Genome-Wide Identification and Characterization of YABBY Gene Family in Juglans regia and Juglans mandshurica
, Jiangtao Wang 1, Shenqun Chen 2,†, Mengdi Li 1, Gang Wang 2, Na Hou 2,* and Peng Zhao 1,*
Luciano Calderón
Round 1
Reviewer 1 Report
Dear authors, I have read your work Genome-Wide Identification and Characterization of YABBY Gene Family in Juglans regia and Juglans mandshurica, I have to say that your work is consistent and well presented. The only recommendation I have to make is that you could improve the resolution quality of some of your images (1, 2, 3 and 5). Finally, I understand that you have conducted a bioinformatic approach to study different aspects of the YABBY gene family. However, it is always recommendable to conduct experimental lab work to support at least some of the observations made, otherwise you remain always the field of speculations, drastically lowering the strength of the statements performed.
Author Response
Response to Reviewer 1 Comments
Thank you for your valuable comments. We have studied the valuable comments from you carefully, tried our best to revise the manuscript. The point to point responds to the reviewer’s comments as following:
Open Review
( ) I would not like to sign my review report
(x) I would like to sign my review report
English language and style
( ) Extensive editing of English language and style required
( ) Moderate English changes required
(x) English language and style are fine/minor spell check required
( ) I don't feel qualified to judge about the English language and style
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Comments and Suggestions for Authors
Dear authors, I have read your work Genome-Wide Identification and Characterization of YABBY Gene Family in Juglans regia and Juglans mandshurica, I have to say that your work is consistent and well presented. The only recommendation I have to make is that you could improve the resolution quality of some of your images (1, 2, 3 and 5). Finally, I understand that you have conducted a bioinformatic approach to study different aspects of the YABBY gene family. However, it is always recommendable to conduct experimental lab work to support at least some of the observations made, otherwise you remain always the field of speculations, drastically lowering the strength of the statements performed.
Point 1: Dear authors, I have read your work Genome-Wide Identification and Characterization of YABBY Gene Family in Juglans regia and Juglans mandshurica, I have to say that your work is consistent and well presented. The only recommendation I have to make is that you could improve the resolution quality of some of your images (1, 2, 3 and 5).
Response: Dear editor, thank you for your positive comments and suggestions. We have improved the resolution quality of images (Figure1, 2, 3 and 5) according to your nice and useful suggestions. All figures were improved as high dpi in the revision. We also improved the figure 4 and figure 6 as high dpi in the revision. We have revised the relevant figures and we have re-inserted it in our manuscript.
Point 2: Finally, I understand that you have conducted a bioinformatic approach to study different aspects of the YABBY gene family. However, it is always recommendable to conduct experimental lab work to support at least some of the observations made, otherwise you remain always the field of speculations, drastically lowering the strength of the statements performed.
Response: Thank you for your warm suggestions. In this study, to investigate tissue-specific YABBY gene expression patterns in J. regia and its wild related species J. mandshurica, we analyzed the gene expression profiles used the transcriptome data from female flowers, male flowers, leaves and green pericarp. The expression profile analysis indicated that the existence of these identified YABBY genes. There was no doubt that your suggestions were absolutely right and we really appreciated it. We also realize the importance of experiment, field work, and morphology observations. The important tree species J. regia and its wild related species J. mandshurica were the major research object in our lab for a long time. As you suggested, in future research, we will do more experiments in the lab and field investigations to provide more strength for our scientific researches. Especially, focused on the YABBY, to prove our point of view more effectively, the gene function verification and regulatory mechanism will be deeply investigated via experiments. Thank you again, deeply, hope that above explanation can be acceptable to you
Thank you for your consideration our manuscript of “Genome-Wide Identification and Characterization of YABBY Gene Family in Juglans regia and Juglans mandshurica " publish on journal of Agronomy.
Sincerely,
Prof. Peng Zhao
Author Response File: 
Author Response.docx
Reviewer 2 Report
The manuscript describes the identification and characterization of YABBY genes in two Juglans species through a genome wide approach.
In total, the authors identified 19 YABBY genes. They performed a phylogenetic analysis including the YABBY gene sequences of Arabidopsis and rice, analyzed the protein domain and gene structure, investigated the chromosomal localizations and determined the expression profiles of YABBY genes by analyzing the available transcriptome data. I believe that a lot of work was done and the research was correctly conducted. the results are convincing and appropriately shown. However, I think that a few improvements are necessary before the publication:
1. In the first paragraph of the Introduction, the authors mentioned the abiotic stresses however the YABBY genes are involved in the regulation of various processes, such as the plant developmental, flowering, abiotic and biotic responses. Therefore, I believe that opening the Introduction section by talking about the biotic stresses is not appropriate. I suggest focusing on the studies performed so far about the YABBY genes in other species. For example, some recent studies should be mentioned: DOI: 10.1038/s41438-021-00467-5 DOI: 10.3390/agronomy10081189 DOI: 10.3390/plants10010021
2. Please check all the references. Some of them are not relevant, e.g. [12] (line 46) and [26] (line 68).
3. Check lines 279-281.
4. The figure 6 capture should be revised. The panels are not properly described. Panel c is not clear to me. In which tissue the transcriptome was analyzed? Which varieties were used?
5. I suggest reorganizing the Discussion section discussing the results in the same order they appear in the Results section in order to make this section more clear for the reader.
6. Please, check all the typos and errors, e.g. “JRYABBY and JRYABBY” (line 136), “members on chr5, chr13, and chr4 chromosomes” (line 206), “on other the chromosomes” (line 209).
Author Response
Response to Reviewer 2 Comments
Thank you for your valuable comments. We have studied the valuable comments from you carefully, made a significant effort to make the work clearer, and tried our best to revise the manuscript. The point to point responds to the reviewer’s comments as following:
Open Review
(x) I would not like to sign my review report
( ) I would like to sign my review report
English language and style
( ) Extensive editing of English language and style required
( ) Moderate English changes required
(x) English language and style are fine/minor spell check required
( ) I don't feel qualified to judge about the English language and style
|
Yes |
Can be improved |
Must be improved |
Not applicable |
|
|
Does the introduction provide sufficient background and include all relevant references? |
( ) |
(x) |
( ) |
( ) |
|
Are all the cited references relevant to the research? |
( ) |
( ) |
(x) |
( ) |
|
Is the research design appropriate? |
(x) |
( ) |
( ) |
( ) |
|
Are the methods adequately described? |
(x) |
( ) |
( ) |
( ) |
|
Are the results clearly presented? |
( ) |
(x) |
( ) |
( ) |
|
Are the conclusions supported by the results? |
(x) |
( ) |
( ) |
( ) |
Comments and Suggestions for Authors
The manuscript describes the identification and characterization of YABBY genes in two Juglans species through a genome wide approach. In total, the authors identified 19 YABBY genes. They performed a phylogenetic analysis including the YABBY gene sequences of Arabidopsis and rice, analyzed the protein domain and gene structure, investigated the chromosomal localizations and determined the expression profiles of YABBY genes by analyzing the available transcriptome data. I believe that a lot of work was done and the research was correctly conducted. the results are convincing and appropriately shown. However, I think that a few improvements are necessary before the publication:
Response: Thank you for your professional and positive comments and suggestions. We have studied the valuable comments from you carefully, and tried our best to revise the manuscript.
Point 1: In the first paragraph of the Introduction, the authors mentioned the abiotic stresses however the YABBY genes are involved in the regulation of various processes, such as the plant developmental, flowering, abiotic and biotic responses. Therefore, I believe that opening the Introduction section by talking about the biotic stresses is not appropriate. I suggest focusing on the studies performed so far about the YABBY genes in other species. For example, some recent studies should be mentioned: DOI: 10.1038/s41438-021-00467-5 DOI: 10.3390/agronomy10081189 DOI: 10.3390/plants10010021.
Response: Thank you for your nice comments. YABBY genes are involved in the regulation of various processes, such as the plant developmental, flowering, abiotic and biotic responses. We added the describes in the Introduction section following your suggestions. We revised our writing from Line 34 to 39 as followings: “The YABBY transcription factor has a prominent role in regulating plant growth and developmental activities, such as the plant developmental, flowering, abiotic, and biotic responses [1-5]. YABBY proteins are comprised of two highly conserved DNA-binding domains, namely the zinc finger-like domain (C2C2) and helix–loop–helix domain (YABBY), respectively [2]. In important crops, YABBY genes have been examined in their related genomes, including 21 in Wheat [3], 17 in soybean [4], 8 in rice [5] and 30 in Cucumber [6]. In woody plants, YABBY genes have been examined in their related genomes, namely 55 genes in Seven Species of Magnoliids [7].”
We also added sentences from Line 68 to 71 in the revision as followings: “INO and its role in ovule development were mainly characterized in the model plant species Arabidopsis. Arabidopsis INO was restrictively expressed in the furthermost cell layer of the outer integument in ovules to promote its growth [7,25,26].”
We added the new references as followings:
- Liu, X.; Liao, X.-Y.; Zheng, Y.; Zhu, M.-J.; Yu, X.; Jiang, Y.-T.; Zhang, D.-Y.; Ma, L.; Xu, X.-Y.; Liu, Z.-J.; et al. Genome-Wide Identification of the YABBY Gene Family in Seven Species of Magnoliids and Expression Analysis in Litsea. Plants 2021, 10, 21.
- Buttar, Z.A.; Yang, Y.; Sharif, R.; Nan Wu, S.; Xie, Y.; Wang, C. Genome Wide Identification, Characterization, and Expression Analysis of YABBY-Gene Family in WHEAT (Triticum aestivum L.). Agronomy 2020, 10, 1189.
- di Rienzo, V.; Imanifard, Z.; Mascio, I.; Gasser, C.S.; Skinner, D.J.; Pierri, C.L.; Marini, M.; Fanelli, V.; Sabetta, W.; Montemurro, C.; et al. Functional conservation of the grapevine candidate gene INNER NO OUTER for ovule development and seed formation. Hortic Res 2021, 8, 29-29, doi:10.1038/s41438-021-00467-5.
Point 2: Please check all the references. Some of them are not relevant, e.g. [12] (line 46) and [26] (line 68).
Response: Thank you for your comments. We have corrected the references in the manuscript. Thank you again for your rigorous attitude. We checked all reference orders and numbers in the text again.
Point 3: Check lines 279-281.
Response: Thank you for your careful comments. We have deleted this part of the manuscript.
Point 4: The figure 6 capture should be revised. The panels are not properly described. Panel c is not clear to me. In which tissue the transcriptome was analyzed? Which varieties were used?
Response: Thank you for your valuable comments. The Panel c showed the expression patterns of identified YABBY genes in J. regia under biotic stress. F26 indicates anthracnose-resistant varieties, F423 indicates anthracnose-susceptible varieties. Numbers after ‘-’ represent time after infection (unit: hour). Colored scale reflects gene expression levels. We have revised the contents of the figure legends in Figure 6. We have revised the relevant figures and we have re-inserted it in our manuscript.Thank you again.
Figure 6. Expression patterns of YABBY genes in J. regia and J. mandshurica. (a) Expression patterns of identified YABBYs in female flowers, male flowers, leaves, and green pericarps of J. regia.; RF, female flowers of J. regia; RM, male flowers of J. regia; RL, leaves of J. regia; RG, green pericarp of J. regia; (b) Expression patterns of identified YABBYs in female flowers, male flowers, leaves, and green pericarps of J. mandshurica. MF, female flowers of J. mandshurica; MM, male flowers of J. mandshurica; ML, leaves of J. mandshurica; MG, green pericarps of J. mandshurica; (c) Expression patterns of identified YABBY genes in J. regia under biotic stress. F26 indicates anthracnose-resistant varieties, F423 indicates anthracnose-susceptible varieties. Numbers after ‘-’ represent time after infection (unit:hour). Colored scale reflects gene expression levels.
Point 5: I suggest reorganizing the Discussion section discussing the results in the same order they appear in the Results section in order to make this section more clear for the reader.
Response: Thank you for your comments. We adjusted the order of discussion part in the manuscript according to your suggestions from Line 320 to 322, Line 335 to 342, Line 381 to 386.
Point 6: Please, check all the typos and errors, e.g., “JRYABBY and JRYABBY” (line 136), “members on chr5, chr13, and chr4 chromosomes” (line 206), “on other the chromosomes” (line 209).
Response: Thank you for pointing this out. We are very sorry for our clerical errors and we have corrected the misspelling in the manuscript. We double checked typos and errors in the whole manuscript, e.g., gene name consistent, chromosome numbers, italic format, and reference numbers etc. Thank you very much for your professional suggestions.
Thank you for your consideration our manuscript of “Genome-Wide Identification and Characterization of YABBY Gene Family in Juglans regia and Juglans mandshurica " publish on journal of Agronomy.
Sincerely,
Prof. Peng Zhao
Author Response File: Author Response.docx
