownia fortunei
Round 1
Reviewer 1 Report
This manuscript titled “Genome-wide Identification and Expression Analyses of the PP2C Gene Family in Paulownia fortunei” presents essential new data about PP2C gene family.
Some minor remarks:
Line 15-16: In the abstract, "with the main motif structure being motifs 3-16-13-10-2-6-12-4-14-1-18-8" could be avoided. Please rearrange the sentence as well.
Line 72: “Phyllostachys heterocycle” should be in italic form “Phyllostachys heterocycle”.
Line 100: Webtool spontaneously modified their database. So, please add the access date of each webtool. Example: TAIR database (accessed on 16 November 2022).
Line 106: “of≤10-2” should be “of ≤10-2”
Line 108-109: Please use weblink, references and accessed date where it is applicable like SMART (http://smart.embl-heidelberg.de/) (accessed on 17 November 2022).
Line 134: “2000-bp sequence upstream” better to use “2000-bp upstream sequence”
Line 134-135: A recent study that looked at cis-elements with a 2000-bp promoter could be cited.
Line 135 and so on: “cis-acting” and “cis-elements” should be changed throughout the manuscript to “cis-acting” and “cis-elements”.
Line 204: In Figure 1, Could you please clear or darkened the subfamily names?
Line 238-239: Could you please add intron phase in the Figure 4b and describe it in the manuscript?
Line 287: Instead of “not” please use “uninfected”.
Line 318: Figure 1 should be Figure 6. Please check the names carefully.
Line 318: “P. fortunei” should be “P. fortunei”
Line 173 and so on: “P. fortunei(Figure 1)” should “P. fortune (Figure 1)”. Please follow the same style throughout the manuscript.
Some major remarks:
#1: Could you please analyze the subcellular localization using webtools such as "Cell-PLoc 2.0," WoLF PSORT, PredSL, and so on? If possible, please include GFP localization to demonstrate that the prediction is valid.
#2: Could you please analyze and include the PP2C miRNA target in the manuscript?
#3: It is better to use RNA-Seq data for co-expression network analysis and gene set enrichment analysis. Could you please conduct a "Gene Set Enrichment Analysis" (GSEA) and co-expression network analysis from the RNA-Seq data and include the results in the manuscript? It will help researchers better understand the biological role of the PP2C gene in Paulownia fortunei.
Author Response
Please see the attachment.
Author Response File: 
Author Response.docx
Reviewer 2 Report
It is advisable to provide photos of healthy and infected plants.
It is necessary to correct the signature in the figure 6.
The authors write about the effects of low temperature and stress. Aren't low temperatures included in the concept of stress?
In section 3.6, the authors point to a small number of promoters of the PfРР2С gene. It is necessary to give exact figures.
The list of references should be brought in line with the requirements of the journal.
Author Response
Please see the attachment.
Author Response File: Author Response.docx
Reviewer 3 Report
METHODS:
Why did the authors perform the sequence alignment in MEGA X, while the phylogenetic inference was conducted in MEGA 7? Instead, I recommend to conduct the alignement and phylonetic inferences from the newest versions of MEGA (MEGA 11). Also, the authors should test for the best nucleotide substitution model to be used before proceeding to the phylogenetic inference. With the most adequate model to be found, they could proceed with the phylogenetic inference using maximum-likelihood method including the best substitution model with 500 bootstrap replications. I do not object to neighbor-joining inference, but since maximum-linkelihood is available, I would rather use the latter because distinct species were involved. Neighbor-joining inference deals with distance-based measurements, which is best suited for genes within a species.
MOTIFS SEARCH: why did the authors set the motifs search to 20? Which criterion was used for that? The threshold for motif detection should be determined as the maximum number of motifs that could be detected without having a significant similarity among each other. That should be analyzed carefully.
FIGURES:
Figure 1 has poor resolution and needs to be improved. Also, the authors could color the gene IDs with the same color that they are represented with the phylogenetic tree. It assists the reader to understand putative gene duplications in the map as well as what the authors wrote: "Most genes on the same chromosome did not belong to the same subclade in 182 the evolutionary tree. These results suggested that different genes on the same chromo- 183 some may encode proteins with different functions".
Figure 2 also has poor resolution. Actually, all figures need to be improved for resolution. Attention to the figure that represents the expression profiles. It has the wrong number.
Figure 3: the protein representation could be "aligned" by their main DOMAIN, which is green. The same could be conducted for the motifs.
GENERAL OBSERVATIONS
Please italicize the name of the species in some lines, such as 143 and 144. Check the manuscript thoroughly for that.
Please italicize gene abbreviations and names when they refere to the gene (DNA sequence) itself, to distinguish from proteins. Example: PP2C genes. PP2C proteins.
Line 390: "has lagged behind". I think "is lagged behind" is better.
Lines 500-end of document: eliminate as they represent reference format.
Author Response
Please see the attachment.
Author Response File: Author Response.docx
Round 2
Reviewer 1 Report
The revised manuscript is well represented, but some minor changes are required. Furthermore, it is preferable to create some more distinct paragraphs with headings such as Future perspectives and conclusion.
Line195: “The members of protein prediction sites in chloroplasts are distributed in all but the D, I, J, and L subfamilies, and the distribution of members in the K subfamily reaches 100%.” should be changed to “Members of protein prediction sites in chloroplasts are distributed in all but the D, I, J, and L subfamilies, with the K subfamily having a 100% distribution.” Alternatively, rephrase.
Author Response
The revised manuscript is well represented, but some minor changes are required. Furthermore, it is preferable to create some more distinct paragraphs with headings such as Future perspectives and conclusion.
Answer: Listened to the experts and reorganized the end of the article and added a "Conclusion" heading. (line 433)
Line195: “The members of protein prediction sites in chloroplasts are distributed in all but the D, I, J, and L subfamilies, and the distribution of members in the K subfamily reaches 100%.” should be changed to “Members of protein prediction sites in chloroplasts are distributed in all but the D, I, J, and L subfamilies, with the K subfamily having a 100% distribution.” Alternatively, rephrase.
Answer: Already listened to the reviewers' comments and changed “The members of protein prediction sites in chloroplasts are distributed in all but the D, I, J, and L subfamilies, and the distribution of members in the K subfamily reaches 100%.” to “Members of protein prediction sites in chloroplasts are distributed in all but the D, I, J, and L subfamilies, with the K subfamily having a 100% distribution.”. (line 196)
I am very grateful to the reviewers for their noble suggestions on my article.
