Genome-Wide Analysis of TCP Transcription Factors and Their Expression Pattern Analysis of Rose Plants (Rosa chinensis)
Round 1
Reviewer 1 Report
The authors present an extensive study of the TCP genes family in Rose. The results are well presented, and the bioinformatics analysis is well performed.
The English language requires extensive revisions since I spotted several syntax and spelling mistakes (see more details in "Quality of English Language"). I suggest some results presentation improvements and discussion points make the manuscript more robust scientifically.
Methods
0) All methods - please add version for ALL the software in your methods. If it's an online tool, specify the day when it was used
1) Lines 291-293: Remove file names for the reference genomes/annotations and include the Rose species Ensembl ids and version
2) Line 301 - change "for sequence extracting" to "as query."
3) Line 302 - What is the 0.01 cutoff, in which tool? It's not clear; specify it better
4) Line 311 - "were got" is not correct English. Use "were obtained"
5) Line 325 - How did you root? On which outgroup? Please specify
6) Line 353 - How did you calculate the row Z-score for the heatmap? What is the row Z-score?
7) Line 367 - there is an underscore after 95_ <-. Please correct
Results
1) Line 76 - Never start the line with a number; please write 18 as eighteen
2) Line 81 - Rephrase "proteins are between 28087.84 and 50039.06 Da" to "protein weight ranges between .... Da"
3) Line 86 - " functional divergence among these protein". This statement is generic and may not be relevant in the case of TF. Please rephrase that to "there may be different groups of TF"
4) Table 1 - Remove the prefix of Gene ID "RchiOBHm_" This is the same for all the entries
5) Figure 2 - What is the phylogeny on the right? You don't describe it. Divide Figure in A and B and describe B
6) Figure 4 - Remove the bottom part, "Motif symbol...". The consensus can be seen from the logos. Also: please rename "logo1", "logo2" to "motif1", "motif2"...
7) Paragraph 2.6 + Figure 6: Polish figure by removing "RchiOBHm_" from text and Figure. This is a redundant info
8) Line 181 - I wonder why you randomly selected these genes. Are these relevant genes for you? Please rephrase to highlight the importance of this section. It looks like this is just a random experiment, and I strongly discourage describing it as such
9) Figure 7 - missing legend
General
1) Species names need to be in italics. Ex. lines 101-102. Check throughout the text
Please carefully check the sentence structure and syntax. I spotted several mistakes.
1) Lines 24-28: sentence too long. Please rephrase, especially "also are able to respond to stimulatory or inhibitory signals originating from within and outside the organism."
2) Line 34 - "a 59 amino acid which forming a basic-helix" change to "which form...."
3) Check all the verbs; 3rd person singular needs an "s". This is an example but please check through the manuscript: Lines 38-39 "Class I...., always bind" requires an "s" (binds). Same for line 42, "participate" needs to be "participates"
4) Line 58 - "and so on". Please remove this expression or rephrase. It's not suitable for a scientific manuscript
5) VERY IMPORTANT - Please use an active verb form. The manuscript is difficult to read. An example is on line 66 "was performed". Rephrase to the active form
Author Response
The authors present an extensive study of the TCP genes family in Rose. The results are well presented, and the bioinformatics analysis is well performed.
The English language requires extensive revisions since I spotted several syntax and spelling mistakes (see more details in "Quality of English Language"). I suggest some results presentation improvements and discussion points make the manuscript more robust scientifically.
Answer: Thanks a lot for your positive comments to our MS, we have tried our best to revise all the syntax and spelling mistakes with the help of MDPI editing service (https://www.mdpi.com/authors/english), all the corrections has been highlighted in red in the revised MS. Thanks again.
Methods
0) All methods - please add version for ALL the software in your methods. If it's an online tool, specify the day when it was used
Answer: Thank you very much for your valuable suggestion, I totally agree with the reviewer’s opinion, and we have added the version and used data in the revised MS, which has been highlighted in red in the methods part.
1) Lines 291-293: Remove file names for the reference genomes/annotations and include the Rose species Ensembl ids and version
Answer: Thanks a lot for your valuable suggestion, we have removed this file name in the revised MS.
2) Line 301 - change "for sequence extracting" to "as query."
Answer: Thanks a lot for your valuable suggestion, we have changed the "for sequence extracting" to "as query" in the revised MS, which has been highlighted in red in Line 304.
3) Line 302 - What is the 0.01 cutoff, in which tool? It's not clear; specify it better
Answer: Thanks a lot for your valuable suggestion, the new hidden Markov model file was built by Clustalw (version 2.1) software with E-value, so 0.01 as the cutoff to filter the sequences in our method. We have added the file in the revised MS, which has been highlighted in red in Line 305.
4) Line 311 - "were got" is not correct English. Use "were obtained"
Answer: Thanks for your careful works on our manuscript. we have changed the " were got " to " were obtained " in the revised MS, which has been highlighted in red in Line 315.
5) Line 325 - How did you root? On which outgroup? Please specify
Answer: Thank you very much for your careful work, but I'm sorry that I didn't quite understand your question. Line 325 is "The Gff3 file was used to analyze the transcript structure. The Gtf file was extract using the gffread command from the cufflinks package (version 2.2.1).", Gff3 file download from ensembl website (https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-56/gff3/rosa_chinensis/), The gtf file is obtained by extracting specific lines using the gffread command (gffread XX.gff3 -T -o XX.gtf).
6) Line 353 - How did you calculate the row Z-score for the heatmap? What is the row Z-score?
Answer: Thanks for your careful works on our manuscript. Actually, Z-score is the difference between a number and the average divided by the standard deviation. In our calculation, the difference is the expression data of the gene in a particular tissue subtracted from the average expression data of this gene in all tissues, and the standard deviation is the expression data of the gene in all tissues. z score in the heat map can be calculated by the difference and standard deviation.
In our heat map, the row Z-score is calculated by the expression of the same gene in different tissues, rather than the expression of different genes in the same tissue.
7) Line 367 - there is an underscore after 95_ <-. Please correct
Answer: Thanks for your careful works on our MS. We have corrected this mistake in the revised MS.
Results
1) Line 76 - Never start the line with a number; please write 18 as eighteen
Answer: Thanks for your careful works on our MS. We have corrected this mistake in the revised MS, which has been highlighted in red in Line 76, 89, 114 and so on.
2) Line 81 - Rephrase "proteins are between 28087.84 and 50039.06 Da" to "protein weight ranges between .... Da"
Answer: Thanks for your careful works on our MS. We have changed this description in the revised MS, which has been highlighted in red in Line 78.
3) Line 86 - " functional divergence among these protein". This statement is generic and may not be relevant in the case of TF. Please rephrase that to "there may be different groups of TF"
Answer: Thanks for your careful works on our manuscript. We have changed this description in the revised MS, which has been highlighted in red in Line 83.
4) Table 1 - Remove the prefix of Gene ID "RchiOBHm_" This is the same for all the entries
Answer: Thanks for your careful works on our MS. We have deleted the prefix of Gene ID "RchiOBHm_" in the whole MS in the revised MS.
5) Figure 2 - What is the phylogeny on the right? You don't describe it. Divide Figure in A and B and describe B
Answer: Thanks a lot for your valuable suggestion, we have corrected this in Figure 2 in the revised MS.
6) Figure 4 - Remove the bottom part, "Motif symbol...". The consensus can be seen from the logos. Also: please rename "logo1", "logo2" to "motif1", "motif2"...
Answer: Thanks a lot for your valuable suggestion, we have corrected this in Figure 4 in the revised MS.
7) Paragraph 2.6 + Figure 6: Polish figure by removing "RchiOBHm_" from text and Figure. This is a redundant info
Answer: Thanks a lot for your valuable suggestion, we have deleted the "RchiOBHm_" in Paragraph 2.6 and Figure 6 in the revised MS.
8) Line 181 - I wonder why you randomly selected these genes. Are these relevant genes for you? Please rephrase to highlight the importance of this section. It looks like this is just a random experiment, and I strongly discourage describing it as such
Answer: Thank you very much for your careful work. In the revised MS, we have added the reason, that is “The genes we selected are all TCP genes. According to the results of transcriptome analysis, three of the eight representative genes belong to specific tissue expression genes, and the remaining five genes are expressed in multiple tissues”, which has been highlighted in red in Line 178-180.
9) Figure 7 - missing legend
Answer: Thanks a lot for your valuable suggestion, we have added this figure legend in the revised MS, which has been highlighted in red in Line 197-198.
General
1) Species names need to be in italics. Ex. lines 101-102. Check throughout the text
Answer: Thanks a lot for your valuable suggestion, we have checked all the italics problem and corrected it in the revised MS, which has been highlighted in red.
Comments on the Quality of English Language
Please carefully check the sentence structure and syntax. I spotted several mistakes.
1) Lines 24-28: sentence too long. Please rephrase, especially "also are able to respond to stimulatory or inhibitory signals originating from within and outside the organism."
Answer: Thanks a lot for your valuable suggestion. We have changed this description in the revised MS, which has been highlighted in red in Line 26-29.
2) Line 34 - "a 59 amino acid which forming a basic-helix" change to "which form...."
Answer: Thanks a lot for your valuable suggestion. We have changed this description in the revised MS, which has been highlighted in red in Line 33-34.
3) Check all the verbs; 3rd person singular needs an "s". This is an example but please check through the manuscript: Lines 38-39 "Class I...., always bind" requires an "s" (binds). Same for line 42, "participate" needs to be "participates"
Answer: Thanks a lot for your valuable suggestion, we have corrected these 3rd person singular “s” problem in the revised MS, which has been highlighted in red in Line 39 and 40, and also we have checked all the MS to avoid this problem.
4) Line 58 - "and so on". Please remove this expression or rephrase. It's not suitable for a scientific manuscript
Answer: Thanks a lot for your valuable suggestion. We have deleted this description in the revised MS.
5) VERY IMPORTANT - Please use an active verb form. The manuscript is difficult to read. An example is on line 66 "was performed". Rephrase to the active form
Answer: Thanks a lot for your valuable suggestion. We have changed this sentence into active verb form, which has been highlighted in red in Line 64. And also, we have checked all the MS to avoid this problem.
Reviewer 2 Report
Title and introduction: it is better to provide TCP description before inserted abbreviation.
Line17: “may have led to the generation of new gene functions.” ??
Lines 24-27: complicated and confusing sentence. Please, rewrite in another way.
Line 28: “-ROLIFERATING CELL FACTOR1” PROLIFERATING???
Line 29: “gene family is one of the major TF specific and superfamily in plants” ??
Line 41: “always” - redundant.
Line 58: why “and tee”? and is redundant.
Line 70: “through reverse transcription-polymerase chain reaction (RT-
PCR) ???
Line 76: “were identified and renamed”? If you identified for the first time, you can nit renamed. You can give a name.
Line 105: “we” = We.
Line 137: Arabidopsis is not rose family. Please, be carefully during writing.
Lines 140-149: please, describe species in order as you described on lines 137-138.
Figure 5: in some screen gray lines almost not visible. Maybe you can change color to more dark.
Line 219; “For root development, lateral root formation, and root hair development and they also play a critical role in hormone…”??? Please, re-write.
Lines 206 - 221: this part of the text not have too much sense here. There is no any link/evidence with your data in Rose. Please, provide some link.
General, discussion require re-writing with more clear link with your own data.
Line 359: “reverse transcription-polymerase chain reaction (RT-PCR)” = qPCR.
Lines 360: please, provide more details about RNA isolation and qPCR analysis.
moderate corrections
Author Response
Comments and Suggestions for Authors
Title and introduction: it is better to provide TCP description before inserted abbreviation.
Answer: Thanks for your careful works on our manuscript. We have added the description of TCP at the first time in the revised MS, which has been highlighted in red in Line 28-29.
Line17: “may have led to the generation of new gene functions.” ??
Answer: Thanks for your careful works on our manuscript. We have corrected this description in the revised MS, that is “Segmental duplication events have contributed to the evolution of the TCP gene family and may generated new functions.” which has been highlighted in red in Line 17-18.
Lines 24-27: complicated and confusing sentence. Please, rewrite in another way.
Answer: Thanks for your careful works on our manuscript. We have corrected this sentence in the revised MS, which has been highlighted in red in Line 27-28.
Line 28: “-ROLIFERATING CELL FACTOR1” PROLIFERATING???
Answer: Thanks for your careful works on our manuscript. We have corrected this careless error in the revised MS, which has been highlighted in red in Line 29.
Line 29: “gene family is one of the major TF specific and superfamily in plants” ??
Answer: Thanks a lot for your valuable suggestion. We have corrected this obscure description in the revised MS, which has been highlighted in red in Line 28-30.
Line 41: “always” - redundant.
Answer: Thanks for your careful works on our manuscript. We have deleted this word “always” in the revised MS.
Line 58: why “and tee”? and is redundant.
Answer: Thanks for your careful works on our manuscript. We have deleted this word “and” in the revised MS.
Line 70: “through reverse transcription-polymerase chain reaction (RT-PCR) ???
Answer: Thanks a lot for your valuable suggestion. Actually, we used RT-PCR to certificate the RNA-seq data, and in the revised MS, we have corrected this description, which has been highlighted in red in Line 68.
Line 76: “were identified and renamed”? If you identified for the first time, you can nit renamed. You can give a name.
Answer: Thanks a lot for your valuable suggestion. We have corrected this in the revised MS, which has been highlighted in red in Line 74.
Line 105: “we” = We.
Answer: Thanks for your careful works on our MS. We have corrected this “we” in the revised MS, which has been highlighted in red in Line 102.
Line 137: Arabidopsis is not rose family. Please, be carefully during writing.
Answer: Thanks for your careful works on our manuscript. Sorry for this careless error, we have corrected this sentence in the revised MS, which has been highlighted in red in Line 135-136.
Lines 140-149: please, describe species in order as you described on lines 137-138.
Answer: Thanks a lot for your valuable suggestion. We have corrected this description in the revised MS, which has been highlighted in red in Line 140-148.
Figure 5: in some screen gray lines almost not visible. Maybe you can change color to more dark.
Answer: Thanks a lot for your valuable suggestion. We have changed the color in Figure 5 in the revised MS.
Line 219; “For root development, lateral root formation, and root hair development and they also play a critical role in hormone…”??? Please, re-write.
Answer: Thanks a lot for your valuable suggestion, we have deleted this obscure description in the revised MS.
Lines 206 - 221: this part of the text not have too much sense here. There is no any link/evidence with your data in Rose. Please, provide some link.
Answer: Thanks a lot for your valuable suggestion. We have deleted some nonsense sentence and rewritten this part in the revised MS, which has been highlighted in red in Line 200-207.
General, discussion require re-writing with more clear link with your own data.
Answer: Thanks a lot for your valuable suggestion. We almost have rewritten the discussion part in the revised MS, deleted some sentences, added some other sentences, which has been highlighted in red in Line 271-295.
Line 359: “reverse transcription-polymerase chain reaction (RT-PCR)” = qPCR.
Answer: Thanks a lot for your valuable suggestion. Actually, they are not the same, we have corrected this qPCR into RT-PCR in the revised MS, which has been highlighted in red in Line261, 264, and 268.
Lines 360: please, provide more details about RNA isolation and qPCR analysis.
Answer: Thanks a lot for your valuable suggestion. Actually, we thought the RNA extraction and RT-PCR analysis are very detailed, and we have corrected some obscure description in the revised MS, which has been highlighted in red in Line 366-377.
Comments on the Quality of English Language moderate corrections
Answer: Thank you very much for your positive affirmation to our manuscript. We have tried our best to revise the English language with the help of MDPI editing service (https://www.mdpi.com/authors/english), all the corrections has been highlighted in red in the revised MS. Thanks again.
Round 2
Reviewer 2 Report
Thank you for detailed answers and corrections. There are many minor points need to be further carefully checked and corrected. As one example: line 125: must be: "branch was" not were.
Line 367: please, clarify what do you really do: "reverse transcription-polymerase chain reaction (RT-PCR)" or real-time PCR (qPCR)?
I would suggest to mention in the text qPCR what combine reverse transcpription and real-time monitoring of gene expression.
moderate edition: were = was etc.
Author Response
Thank you for detailed answers and corrections. There are many minor points need to be further carefully checked and corrected. As one example: line 125: must be: "branch was" not were.
Answer: Thanks for your careful work on our manuscript. we have changed the "branch were" to "branch was" in the revised MS, which has been highlighted in red in Line 124.
Line 367: please, clarify what do you really do: "reverse transcription-polymerase chain reaction (RT-PCR)" or real-time PCR (qPCR)?
Answer: Thank you very much for your valuable suggestion and patient explanation. I totally agree with the reviewer’ point. So, we have corrected this error description "reverse transcription-polymerase chain reaction (RT-PCR)" into "quantitative real-time polymerase chain reaction (qPCR)" in the revised MS, which has been highlighted in red in Line 67-68.
I would suggest to mention in the text qPCR what combine reverse transcpription and real-time monitoring of gene expression.
Answer: Thank you very much for your valuable suggestion. I totally agree with the reviewer’ point. So, we have checked although the MS and corrected the "RTPCR" to "qPCR" in the revised MS, which has been highlighted in Line 267, 272, 275, 277, 279, 282, 392, 395, 397 and 400.
Comments on the Quality of English Language
moderate edition: were = was etc.
Answer: Thanks for your careful work on our MS. We have corrected these mistakes in the revised MS, which has been highlighted in Line 39, 59, 60, 66, 104, 124.
