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[# PeerJ Staff Note - this decision was reviewed and approved by Brenda Oppert, a PeerJ Section Editor covering this Section #]
The manuscript is somewhat improved but a Secrtion Editor identified some problems that will need to be addressed:
1. Some typos: analyses, not analyzes in title. Venn, not veen. etc.
2. In the abstract, recommend changing the objective to "The classification and clinical usage of the different species of bead ginseng are often confused. Therefore, we conducted an integrated metabolomics and transcriptome analysis of three main species of . . .
3. What is the difference in YY and YYB, XL and XLB, DY and DYB? I do not find it defined.
4. Starting in line 453, the authors make the jump from "phenolics have antiviral properties" to COVID, but didn't provide any evidence that ginseng has been used as a COVID treatment. You should add this reference:
Ratan ZA, Rabbi Mashrur F, Runa NJ, Kwon KW, Hosseinzadeh H, Cho JY. Ginseng, a promising choice for SARS-COV-2: A mini review. J Ginseng Res. 2022 Mar;46(2):183-187. doi: 10.1016/j.jgr.2022.01.004. Epub 2022 Jan 22. PMID: 35095288; PMCID: PMC8783644.
. . . and mention that ginseng has been studied as a covid therapeutic.
**Language Note:** The Academic Editor 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
As Academic Editor, I am satisfied with the revisions. Congratulations on your work
However, one of the Section Editors has provided the following comments. Therefore, you must address these concerns (by seeking language editing from someone familiar with the subject) before the article can be Accepted:
"I am having difficulty in understanding the basis of this paper and think that someone should edit for English and also with expertise in this medicinal plant. Maybe someone working in this field can follow what was done and why, but I was unable.
For example, the sentence in the abstract "To solve the confusion in the classification and clinical usage of the original plants of Panacis Majoris Rhizoma (bead ginseng), we made the integrated metabolomics and transcriptome analysis of the three species of Panax, including Panax japonicas, Panax pseudoginseng, and Panax pseudo-ginseng var. elegantior." doesn't make any sense until you read the explanation in the introduction "Panacis Majoris Rhizoma (PMR) is the dry rhizome of Panax japonicus, Panax pseudoginseng, and Panax pseudoginseng var. elegant." You abbreviate PMR, but then continue to use the full name throughout. I think it would be better to use PMR after this because you are talking about the rhizome, not a plant genus/species. The first time you state the genus Panax, it should be followed by subsequent instances of abbreviated with a P.
Equally confusing is the sentence "To address the confusion in the classification of the original plants of Panacis Majoris Rhizoma and to ensure the medicinal safety and effectiveness of Panacis Majoris Rhizoma, we conducted an in-depth study of the metabolome and transcriptome to explain the similarities and differences of the three origins of Panacis Majoris Rhizoma." Do you mean that PMR can originate from one of the 3 species of Panax that you are studying and that the metabolome and transcriptome can distinguish which plant the rhyzome came from? If so, this could be more clearly written.
In figure 2, you say "Overview of the detected metabolites in the three originals of Panacis Majoris Rhizoma." Do you mean "metabolites from three Panax spp? In that figure A, there are three columns with the same color, do those represent the 3 Panax spp? If so, need to label or at least explain this in the figure legend. Are these replicates? This confusion about samples carries through to the other figures as well. But, then when I got to figure 5, I saw this "KEGG analysis of metabolites in yellow (YY), brown (XL), and cyan (DY) modules" that made me question what exactly is YY, XL, and DY and what are the modules???
In figure 7, "HMGR is a key regulatory body in the MVA pathway. Showed about 1.5 times higher expression in YY than in XL.", put these sentences together."
The article is well-structured and presented clearly.
Literature references are generally adequate and sufficient background/context is provided.
The paper describes a solid and comprehensive research work that fits the Aims and Scope of the journal. Experimental procedures are adequate and carefully described.
The results are presented in an organized way and have been well analyzed. In general, the manuscript is well-stated.
The authors have done an excellent job in refining the basic reporting of the study. They have presented the background information, experimental procedures, and results in a clear and concise manner. The revised manuscript is well-structured and easy to read, and the authors have provided all necessary details, figures, and tables to support their work. They have also added missing references, corrected errors in terminology, and have ensured that all terms and abbreviations are adequately defined.
The experimental design of this study is well-planned and executed. The authors have clearly explained the rationale behind their experiments, and the methods used are standard and appropriate for the research questions. The statistical analysis is sound and appropriately used. Furthermore, they have addressed my earlier concerns about the calibration of their instrument and the source of their MRM transition list.
The findings of the study are valid and supported by the data presented. The authors have carried out a detailed analysis of the data and have been careful to avoid overinterpretation of the results. The revisions have only served to strengthen the validity of the findings. They have provided a clearer explanation of how the identified metabolites contribute to the differences in the three plant species and have ensured that the implications of their findings are realistically presented.
In general, the authors have done a commendable job in revising the manuscript in response to the review comments. They have addressed all the concerns raised and have made necessary changes to improve the clarity and quality of the manuscript. The revised manuscript presents a solid piece of work that contributes new insights into the comparative analysis of the metabolomics and transcriptome of Panacis Majoris Rhizoma from three different sources. The findings have potential applications in the fields of plant biology, traditional medicine, and pharmacology. I highly recommend the acceptance of this manuscript for publication.
Please revise your manuscript according to the reviewers' comments.
[# PeerJ Staff Note: Please ensure that all review and editorial 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. #]
The article is well-structured and presented clearly. However, the text has some minor English errors that must be corrected. Please see "Comments for the author" for suggestions.
Literature references are generally adequate and sufficient background/context is provided.
The paper describes a solid and comprehensive research work that fits the Aims and Scope of the journal. Experimental procedures are adequate and carefully described.
The results are presented in an organized way and have been well analyzed. In general, the manuscript is well-stated.
The manuscript appears to be well-written and informative. However, there are a few minor errors in grammar and punctuation that could be corrected for clarity. For example:
Line 2: ‘’ Panax Linn,’’ The scientific name should be in italics.
Line 9: add a comma ‘’thus,’’
Line 12: Replace ‘’is’’ by ‘’are’’
Line 17: Please correct ‘’how to accurately identify’’ by ‘’how accurately identifying’’
Line 42: add a comma ‘’it has a long growth cycle,’’
Line 60: Replace ‘’ 3 groups of samples were selected, and each group consisted of 3 biological replicates.’’
Line 62, 429: ‘’ Panax japongicus’’ The scientific name should be in italics.
Line 64: ‘’the sample was deposited at Shaanxi’’
Line 84: ‘’Further DP and CE optimization were used’’
Line 87: remove ‘’an’’
Line 91: remove ‘’in order’’; correct ‘’ three’’ and replace ‘’duplicates’’ by ‘’replicates’’
Line 97: Replace ‘’ concentrations’’ by ‘’concentration’’
Line 99: ‘’cDNA’’
Line 109: ‘’The prediction of transcription factors was carried out with iTAK (Zheng Y et al.,2016), and the quantification of gene expression was performed using FPKM’’
Line 117: Replace ‘’original’’ by ‘’originals’’
Line 120: verify if there are 830 or 829 metabolites.
Line 131: Please correct ‘’flavonoids in the XL. While YY was rich in lipids, nucleotides and derivatives’’
Line 140: add ‘’and green’’
Line 141: replace ‘’group’’ by ‘’grouped’’
Line 143: Replace ‘’So’’ by ‘’thus,’’
Line 146: add s for the plurals ‘’acids’’
Line 147: add species ‘’showed that all three species’’
148: remove ‘’that’’ and replace ‘’small’’ by ‘’negligible’’
Line 150: Please respect the same formatting for titles (with or without first letter of capitalized words)
Line 159: Replace ‘’amount’’ by ‘’number’’
Line 178: Please correct punctuations and singular ‘’ 1 amino acid and derivatives 1 flavonoids.’’
Line 187: Please check the numbers ‘’In group A, a total of 242 sequences (131 down-regulated and 116 up-regulated)’’
Line 188-190 and 192-194: please remove repetition by paraphrasing.
Line 201: Please mention the meaning of each abbreviation cited in the manuscript.
Line 229 and 230: add ‘’the’’ “the three plant”
Line 233: replace ‘’class’’ by ‘’classes’’
Line 243: replace ‘’duplicates’’ by ‘’replicates’’
Line 288: Correct ‘’according’’
Line 345: what do you mean by “qi and yin”
Line 376: scientific names should be always in italics ‘’Lonicera japonica thunb’’
The conclusions are badly written and must be rewritten.
Line 434, 501, 506, 509, 511, 514 … : Remove capital letters and stick to one style.
The quality of Figure 7 must be ameliorated.
Fail. See "4. Additional comments".
Pass.
Pass.
Dear Editor,
I have reviewed the manuscript entitled "Metabolome and transcriptome analyzes identify the characteristics and expression of related saponins of the three genealogical plants of Panacis Majoris Rhizoma" submitted by Yihan Y and Nan M et al.
The manuscript presents an interesting and comprehensive investigation into the transcriptomics and metabolomics profiles of three Panax (ginseng) plant species. By performing targeted metabolomic analysis with LC-MS/MS and RNAseq, the authors are able to quantify 830 metabolites, identify 16,074 differentially expressed genes within these plants, and suggest these plants differ mainly in metabolite contents of flavonoids, phenolic acids, and terpenes. The authors also lead an extensive discussion on medicinal properties of these bioactive compounds and conclude with the sizable contribution of this study to the field of herbal medicine.
Overall, the authors have conducted a comprehensive multi-omics study for characterizing the medicinal properties of 3 ginseng species. The manuscript is informative and presents a scientific deliverable that adds value to the field of herbal medicine research.
However, I have some concerns and suggestions that I believe would strengthen the manuscript and improve its clarity. I have outlined these points below, and I recommend the authors address these issues before the manuscript can be considered for publication on Peer J.
Major Concern:
1. The manuscript lacks discussion surrounding analytical method-related variabilities and limitations. It is widely known that both RNAseq based transcriptomics and LC-MS/MS based metabolomics have several variabilities in biological sampling, sample preparation, instrumental performance, and low-abundance analyte detectability. In the discussion section (Line 344 to 417), it is crucial to address potential biases introduced by the choice of sample preparation, reference standards, data normalization, and statistical analysis methods in both transcriptomics and metabolomics experiments. Moreover, the manuscript would benefit from a more in-depth exploration of the impact of technical variability, batch effects, and biological variability on the results. A thorough evaluation of these factors would not only strengthen the reliability and reproducibility of the findings but also help identify potential areas for improvement in future studies. By addressing these methodological concerns, the authors can provide a more robust and comprehensive understanding of the observed patterns and underlying biochemical processes.
Minor Concerns:
There are several instances throughout the manuscript where the language could be refined for better clarity and readability. For example:
1. Line 17, 44, and 47: The authors have mentioned there is a great need for accurate identification of Japanese ginseng or Panax japonicus. However, this topic appears slightly redundant. The authors may consider re-organizing this section.
2. Line 76 and 77: It is not clear how the “High collision-activated dissociation” was used. The authors may elaborate more on whether it is configured as part of the in-source fragmentation or fragmentation in the collision cell. It is also not clear how both linear ion trap mass analyzer and QqQ are used in the metabolomics experiments.
3. Line 80: Collision activated dissociation (CAD) gas.
4. Line 81: It is not clear how the authors used polypropylene glycol to calibrate the instrument, on what m/z values?
5. Line 86: The reference (Li et al., 2021) cannot be found in the reference section. The authors need to provide more details on the source of the MRM transition list used in this study.
6. Line 91: the term “tree biological duplicates” is confusing.
7. Line 93: “gel electrophoresis”.
8. Line 120: “The levels of 830 metabolites were determined” may be rephrased as “of 830 metabolites were quantified”.
9. Line 126: orthogonal partial least squares discriminant analysis (OPLS-DA) may need a reference.
10. Line 150: “…Among three original (plants?)”
11. Line 318: “MVP pathway”, do the authors mean “MEP” pathway here? If so, Figure 7E may be mentioned here.
12. Line 201: WGCNA needs a reference.
13. Line 345: the term “qi and yin deficiency” is not common. The authors may rephase it or put a reference here.
14. Line 355 and 356: it is not clear whether 830 metabolites are common metabolites detectable in all samples or 830 is the cumulative number of all metabolites detected in this study.
15. Line 417: the statement “This will contribute to more specific targeted programming for clinical use” is not clear.
16. Line 427 and 428: “…three species of primitive plants, Panax pseudoginseng and Panax pseudo-ginseng var. elegantior, missing Panax japonicus?
17. Figure 2: Figure 2B is not mentioned in manuscript. Figure 2E x-axis does not have a unit.
18. Figure 4: bottom barchart x-axis does not have a unit.
19. Figure 5: figure description appears incomplete.
20. Figure 7: this figure is not mentioned in the manuscript.
In conclusion, I believe that the manuscript has the potential to be a valuable addition to Peer J, but it requires some revisions to address the concerns mentioned above. I recommend that the authors address these concerns and resubmit their manuscript for further consideration.
Sincerely,
Reviewer
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