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[# PeerJ Staff Note - this decision was reviewed and approved by Paula Soares, a PeerJ Section Editor covering this Section #]
Please address the final comments of reviewer one.
"Few minor suggestions have been mentioned in the edited version of the manuscript provided here."
Authors have revised the manuscript well. Few minor suggestions have been mentioned in the edited version of the manuscript provided here.
No comments
No comments
No comments
The article must be written in English and must use clear, unambiguous, technically correct text. The article must conform to professional standards of courtesy and expression.
No
Decisions are not made based on any subjective determination of impact, degree of advance, novelty or being of interest to only a niche audience. We will also consider studies with null findings. Replication studies will be considered provided the rationale for the replication, and how it adds value to the literature, is clearly described. Please note that studies that are redundant or derivative of existing work will not be considered. Examples of "acceptable" replication may include software validation and verification, i.e. comparisons of performance, efficiency, accuracy or computational resource usage.
No
no commen
no commen
no commen
Thank you for your submission. Please note that all reviewers have recommended Major Revisions, Please address all comments carefully!
**PeerJ Staff Note:** Please ensure that all review and editorial comments are addressed in a response letter and that any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate.
**Language Note:** The review process has identified that the English language must be improved. PeerJ can provide language editing services - please contact us at [email protected] for pricing (be sure to provide your manuscript number and title). Alternatively, you should make your own arrangements to improve the language quality and provide details in your response letter. – PeerJ Staff
Authors have performed the bioinformatic analysis to identify the bHLH genes in Populus canescens. They identified the cis-elements of these genes and also performed evolutionary analysis using the bioinformatic tools that are commonly used. Authors have also performed some expression analysis of selected bHLH genes in response to cadmium stress using different plant tissues.
The major concern of the study is the source from which the genome sequence of Populus canescens is retrieved to select the bHLH genes (which forms the main basis of their study). The link authors have provided as source for the genome doesn't match and P. canescens, which is a hybrid of P. tremula X P. alba genome is available in Phytozome. The ID's provided for the selected bHLH genes (Table S1) are from P. trichocarpa and authors have not mentioned gene IDs used from P. canescens anywhere in the manuscript. Secondly, the expression analysis performed in the study was represented as a heat map and no raw data was provided to validate their experiment.
Authors are advised to revise their manuscript appropriately with clear details of the source of genome information and genes used for their study.
Scientific writing has to be improved and the manuscript along with figure legends should be thoroughly checked for all spelling and grammatical errors. Further corrections and comments are mentioned in the edited version of the manuscript.
No comment
No comment
No comment
Clear and unambiguous, professional English used throughout
Research question well defined, relevant & meaningful. It is stated how research fills an identified knowledge gap.
Conclusions are well stated, linked to original research question & limited to supporting results.
I have carefully read the manuscript entitled "Genome-Wide Identification of bHLH Gene Family and its Response to Cadmium Stress in Populus × canescens". Overall, this is a very good study involving the systematic identification and expression analysis of the bHLH transcription factor family in poplar at the genome level. The research content has a certain novelty and significance. However, before submission, I still suggest that the authors further improve the following aspects:
1. The overall writing of the article is somewhat verbose and could be appropriately concise. In particular, the introduction section is too lengthy in discussing the bHLH gene family and cadmium stress. It is recommended to focus on introducing the background knowledge directly relevant to this study.
2. There is some repetition between the results and discussion sections, which could be considered for merging. At the same time, there is a lack of in-depth discussion of certain key findings, such as the conservation of gene structure, expansion of the subfamilies, expression patterns of bHLH genes, etc.
3. The synteny analysis results in Figure 6B need a clearer legend explanation, as currently readers do not fully understand the meaning of this figure.
4. The experimental section lacks an explanation of the cadmium stress treatment concentration, which should be supplemented. Additionally, the screening criteria for the 14 candidate genes also need to be clarified.
5. In general, the conclusion section should be highly summarized and concise, while the conclusion section of this manuscript is too lengthy. It is recommended to concise the conclusion and highlight the main innovations of the research.
6. There are some language issues that need to be revised, such as the lack of a semicolon before and after "in plants" on line 48; the misspelling of "cromosomes" on line 189, etc. It is suggested that the entire manuscript be polished for language.
Overall, this is a high-quality research paper, and the research content has a certain degree of innovation, but some further modifications and improvements are still needed before submission. I hope the authors will consider the above comments, which will make the paper more complete. Please feel free to provide any other feedback if you have any other questions.
The writing level of this article was on the low side.
There are too many writing and grammar mistakes, and this manuscript must be thoroughly revised.
For example,
Line 33 ‘about the of’ should be corrected to ‘about the roles of’
Line 35 ‘location’ should be corrected to ‘locations’
Line 37 ‘are’ should be corrected to ‘were’
Line 39 ‘PcbHLHs’ should be italic
Line 86 ‘And’ should be deleted
Line 89, Line 103, Line 133, Line 187, Line 193, Line194, Line 195, Line 207, Line 213, there were many mistakes behind, which were not listed one by one
1. Line 118-119: There was an error in the method, BLASTp should be applied to P. canescens protein sequence data, not genomic sequence data.
2. Line 171-173: qRT-PCR needed technical repetition and biological repetition. If there was no repetition, the results were unreliable.
no comment
1. Line 74 :‘IREG2, MTP3, HMA3’ change the abbreviation to the full name.
2. Line188: PcbHLH170 could be mapped to the Scaffords, which needed to be explained.
3. Phylogenetic analysis was too simple to reflect the evolutionary relationships between the PcbHLHs and the AtbHLHs.
4. Which motif was shared by 170 proteins?
5. Explain the reasons for the intron lack.
6. Line 238-240, members contained phytohormone-related cis-acting elements were involved in responses to different abiotic stressors. What was the basis?
7.Tandem duplication gene pairs were close to each other, however, Figure 1showed that PcbHLH48 and PcbHLH58 were far apart.
8. Line 346 Explain how to regulate and what regulation mechanism
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