Metabolomic Analysis of Lycoris radiata across Developmental and Dormancy Stages
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsAuthors performed a metabolomic analysis of Lycoris radiata during six developmental stages to determine the metabolic changes . Previously authors had performed proteomic (https://doi.org/10.1007/s11738-020-03179-w) and transcriptomic (DOI: http://dx.doi.org/10.30848/PJB2023-3(21)) analyzes on these six developmental stages of Lycoris radiata. The present study is interesting but there are some major and minor points to be addressed.
Major points:
1.- In the manuscript is not mentioned how authors identified the metabolites neither if the identities were confirmed with authentic standards. Even worst, the full list of metabolites is not provided. Authors must include a supplementary material a table indicating the retention time, m/z, error, mode, adduct, fragments (if are there) etc., This information is very important to determine the scientific soundess of the study.
2.- I am really worried when authors declare in the abstract "the biosynthesis of neomycin, kanamycin and gentamicin were uniquely identified during the transition from Dormancy to Flowering". How do authors explain this pathway when neomycin, kanamycin and gentamicin are microbial compounds. Again, did you confirm the identity of these compounds with authentic standards? Or did you use a plant database to perform the enrichment pathways? In figure 7 authors show that the compounds UDP-N-acetylglucosamine, UDP-D-glucose and L-glutamate belong to the Neomycin, kanamycin and gentamicin biosynthesis pathway. None of the three compounds (UDP-N-acetylglucosamine, UDP-D-glucose and L-glutamate) are neomycin, kanamycin and gentamicin. I think the big issue is that authors did not use a plant database to perform the enrichment pathways analyzes.
3.- In consequence of using a not specialized plant platform for compound identification and pathway analyzes, Amaryllidaceae well-known compounds are missing at all. Which metabolome was used as reference? Authors must include in the study the dynamic of Lycoris radiata alkaloids. In other words, it should be included the chemotaxonomic criterion in the study. It would be very interesting to determine the dynamics of compounds that are taxonomically restricted (e.g. alkaloids).
4.- In figure 1, you can join the datasets (positive and negative) to perform a single PCA and it should be properly described. What is the importance of performing the PCA? What is the information you get with PCA? These comments are also for Figure 2.
5.- In figure 4 only is shown the subclass distribution of negative mode DEMs [by the way, in metabolomics is frequently used DAMs (differentially Accumulated Metabolites), considering that metabolites are not regulated like genes, metabolites are accumulated]. So, what about of those positive mode DEMs? I strongly suggest to change Figure 4 by a new one that considers positive and negative modes DEMs. At the end, the aim is to show the subclass distribution of DEMs regardless the ionization mode.
6.- Figure S3 giver more information than Figure 5. I strongly suggest to delete figure 5 and use Figure S3.
7.- Now if you already have transcriptomic and proteomic data, I strongly suggest to perform an integrative analysis, considering trancriptomics/metabolomics or proteomics/metabolomics. This analysis will allow the study to be more robust and reliable. Above all, considering that apparently the compound identification was not confirmed for any of the metabolites.
Minor points are included in the attached file.
Comments for author File: 
Comments.pdf
The quality of English is good.
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsAfter reading the manuscript, I consider the manuscript to be well organized and robust, with well presented images. However, I present some observations I made.
Keywords. Please, replace keywords present in the title
line 142. what about QC?
item. 3.2 I believe it is possible to elucidate better the results according to the groups tested.
item 3.4 It’s possible to note in Figure 5 that “others” are most part of the components, why that gap? Why didn’t you classify them?
item 4. Discussion. Once this study objective is to offer insights through metabolism knowledge, I believe it could be pretty interesting for the authors to discuss a little how their achievements could help the growing technics of this species. Maybe a topic 4.4.
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
Round 2
Reviewer 1 Report
Comments and Suggestions for AuthorsI think the revised version of the manuscript has improved significantly. Authors performed many changes according to my suggestions. I only recommend to check that metabolomics (with s) is used as a noun (e.g. Metabolomics is a chemical science) and metabolomic (without s) is an adjective (e.g. Metabolomic analysis, metabolomic data, metabolomic studies). In the revised manuscript these terms are used indistinctly.
Author Response
Thank you for recognizing the improvements made in the revised version of our manuscript. We acknowledge your point regarding the proper use of the terms "metabolomics" and "metabolomic". We have carefully reviewed the manuscript and corrected any misuse of these terms. Please refer to line 14 (metabolomic analysis), line 144 (metabolomic data), line 351 (metabolomic study).
