Comparative Transcriptome Analyses Reveal Different Regulatory Mechanisms in Ecological Adaptation between Chrysanthemum vestitum and Chrysanthemum mongolicum
Round 1
Reviewer 1 Report
The manuscript, entitled "Comparative transcriptome analyses reveal different regulatory mechanisms in ecological adaptation between Chrysanthemum vestitum and Chrysanthemum mongolicum", provides new information about the adaptation of the two Chrysanthemum species in extreme environments. The results of this manuscript will be useful for further studies on transcriptomics and metabolomics of Chrysanthemum in particular and Asteraceae in general.
I have some suggestions as the followings:
1/ Please check English because there are typing and grammar errors in the text. For example, in the abstract, "Chrysanthemu mongolicum", "occupy a wider range of ecological niches representing an extensive biotic resistance and abiotic tolerance"; "21,856 DEGs differentially expressed genes (DEGs) were identified between C. vestitum and C. mongolicum, of which 12,076 DEGs were upregulated and 9,780 were down regulated in C. vestitum compare to C. mongolicm".
2/Line 111: "The genome of C. nankingense" Please use the full name for the first mention.
3/ Line 124: "Specific primers designed by Primer Express 3.0 were list in Table 1.". Table 1 does not contain primer information.
4/ Please increase the size of letters/words/names... in the figures. The current format is too small to get the information.
5/ Please clarify the sampling section with the information about the time of collecting samples. Fresh leaves were collected directly from the plant living in Baotou or from the transplants being cultivated in the nurse garden of Northeastern University? This question was raised because changes in the environment (differences between Baotou and nurse garden habitats) will affect gene expression in plants.
6/ Please clarify the habitats of Chrysanthemum mongolicum and C. vestitum because this information will be helpful for interpreting the transcriptomic data related to adapting to environmental stress in this manuscript.
Thank you.
English should be checked again before publication.
Author Response
Dear reviewer,
Thank you for your comments concerning our manuscript entitled Comparative transcriptome analyses reveal different regulatory mechanisms in ecological adaptation between Chrysanthemum vestitum and Chrysanthemum mongolicum’ (Horticulturae-2471553). Those comments are very valuable and very helpful for revising and improving our paper. We have revised the manuscript, according to your comments and suggestions, and responded point by point, please see the attachment.
Author Response File: 
Author Response.docx
Reviewer 2 Report
The study “Comparative transcriptome analyses reveal different regulatory mechanisms in ecological adaptation between Chrysanthemum vestitum and Chrysanthemum mongolicum” present potential molecular mechanisms for the ecological adaptation of the two Chrysanthemum species during stress. The study is well designed but there are some questions which must be addressed.
Line 13 the leaf transcriptome of the two Chrysanthemum species were investigated. The author should provide information that it was from a stressed plant or normal plant. Also replace were with was in this sentence.
Line 17-23 the sentence is long and complex and not clear. It should be revised.
Line 14-15 the authors should provide numbers of up regulated and down regulated genes of both species.
Paragraph first of the introduction, add information about the habitat range of wild Chrysanthemum.
Line 49 it would be better to inform the readers specifically about wild hexaploid relative of cultivated chrysanthemums.
Line 50 “different distinguishable” use different or distinguishable.
Line 64 add a full stop
Line 69 it would be better to add some recent studies. The following studies would be helpful. https://doi.org/10.1016/j.ygeno.2023.110635, https://doi.org/10.3389/fgene.2021.635043
Add novelty of the study in last paragraph of the introduction.
Section Plant material provide information of the plant growth conditions, time of harvesting.
Morphological analysis section could be cited with a recent study. The following study could be added.
https://doi.org/10.3390/agronomy12102500
Figure 2 the graphs should show number of DEGs of both species. As it is comparative study.
Line 273-275 should be cited with relevant study https://doi.org/10.1016/j.plipres.2022.101199
The experiments do not cover or justify the aims of the study so the following analysis would further strengthen this study.
Identify modules or clusters of co-expressed genes and investigate their functional enrichment. This analysis can reveal potential gene regulatory networks and provide insights into the coordinated regulation of genes involved in ecological adaptation. As the aim of the study to understand molecular mechanisms for the ecological adaptation.
functional enrichment analysis using gene ontology (GO) can also help in understanding functional insights into the regulatory mechanisms underlying ecological adaptation.
identify conserved and divergent genes involved in ecological adaptation and help understand the evolutionary processes underlying adaptation of both species.
Analyze the network topology and identify key TFs that may play crucial roles in ecological adaptation.
Add future perspective and study gap in conclusion.
Some minor corrections are required which are mentioned in my comments to authors
Author Response
Please see the attachment.
Author Response File: Author Response.docx
