All reviews of published articles are made public. This includes manuscript files, peer review comments, author rebuttals and revised materials. Note: This was optional for articles submitted before 13 February 2023.
Peer reviewers are encouraged (but not required) to provide their names to the authors when submitting their peer review. If they agree to provide their name, then their personal profile page will reflect a public acknowledgment that they performed a review (even if the article is rejected). If the article is accepted, then reviewers who provided their name will be associated with the article itself.
The authors have made changes according to the comments and the current form of the article can be accepted for publication.
[# PeerJ Staff Note - this decision was reviewed and approved by Julin Maloof, a PeerJ Section Editor covering this Section #]
**PeerJ Staff Note:** Although the Academic and Section Editors are happy to accept your article as being scientifically sound, a final check of the manuscript shows that it would benefit from further editing. Therefore, please identify necessary edits and address these while in proof stage.
there is a minor error, I dont know why authors to get the absolute of R2? R2 all > 0, why? please check this.
no comment
no comment
no comment
The author modified the manuscript based on review's suggestion
Although there are some results, such as the HPLC/MS chromograph of some compounds, still not solid enough, but the author make an explanation fot them.
a novel and interseting finding
no
I agree with the reviewers and the article can be accepted after minor revisions.
**PeerJ Staff Note:** Please ensure that all review, editorial, and staff comments are addressed in a response letter and 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 copyediting@peerj.com 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 conducted HPLC-MS/MS analysis to identify 13 diosgenin metabolites in D. cirrhosa tuber, and utilized transcriptome data to identify 21 key enzymes and 43 unigenes. The results reveal 22 TFs are strongly associated with diosgenin biosynthesis genes. The work is important to aim improving the biosynthesis of diosgenin compounds in plants.
Authors conducted HPLC-MS/MS analysis to identify 13 diosgenin metabolites in D. cirrhosa tuber, and utilized transcriptome data to identify 21 key enzymes and 43 unigenes. Based on the gene family analysis to identified the CYP450 gene family and TF, and to verify the expression of diosgenin-related genes. The work included the bioinformatic analysis and experimental verify.
Authors identified 206 CYP450 genes including 40 being potential CYP450s. these CYP450s were associated with sterol C-22 hydroxylase, sterol-14-demethylase and amyrin oxidase in diosgenin biosynthesis. There some comments as below:
1. Figure 10 should check, for the remake of the "*", what is the NS?
2. the tools should be cite, as what software to get the heatmap
3. I sugget authors to compare the expression of hub gene in different population to verify the Dao-Di Herb.
The manuscript “Diosgenin biosynthesis pathway and its regulation in Dioscorea cirrhosa L.” by Yan Lin analyzes the diosgenin synthesis pathway through transcriptome and metabolism data. 13 diosgenin metabolites, 21 key enzymes, and 43 unigenes were identified, which will apply the guidance for future research aimed at improving the diosgenin biosynthesis ability in plants. The manuscript includes a large amount of data and analysis, but it still needs more evidence to support the results and do a thorough investigation of the diosgenin biosynthesis.
1. In line 280, the author said that no “no CYP450 or UGT genes involved in diosgenin biosynthesis have been identified in Dioscoreae or other diosgenin producing plants”, which is not accurate. There are some papers that identified the CYP450 genes involved in diosgenin biosynthesis, such as, “Zhou, Chen, et al. The Plant Journal 109.4 (2022): 940-951.” and “Cheng J., Chen J., Liu X., et al. Plant Communications. 2020. 2(1):100079.” The author should reinvestigate the related paper carefully and correct your manuscript.
2. As there are many studies on other diosgenin-producing plants, the author should make a comparison between your results and previous results and discuss the similarities and differences.
1. The author introduced and compared several important diosgenin metabolites in the manuscript, some of which are not easy to identify. Can the author apply the HPLC/MS chromograph of these compounds?
The finding is important.
in all text some times you do not need use some extra words like here PATHWAY
AND There are many examples in the text should be improved
Please see attached file with highlighted to be consider
In gene expression analysis It was written:
The significance of diosgenin metabolite data and gene expression data was analyzed by t-
150 test method with ggsignif package in R.
T-test compares between two group while they have replicates and may have done Analysis of variance
please MAKE CLEAR AND UNDERSTANDABLE THESE SECTION
2.7. Gene Expression Analysis Using qRT-PCR
what kind of primer used for cDNA synthesis?
Is there any expression analysis for leaf tissue?
no comment
In paragraph starting line 378:
In this paragraph you should speak about transcription factors rather than hormones since you haven't treat plants with hormone
there fore you don't have data to discuss here
please give reference to this:
Combining the
418 genetic screening of mutants with impaired triterpene biosynthesis and the availability of
419 integrated genomic and transcriptome resources, some CYP450s involved in the structural
420 modification of plant triterpenes has been identified.
All text and materials provided via this peer-review history page are made available under a Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.