Molecular Regulation of Bud Regeneration from Callus of Hybrid Sweetgum (Liquidambar styraciflua × Liquidambar formosana)
Round 1
Reviewer 1 Report
Comments from the reviewer:
- The authors attempted to investigate the Regulation of Bud Regeneration at the molecular level from Callus of Hybrid Sweetgum. The work seems interesting, but there are certain issues that need to be addressed by the authors before the manuscript (MS) is recommended for acceptance.
- The authors may provide a more detailed explanation of "pluripotency" and "totipotency" in plant cells for readers who might not be familiar with these terms. Also, the authors may add the importance of adventitious bud regeneration in plant research and its applications briefly for the general audience.
- Line-46, KCS should be first written in long form and then give the abbreviated form in the bracket.
- Line-51, BGLU should also be written in the long form when first mentioned in the MS, and the abbreviated form can be used later in the MS.
- Line 53-54, please change the English writing.
- Line 57-58, please change the style of English writing.
- The authors may include more details about the specific growth conditions, culture media, and hormone concentrations used for callus induction and bud regeneration. This will help others to replicate the culture experiment.
- Why is the transcriptomic analysis needed for NRC, as they normally do not give rise to new plants?
- Line 166-170, the authors compared the upregulated genes of RC with NRC. However, the results of NRC were not mentioned in the MS.
- Line 173-175, the same thing is found here also; if the comparison is made between two entities, their respective values should be highlighted. If there are similar cases in the other parts of the MS, kindly rectify them.
- Line 213, Put a comma after “metabolism”.
- The authors may add briefly the possible biological significance of the upregulated and downregulated genes in the Phenylpropanoid biosynthesis pathway in the discussion part of the MS.
- The authors may also include the possible impact of differentially variable splicing events identified in this study on the regulation of gene expression and cellular processes related to bud regeneration.
- The conclusion part is missing in the MS. Kindly insert it.
- There are also some minor grammar errors in the MS. The authors are requested to rectify those. The authors need to make modifications in MS as suggested by the reviewer before the MS is accepted for publication in the journal.
Some minor grammar errors and some modification needed in style of English writing in MS which I have already mentioned in the comments. Please do the needful.
Author Response
Dear reviewer,
Thank you for your comments concerning our manuscript entitled “Molecular Regulation of Bud Regeneration from Callus of Hybrid Sweetgum” (ID: 2591991). Those comments are all valuable and very helpful for revising and improving our paper, as well as the important guiding significance to our researches. We have studied comments carefully and have made correction which we hope meet with approval. We have submitted documents with tracked changes to highlight the revisions. (The file uploaded below is the revised paper.)The main corrections and the responds to the comments are as following:
- Comment: The authors may provide a more detailed explanation of“pluripotency”and “totipotency” in plant cells for readers who might not be familiar with these terms.
Response: Accept it. We appreciate it very much for this good suggestion. This article is about the regenerability of callus, it is appropriate to mention “pluripotency”, and “totipotency” has been removed. In addition, “pluripotency” has been explained in the introduction section on page 1, lines 37 to 39.
- Comment: Also, the authors may add the importance of adventitious bud regeneration in plant research and its applications briefly for the general audience.
Response: Accept it. We appreciate it very much for this good suggestion, and we have made modification of language in the introduction section on page 1, lines 39 to 41.
- Comment: Line-46, KCS should be first written in long form and then give the abbreviated form in the bracket.
Response: Accept it. We appreciate it very much for this good suggestion, and we have made changes to relevant parts of the original text (page 2, lines 55).
- Comment: Line-51, BGLU should also be written in the long form when first mentioned in the MS, and the abbreviated form can be used later in the MS.
Response: Accept it. We appreciate it very much for this good suggestion, and we have made changes to relevant parts of the original text(page 2, lines 58).
- Comment: Line 53-54, please change the English writing.
Response: Accept it. We appreciate it very much for this good suggestion, and we have made modification of language in the introduction section on page 2, lines 60 to 61.
- Comment: Line 57-58, please change the style of English writing.
Response: Accept it. We appreciate it very much for this good suggestion, and we have made modification of language in the introduction section on page 2, lines 64 to 65.
- Comment: The authors may include more details about the specific growth conditions,culture media, and hormone concentrations used for callus induction and bud regeneration. This will help others to replicate the culture experiment.
Response: Accept it. We appreciate it very much for this good suggestion, and we add detailed introduction of cultivation environment on page 2, lines 87 to 90.
- Comment: Why is the transcriptomic analysis needed for NRC, as theynormally do not give rise to new plants?
Response: The purpose of this experiment is to study the differential expression of RC and NRC genes and to explore their mechanism of action. Therefore, transcriptome analysis is needed for both RC and NRC, so that the results are more accurate and convincing.
- Comment: Line 166-170, the authors compared the upregulated genes of RC with NRC. However, the results of NRC were not mentioned in the MS.Line 173-175, the same thing is found here also; if the comparison is made between two entities, their respective values should be highlighted. If there are similar cases in the other parts of the MS, kindly rectify them.
Response: We appreciate it very much for this good suggestion. The purpose of this experiment is to study the differential expression of RC and NRC genes and to explore their mechanism of action. NRC is the control group, and the difference of most genes expression in RC and NRC is not obvious. Due to the limitation of research time and article length, we mainly present the differentially expressed genes in RC, so that the subsequent exploration of the influence mechanism of these genes can be more intuitive and concise. (The gene expression of the samples and the differences between RC and NRC gene expression are shown in the attached table)
- Comment: Line 213, Put a comma after “metabolism”.
Response: Accept it. We appreciate it very much for this good suggestion, and we have made modification of language in the introduction section on page 7, lines 236.
- Comment: The authors may add briefly the possible biological significance of the upregulated and downregulated genes in the Phenylpropanoid biosynthesis pathway in the discussion part of the MS.
Response: Accept it. We appreciate it very much for this good suggestion, and we have add the possible biological significance of some upregulated and downregulated genes in the Phenylpropanoid biosynthesis pathway on page 11, lines 318 to 325.
- Comment: The authors may also include the possible impact of differentially variable splicing events identified in this study on the regulation of gene expression and cellular processes related to bud regeneration.
Response: Accept it. We appreciate it very much for this good suggestion, and we have made modification of language in the introduction section on page 10, lines 304 to 306.
- Comment: The conclusion part is missing in the MS. Kindly insert it.
Response: Accept it. We appreciate it very much for this good suggestion, and we have added the conclusion part on page 12, lines 358 to 370.
Author Response File: 
Author Response.docx
Reviewer 2 Report
Comments to the Author
The review on the paper by Zhongyao Ai et al. “Molecular Regulation of Bud Regeneration from Callus of Hybrid Sweetgum”
The study was aimed to better understand which molecular processes and genetic factors are involved in establishing of callus pluripotency, leading to formation of adventitious buds using RNA-Seq approaches. Authors sequenced and analyzed 4 mRNA libraries representing regenerable calli (RC) and non-regenerable (NRC) calli of hybrid sweetgum. Large amount of DEGs were defined which were functionally annotated and analyzed.
In general, it is methodologically simple, descriptive paper, defining the set of DEGs in tissues differing in regenerative ability. The authors used responsive hybrid without any comparisons with other genotypes differing in regeneration efficiency. Authors made a great work to characterize obtained transcripts within the selected hybrid, made their annotation, define DEGs and their involvement in specific pathways. They selected phenylpropanoid biosynthesis pathway as a basis for analysis but did not provide any justification for selection of this specific pathway. Despite the obtained results are very interesting from bioinformatics point of view as collection of transcriptomic data, but not clear what authors going to do with obtained data. Huge number of DEGs withing one genotype without any comparisons with any other genotypes does not have any biological meaning and does not look like a finished biological experiment and finished work.
I would suggest below some general and specific comments that may hopefully help the authors to reshape their manuscript in a form more accessible to the readers and revealing its scientific essentials.
Introduction is too small. Nothing is mentioned about the plant species, its importance, why the problem exists. In introduction the aims of study should be clearly defined – analysis of transcriptome is a tool but not the aim of analysis. Also any further use of obtained transcriptomic data not clear, because no aim of study defined.
In M&M
It is not clear how plant material was collected from hybrid “HT-8”. I mean was the collected tissues originate from the same one plant (genotype) or several. What means “sterile vaccine” How many leaves were collected and how many used for sampling.
“Two biological replicates were set for each developmental stage of sampling”. Which developmental stages were meant here?
Please, give more detailed description or give a reference.
Results part is quite good. Presented results most probably from well-elaborated pipeline. I do not know why but no data presented from the RT_PCRs, just mentioned in the text.
Discussion in general repeating the Introduction, following the initial hypothesis of importance of the phenylpropanoid biosynthesis pathway and WUSCHEL-related homeobox gene family members for bud formation. I did not find any clear link to the transcriptomic data and results. No conclusion at all.
Finally, I did not accept the manuscripts without transcriptomic data uploaded to the public resources. I did not find any info of it
Looks like machine translation, should be revised
Author Response
Dear reviewer,
Thank you for your comments concerning our manuscript entitled “Molecular Regulation of Bud Regeneration from Callus of Hybrid Sweetgum” (ID: 2591991). Those comments are all valuable and very helpful for revising and improving our paper, as well as the important guiding significance to our researches. We have studied comments carefully and have made correction which we hope meet with approval. We have submitted documents with tracked changes to highlight the revisions. (The file uploaded below is the revised paper.)The main corrections and the responds to the comments are as following:
- Comment:Introduction is too small. Nothing is mentioned about the plant species, its importance, why the problem exists. In introduction the aims of study should be clearly defined – analysis of transcriptome is a tool but not the aim of analysis.
Response: Accept it. We appreciate it very much for this good suggestion. We have added some content that you mentioned to the article on page 1, lines 19 to 23.
- Comment: It is not clear how plant material was collected from hybrid “HT-8”. I mean was the collected tissues originate from the same one plant (genotype) or several. What means “sterile vaccine” How many leaves were collected and how many used for sampling.
Response: Accept it. We are sorry for this mistake that inadvertently wrote seedling as vaccine. Also, We have added some content about collection of hybrid “HT-8” sample on page 2, lines 83 to 86.
- Comment: “Two biological replicates were set for each developmental stage of sampling”. Which developmental stages were meant here?
Response: Accept it. We appreciate it very much for this good suggestion and added an explanation in the article on page 3, lines 98 to 99.
- Comment: They selected phenylpropanoid biosynthesis pathway as a basis for analysis but did not provide any justification for selection of this specific pathway.
Accept it. We appreciate it very much for this good suggestion and have added our justification on page 8, line 246 to 252.
- Comment: Please, give more detailed description or give a reference.
Response: Accept it. We appreciate it very much for this good suggestion and have added a number of detailed notes and introductions to make the article fuller and more rigorous.
- Comment: “Results part is quite good. Presented results most probably from well-elaborated pipeline. I do not know why but no data presented from the qRT-PCRs, just mentioned in the text.
Response: Accept it. We appreciate it very much for this good suggestion and have added description and figures to make the results more intuitive (page 1, lines 5 to).
- Comment: Discussion in general repeating the Introduction, following the initial hypothesis of importance of the phenylpropanoid biosynthesis pathway and WUSCHEL-related homeobox gene family members for bud formation.
Response: Accept it. We appreciate it very much for this good suggestion, and we have made modification of language in the introduction section on page 11, lines 313 to 316.
In addition, we made several changes to the English presentation to make it more fluent and precise and uploaded transcriptome data.(The data table has been sent to the editor, please contact me if you have any questions.)
Author Response File: Author Response.docx
Round 2
Reviewer 2 Report
Comments to the Author
Comments for the revised version of the paper by Zhongyao Ai et al. “Molecular Regulation of Bud Regeneration from Callus of Hybrid Sweetgum (Liquidambar styraciflua × Liquidambar formosana)”.
The authors partially revised and rewritten the manuscript and most of my comments were met in the revised version. I like the addition of supplementary data. I feel now much more comfortable with the manuscript and would recommend it for publishing
