Allele-Specific Transcriptional Regulation of Shoot Regeneration in Hybrid Poplar
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsReviewer’s Comments
The manuscript entitled, “Allele-specific transcriptional of shoot regeneration in hybrid poplar” would be of significant importance to plant science research community and ecologists. However, before final submission, minor changes needs to be incorporated to make it worth reading.
Introduction: The last paragraph of the this section need to be modified, and authors should clearly states here the objectives of this study. This paragraph should be adjusted in discussion or conclusion section.
Materials and Methods: Methodology adopted for to transcriptional analysis should be mentioned in detail.
Discussion: This section is the most weak part of this manuscript and is also too brief. Author’s must explain/discuss their results and their significance in more details and comprehensive manner.
Conclusion: conclusion is missing.
References: Cite more recent references of 2022 and 2023.
Author Response
Please see the attachment.
Author Response File: 
Author Response.docx
Reviewer 2 Report
Comments and Suggestions for AuthorsThe main idea behind this paper is interesting, however some poinst are unclear and need further explanations:
1. Why authors didn't use Populus tricchocarpa genome to charaterize REGs?
2. There's no information about RNAseq data at all, how is was obtained and processed.
3. What about alternative splicing between alleles?
Author Response
Please see the attachment.
Author Response File: Author Response.docx
Reviewer 3 Report
Comments and Suggestions for AuthorsThe manuscript by Ding et al. presents an analysis of the transcriptomic data for the regeneration-related genes in hybrid poplar. The manuscript starts with a good Introduction, then the authors show a scheme summarizing the molecular mechanisms of plant regeneration based on the earlier published review paper.
However, the following sections of the manuscript raise lot of questions. First, the authors do not provide the detailed figure legends, and it is very hard to understand what is shown in each figure. Therefore, at this round of review, I may not have fully understood the results presented. Secondly, the authors describe the differential gene expression, but it is not evident, what stages (?) were compared. Finally, the analysis of allele-specific expression is fully unclear.
Comments:
1) Line 105: “second data set was from our in-house transcription data”. The detailed description and quality check of these data are missing.
2) Line 127: “Homologous genes of these REGs were also identified in Arabidopsis, including 895 genes from 30 families (Table S2), these genes were termed as REG-homologous genes (REGHs).” I do not understand what is the point of analyzing the expression of such a large number of REG homologues. I am not sure that there is any chance that these genes have any role in the regeneration process of Arabidopsis. For poplar, this chance is even lower.
3) Line 136: “Figure 1. Signal transduction pathways in plant regeneration [3].” Such reference suggests that the figure has been taken from [3]. The authors should say something like “summarized based on [3]”.
4) “Based on the annotation of orthologous pairs between two plants, we first calculated….” Should be “two plant species”, because the authors mean Arabidopsis and poplar. This should be corrected throughout the paper.
5) Line 145: “The results indicated that about half (51) of the gene pairs exhibited positively correlations, nine of them were significantly positive correlated”. How did you select these nine genes? The analysis of significant and non-significant correlations is not presented.
6) Line 166: “Correlations of regeneration-related genes…” The authors describe correlations between the gene expression levels, not between genes. Please, correct it throughout the text.
7) Figure 2: As I understood, panel (a) shows correlations between the levels of gene expression (please specify the units in the legend, (TPM?)), while panel (b) shows differentially expressed genes (DEGs). However, the authors do not specify contrasts, for which the expression was compared in each column. I suggest that they compare different stages. However, no comparisons are mentioned in the Results or Materials and Methods.
8) Line 183: “The expression trends of REGH genes were further analyzed to identify the major expression patterns of differentially expressed genes.” No information about DEGs here either.
9) Supplementary Figures are supplied within the Word document, where they could not be zoomed in, and the labels are not readable.
10) Figure 4 lacks a detailed legend. Nothing is written about the six clusters. What do the trend lines show? What plant species are they associated with?
11) Line 186: “In cluster 1, 86 Arabidopsis and 119 poplar genes were down-regulated during the callus induction stage”. I do not see any up- or down- regulated genes in Figure 4.
12) The meaning of Figure 6 is fully unclear. I suggest that the left-hand side shows the expression for the alleles of subgenomes; however, for some genes, only one allele is shown in the figure, while for others, two alleles are shown. Overall, if the expression of Arabidopsis genes is shown on the right, what is the point of such comparison?
13) The gene names should be italicized throughout the manuscript.
14) Line 15: “in hybrid poplar (Populus alba × P. glandulosa clone 84K) “. Please correct.
Author Response
Please see the attachment.
Author Response File: Author Response.docx
Round 2
Reviewer 1 Report
Comments and Suggestions for AuthorsPaper has been improved considerably and could be considered for publication.
Reviewer 3 Report
Comments and Suggestions for AuthorsDuring the revision, the manuscript by Ding et al. has been substantially improved. The authors fully addressed all my comments.
