Genome Wide Identification, Characterization, and Expression Analysis of YABBY-Gene Family in WHEAT (Triticum aestivum L.)
, Yuan Yang 1, Rahat Sharif 2, Sheng Nan Wu 1, Yanzhou Xie 1 and Chengshe Wang 1,*Round 1
Reviewer 1 Report
In this manuscript, the authors identified 21 YABBY genes in wheat, characterized their structure and potential functions, and analyzed their expressions in tissues, stages, and under abiotic and biotic stress conditions. The authors concluded that the YABBY genes play important role in growth, development, and resistance to various abiotic and biotic stresses. I have some minor comments and edits that may improve the manuscript.
Page 2: “[Li, J, Liu, et al., 2018]” needs be changed to a reference number.
Page 2: Change “The identified YABBY gene Expression levels…” to “expression”
Page 9: A detail description is needed for Figure 5. For example, green and red indicated the expression values increased and decreased, respectively. What was the control tissue or stage?
Page 9: Change “…S. tritici, Powdery mildew…” to “powdery mildew…”
Author Response
Reviewer 1
Comments and Suggestions for Authors
In this manuscript, the authors identified 21 YABBY genes in wheat, characterized their structure and potential functions, and analyzed their expressions in tissues, stages, and under abiotic and biotic stress conditions. The authors concluded that the YABBY genes play important role in growth, development, and resistance to various abiotic and biotic stresses. I have some minor comments and edits that may improve the manuscript.
Comment 1;
Page 2: “[Li, J, Liu, et al., 2018]” needs be changed to a reference number.
Page 2: Change “The identified YABBY gene Expression levels…” to “expression”
Page 9: A detail description is needed for Figure 5. For example, green and red indicated the expression values increased and decreased, respectively. What was the control tissue or stage?
Page 9: Change “…S. tritici, Powdery mildew…” to “powdery mildew…”
Response 1; Thanks for your comments. The following changes have been made according to the given suggestion.
Line 62; “[Li, J, Liu, et al., 2018]” changed to a [23].
Line The identified YABBY gene expression levels changed into “to expression”
Line 173; Detail description for Figure 5 is added, and as far control is concern it is clearly mention in material method that “The expression value of identified genes in response to applied treatments to the control was calculated with the ratio of the expression patterns in response to applied treatments” for further detail please check reference (Ma J, Yang Y et al., 2017).
Ma J, Yang Y, Luo W, Yang C, Ding P, Liu Y, et al. (2017) Genome-wide identification and analysis of the MADS-box gene family in bread wheat (Triticum aestivum L.). PLoS ONE 12(7):e0181443. https://doi.org/10.1371/journal. pone.0181443
Line 179; S. tritici, Powdery mildew is changed to “Powdery mildew”
We are very thankful for your valuable time and kind suggestion to make significant improvement in our final version.
Reviewer 2 Report
In their manuscript, Buttar et al are presenting an in silico analysis of the YABBY genes of wheat including data from public databases on the expression of these genes across tissues, developmental stages, abiotic and biotic stresses. Although this could be a valuable first step in identifying the role of these important genes in wheat, the authors fail to provide a clear message for the significance of their study, for example how this information could be used or be useful for wheat research in the future. However, the most important defect of the manuscript is the english language used that needs to be vastly improved in order for the manuscript to be even comprehensible. Unfortunately, almost every sentence seems to have a problem and I experienced great difficulty in trying to comprehend what the authors want to say. Authors do need to seriously address the issue for the manuscript to be understandable.
More specific comments:
Materials and Methods Section
“Proteins that do not exist were excluded”. What do the authors mean by that? Possibly proteins with no hits in wheat genome? How exactly did they perform the search on the wheatgenome.org website database?
Results Section
Authors include A. thaliana proteins in the phylogenetic tree of Figure 1 without providing any accession number for these proteins, just the names. They need to provide the accession numbers for these proteins.
Arabidopsis thaliana has 6 YABBY genes; FILAMENTOUS FLOWER (FIL), YAB2, YAB3, YAB5, CRABS CLAW and INNER NO OUTER (INO) (Bowman 2000). Genes are indeed grouped in 5 subfamilies. In their introduction authors refer to this without providing any reference and without mentioning the INO gene/subfamily. Yet in the Results section and Table 1, they mention that they find three wheat genes which they group as TaYABBY2-2A, TaYABBY2-2B and TaYABBY2-2D into the ONI (? Possibly INO ?) subfamily. Could the authors please clarify that or at least provide some reference in the introduction section?
In Figure 5 there’s no explanation for the abbreviations used e.g. GTE = grain tissue specific expression at 12 days post anthesis. I had to go to the Supplementary excel file to understand what these abbreviations stand for. Although authors mention in their Materials and Methods section that all abbreviations of treatments and materials are provided in Table S1, I believe that this is vital information that has to be included in the main manuscript. They do provide some abbreviations explanations in the Discussion section but it is too late.
Why do the authors not use the same colors for heatmap of Figure 6 as in Figure 5? In my opinion it would be much easier to use the standard green and red colors for gene expression and keep a consistency throughout the paper. Again, there’s no explanation for the abbreviations included in the figure. Same goes for Figure 7.
How did the authors perform the protein interaction of YABBY proteins? They mention nothing in their Materials and Methods section!
Discussion Section
5.1: “The constructed evolutionary tree sub-divided into five groups, based on their evolutionary similarity with Arabidopsis (Fig-1), obtained results was same as previously identified in Arabidopsis [7].” Reference refers to YABBY family genome-wide analysis in grapevine not Arabidopsis!
“Thus, open a new avenue toward a new study”. This is a bit vague statement. What is exactly the authors’ point here?
5.2: “The transcriptome analyses of FHB recombinant inbreed line carrying resistant (R-RIL) suggested that there the up-regulation of certain group of transcription factors was the backbone of resistance [41]”. This is one of the many sentences that I cannot understand what the authors mean.
Also, in the same section I have a difficulty trying to make a trend out of the expression data that authors discuss as they jump from heat and drought stress to plant development and different tissues and biotic stresses. Authors need to be a bit more specific because presenting data in bulk does not help in drawing a clear picture.
Section 5.2.1 I don’t think the discussion of the validation of expression data fits here. Probably authors are trying to stress out that the RNA-seq data they used to work on are valid since they are validated by two different expression atlases but I don’t think they should discuss this in a whole section. Maybe shorting this section or adding a comment in the previous one should be enough.
Author Response
Reviewer 2
Comments and Suggestions for Authors
In their manuscript, Buttar et al are presenting an in silico analysis of the YABBY genes of wheat including data from public databases on the expression of these genes across tissues, developmental stages, abiotic and biotic stresses. Although this could be a valuable first step in identifying the role of these important genes in wheat, the authors fail to provide a clear message for the significance of their study, for example how this information could be used or be useful for wheat research in the future.
More specific comments:
Comment 1
Materials and Methods Section
“Proteins that do not exist were excluded”. What do the authors mean by that? Possibly proteins with no hits in wheat genome? How exactly did they perform the search on the wheatgenome.org website database?
Response 1; Thanks for your comments; we are very thankful to point out critical mistake. The change has been made in the manuscript as follow. “Proteins which does not contain YABBY domain were excluded”.
Line 69-77 We have rewritten the whole passage with more clarity. For wheatgenome.org website we used ensemble plant (Triticum aestivum IWGSC) database.
Comment 2
Results Section
Authors include A. thaliana proteins in the phylogenetic tree of Figure 1 without providing any accession number for these proteins, just the names. They need to provide the accession numbers for these proteins.
Response 2; Thanks for highlighting this issue. We have added the accession number in the supplementary table (5).
Comments 3
Arabidopsis thaliana has 6 YABBY genes; FILAMENTOUS FLOWER (FIL), YAB2, YAB3, YAB5, CRABS CLAW and INNER NO OUTER (INO) (Bowman 2000). Genes are indeed grouped in 5 subfamilies. In their introduction authors refer to this without providing any reference and without mentioning the INO gene/subfamily. Yet in the Results section and Table 1, they mention that they find three wheat genes which they group as TaYABBY2-2A, TaYABBY2-2B and TaYABBY2-2D into the ONI (? Possibly INO ?) Subfamily. Could the authors please clarify that or at least provide some reference in the introduction section?
Response 3; we have revised the mentioned paragraph and made changes as per reviewer suggestion.
Comments 4;
In Figure 5 there’s no explanation for the abbreviations used e.g. GTE = grain tissue specific expression at 12 days post anthesis. I had to go to the Supplementary excel file to understand what these abbreviations stand for. Although authors mention in their Materials and Methods section that all abbreviations of treatments and materials are provided in Table S1, I believe that this is vital information that has to be included in the main manuscript. They do provide some abbreviations explanations in the Discussion section but it is too late.
Response 4; Thanks for your comments; the complete detail of abbreviations is added in figure legend and further detail is provided in supplementary detail (sheet 1-4).
Comments 5
Why do the authors not use the same colors for heatmap of Figure 6 as in Figure 5? In my opinion it would be much easier to use the standard green and red colors for gene expression and keep a consistency throughout the paper. Again, there’s no explanation for the abbreviations included in the figure. Same goes for Figure 7.
Response 5; We have remade the heatmap according to the reviewer suggestion. Further, the abbreviations have been provided in the manuscript.
Comments 6;
How did the authors perform the protein interaction of YABBY proteins? They mention nothing in their Materials and Methods section!
Response 6; Thanks for the comment. We have included the methodology of protein interaction in M&M section.
Comments 7
Discussion Section
5.1: “The constructed evolutionary tree sub-divided into five groups, based on their evolutionary similarity with Arabidopsis (Fig-1), obtained results was same as previously identified in Arabidopsis [7].” Reference refers to YABBY family genome-wide analysis in grapevine not Arabidopsis!
“Thus, open a new avenue toward a new study”. This is a bit vague statement. What is exactly the authors’ point here?
Response 7; Thanks for your comments. The phylogenetic tree has been revised and inserted in the manuscript according to the reviewer suggestion.
Comments 8;
5.2: “The transcriptome analyses of FHB recombinant inbreed line carrying resistant (R-RIL) suggested that there the up-regulation of certain group of transcription factors was the backbone of resistance [41]”. This is one of the many sentences that I cannot understand what the authors mean.
Response; Thanks for your comments; we are agreeing with your specific point related to 5.2 passage. We have thoroughly revised it and changes has been highlighted in yellow color.
Comments 9;
Also, in the same section I have a difficulty trying to make a trend out of the expression data that authors discuss as they jump from heat and drought stress to plant development and different tissues and biotic stresses. Authors need to be a bit more specific because presenting data in bulk does not help in drawing a clear picture.
Response 9; We have discussed each section in a separate passage as per reviewer suggestion.
Line 320; 5.2.1 given detail under normal conditions
Line 334; 5.2.2 only given detail of biotic stress
Line 341; 5.2.3 only given detail of abiotic stress.
Comments 10
Section 5.2.1 I don’t think the discussion of the validation of expression data fits here. Probably authors are trying to stress out that the RNA-seq data they used to work on are valid since they are validated by two different expression atlases but I don’t think they should discuss this in a whole section. Maybe shorting this section or adding a comment in the previous one should be enough.
Response 10; thanks for your comments; we have made changes as you suggested. Dissolved 5.2.1 passage with mentioning this portion with previous one.
As per English is concern significant revision is done by well-known Professor Rehman, Ata-Ur from Australia and Asgar Farahnaky, PhD Associate Professor in Food Technology and Innovation School of Science, RMIT University, Bundoora West Campus (Building 201, L4, R03) Melbourne, Vic, ,to make manuscript to be even more comprehensible.
Round 2
Reviewer 2 Report
I understand and appreciate authors efforts to improve the manuscript but there are still several issues in most sentences that impair comprehension. Written English needs to be significantly improved in order for the manuscript to be readable. Authors need to address this matter otherwise it is seriously difficult to understand what they are trying to say most of the times.
More specific comments;
For fungi pathogens please provide the latin name (the first time) and then use the common name. Also, authors keep repeating Triticum aestivum full latin name of wheat several times. They should use an abbreviation if they want to use its latin name. Authors do not need to repeat abbreviations they are using, for example they use FILAMENTOUS FLOWER (FIL) abbreviation in full, several times in the text. The same with CRABS CLAW (CRC) which by the way in Line 339 is CABS CLAW. They need to just mention all abbreviations IN FULL the first time they are using them and then use the abbreviation in the rest of the manuscript.
Lines 86-89; “The expression value of identified genes in response to applied treatments in comparison to the control was calculated with the ratio of the expression patterns in response to applied treatments as followed” ; This sentence is one of the many that does not make any sense. How exactly did the authors calculate the expression values of identified genes?
Lines 315-316; “….has been approved” ??? Should the authors use here another verb?
Lines 331-332; “However, in other YABBY1, YABBY5 did not show clear response against FHB”. I do not understand that phrase (and that’s only one of the many I don’t get).
Author Response
More specific comments;
Comment 1;
For fungi pathogens please provide the latin name (the first time) and then use the common name. Also, authors keep repeating Triticum aestivum full latin name of wheat several times. They should use an abbreviation if they want to use its latin name. Authors do not need to repeat abbreviations they are using, for example they use FILAMENTOUS FLOWER (FIL) abbreviation in full, several times in the text. The same with CRABS CLAW (CRC) which by the way in Line 339 is CABS CLAW. They need to just mention all abbreviations IN FULL the first time they are using them and then use the abbreviation in the rest of the manuscript.
Response Thanks for your comments; the whole manuscript in carefully revised is according to given instruction.
Comment 2;
Lines 86-89; “The expression value of identified genes in response to applied treatments in comparison to the control was calculated with the ratio of the expression patterns in response to applied treatments as followed” ; This sentence is one of the many that does not make any sense. How exactly did the authors calculate the expression values of identified genes?
Response; thanks for your comments; Line 84-88 has been revised with more clarity.
Comments 3;
Lines 315-316; “….has been approved” ??? Should the authors use here another verb?
Response 3. Thanks for your comments; revised as suggested.
Comment 4
Lines 331-332; “However, in other YABBY1, YABBY5 did not show clear response against FHB”. I do not understand that phrase (and that’s only one of the many I don’t get).
Response; Thanks for your comments; the following line has been revised.
We are very thankful for your kind assistant to thoroughly improve our manuscript. As per English is concern significant revision is done by well-known Professor Rehman, Ata-Ur from Australia and Asgar Farahnaky, PhD Associate Professor in Food Technology and Innovation School of Science, RMIT University, Bundoora West Campus (Building 201, L4, R03) Melbourne, Vic, ,to make manuscript to be even more comprehensible.
