Genetic Diversity Analysis of Wild Cordyceps chanhua Resources from Major Production Areas in China

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The manuscript describes the genetic diversity analysis of wild Cordyceps chanhua samples collected in China. Samples were confirmed to be Cordyceps chanhua by morphological features and ITS sequencing. This was followed by whole genome resequencing of 12 samples. The whole genome resequencing data was used for analysis of genetic diversity and population structure analyses. The results are useful for the conservation and utilisation of Cordyceps chanhua genetic resources.

In general, the manuscript is well written, and the results and discussion are clearly presented and logical.

Minor comments and suggestions to improve the manuscript:

More details should be provided about the sample collection locations. A map showing the locations, or at least coordinates of where the samples were collected is needed. Samples were collected from four locations, but no further details are provided. What was the distance between collection sites within regions?

Details of STRUCTURE analysis – number of burnin steps, number of step after burnin, the range of K values used and other analysis parameters should be included in the methods section.

In the Conclusions section (lines 421-424), it is stated “The results demonstrate significant genetic differentiation among Cordyceps chanhua resources across various geographic areas, closely associated with their distribution and environmental adaptability.” However, samples from ICY and ICL are found in both major clusters (G1 and G2), indicating that additional factors than geographic distance may influence the genetic clustering. However, as no coordinates are given for the collection sites, this remains unclear. In addition, how is the genetic differentiation associated with environmental adaptability? No information on environmental adaptability is provided in the manuscript, nor is any information on environmental conditions at the collection sites.

Are the whole genome resequencing data available, either from a public depository, or from the authors?

Author Response

Comments 1:More details should be provided about the sample collection locations. A map showing the locations, or at least coordinates of where the samples were collected is needed. Samples were collected from four locations, but no further details are provided. What was the distance between collection sites within regions?

Response 1: Thank you for your comment. Section 2.1 of the manuscript has been updated to include the coordinates of the sampling locations, climate conditions, and distances between collection points within each region.

Comments 2: Details of STRUCTURE analysis – number of burnin steps, number of step after burnin, the range of K values used and other analysis parameters should be included in the methods section.

Response 2: Thank you for your comment. Section 2.3 of the manuscript has been updated to include detailed information on the STRUCTURE analysis, including the number of burn-in steps, the number of steps after burn-in, the range of K values used, and other analysis parameters.

Comments 3: In the Conclusions section (lines 421-424), it is stated “The results demonstrate significant genetic differentiation among Cordyceps chanhua resources across various geographic areas, closely associated with their distribution and environmental adaptability.” However, samples from ICY and ICL are found in both major clusters (G1 and G2), indicating that additional factors than geographic distance may influence the genetic clustering. However, as no coordinates are given for the collection sites, this remains unclear. In addition, how is the genetic differentiation associated with environmental adaptability? No information on environmental adaptability is provided in the manuscript, nor is any information on environmental conditions at the collection sites.

Response 3: Thank you for your comment. Section 2.1 of the manuscript has been updated to include the coordinates of the sampling locations, climatic conditions, and the distances between collection sites within each region. Additionally, Section 4.1 provides a detailed discussion on how genetic differentiation is associated with environmental adaptability, incorporating information on the latitude, longitude, and climatic characteristics of the different sampling sites.

Comments 4: Are the whole genome resequencing data available, either from a public depository, or from the authors?

Response 4: Thank you for your comment. The whole-genome resequencing data is available upon request from the authors.

Author Response File: Author Response.docx

Reviewer 2 Report

Comments and Suggestions for Authors

This manuscript describes an interesting study describing the distribution of the genetic diversity of Cordyceps chanhua (golden cicada flower) among four production areas in China. The authors compared the morphological and genomic variation to suggest that their results should serve to establish adequate management strategies for the conservation of the genetic diversity of this vital resource.

 

However, the authors should change this manuscript to be accepted for publication.

1. The introduction is too long and contains some unnecessary information. The authors should shorten the introduction to about sixty percent of its current length.
2. For example, the first paragraph is too long and may be combined with the second paragraph. Moreover, a reorganization of the introduction would help shorten this section.
3. The short paragraph starting in line 67 is irrelevant to the study.
4. The level of detail in the paragraph starting in line 72 is excessive.
5. The materials and Methods section should be shortened to about half of its current length.
6. For example, the authors should delete the paragraph starting in line 99.
7. The description of the workflow is excessive (starting in line 123). For example, sample quality assessment is routine, and it is not necessary. The authors should reduce the whole section (lines 123-147) to one or two short paragraphs supporting their work with adequate citations.
8. The authors wrote the Results section as a Results and Discussion section. The author's comments on their results do not belong to the Results section.
9. In the paragraph starting in line 155, the authors introduce information about the vegetation that does not belong to this section.
10. Similarly, section 3.2 includes information about the methodology, and the authors discuss the results.
11. Observations similar to item 10 happen across the whole results section.
12. The authors should also present some of their findings as supplementary tables and figures. For example, figure 3 is not key to understanding the results they presented.
13. The discussion section is well presented, but it is redundant with the result section, as the authors tend to discuss their results as they present them.
14. The authors should delete the paragraph starting in line 404.
15. Section 4.4 is too weak. The authors have enough information to write more substantial points about developing strategies for the conservation and use of genetic resources of Cordyceps chanhua.
16. The authors should revise the conclusions section in light of the changes made in section 4.4.
17. There are only six references in the whole discussion section, suggesting that the scope of the article is limited.

Comments for author File: Comments.pdf

Author Response

Comments 1: The introduction is too long and contains some unnecessary information. The authors should shorten the introduction to about sixty percent of its current length.

Response 1: Thank you for your comment. The introduction has been condensed as per your suggestion, reduced from the original 654 characters to 395 characters.

Comments 2: For example, the first paragraph is too long and may be combined with the second paragraph. Moreover, a reorganization of the introduction would help shorten this section.

Response 2: Thank you for your comment. The first and second paragraphs of the introduction have been merged and reorganized.

Comments 3: The short paragraph starting in line 67 is irrelevant to the study.

Response 3: Thank you for your comment. The irrelevant content has been deleted and merged with the following paragraph, which has been rewritten.

Comments 4: The level of detail in the paragraph starting in line 72 is excessive.

Response 4: Thank you for your comment. Redundant content has been removed, and the text has been streamlined while retaining the essential information.

Comments 5: The materials and Methods section should be shortened to about half of its current length.

Response 5: Thank you for your comment. The Materials and Methods section has been streamlined as per your request, and additional details have been added to sections 2.1 and 2.3 based on the suggestions of another reviewer.

Comments 6: For example, the authors should delete the paragraph starting in line 99.

Response 6: Thank you for your comment. The mentioned section has been deleted as per your suggestion.

Comments 7: The description of the workflow is excessive (starting in line 123). For example, sample quality assessment is routine, and it is not necessary. The authors should reduce the whole section (lines 123-147) to one or two short paragraphs supporting their work with adequate citations.

Response 7: Thank you for your comment. The content of "2.2.2. Whole-Genome Resequencing Analysis of C. chanhua" has been consolidated into a single paragraph, and additional references have been cited.

Comments 8: The authors wrote the Results section as a Results and Discussion section. The author's comments on their results do not belong to the Results section.

Response 8: Thank you for your comment. In accordance with your suggestion, the discussion content in the Results section has been removed.

Comments 9:In the paragraph starting in line 155, the authors introduce information about the vegetation that does not belong to this section.

Response 9: Thank you for your comment. The information about the vegetation that does not belong to this section has been removed.

Comments 10: Similarly, section 3.2 includes information about the methodology, and the authors discuss the results.

Response 10: Thank you for your comment. The content related to methodology and discussion in section 3.2 has been removed.

Comments 11: Observations similar to item 10 happen across the whole results section.

Response 11: Thank you for your comment. The entire Results section has been revised.

Comments 12: The authors should also present some of their findings as supplementary tables and figures. For example, figure 3 is not key to understanding the results they presented.

Response 12: We appreciate the reviewer’s suggestion. Figure 3 has been moved to the Supplementary Materials as Supplementary Figure S1, as it is not essential to understanding the primary findings.

Comments 13: The discussion section is well presented, but it is redundant with the result section, as the authors tend to discuss their results as they present them.

Response 13:Thank you for pointing this out. We have revised the discussion section to reduce redundancy with the results section. The results section now focuses solely on presenting data and findings, while the discussion section interprets these findings in the context of existing literature, potential mechanisms, and their broader implications.

Comments 14: The authors should delete the paragraph starting in line 404.

Response 14: Thank you for your comment. The content has been deleted.

Comments 15: Section 4.4 is too weak. The authors have enough information to write more substantial points about developing strategies for the conservation and use of genetic resources of Cordyceps chanhua.

Response 15: Thank you for your comment. Section 4.4 has been significantly revised to include detailed strategies for the conservation and sustainable utilization of Cordyceps chanhua genetic resources, supported by findings from genetic variation and SNP analyses.

Comments 16: The authors should revise the conclusions section in light of the changes made in section 4.4.

Response 16: Thank you for your comment. The Conclusion section has been revised according to the changes made in the Discussion section.

Comments 17: There are only six references in the whole discussion section, suggesting that the scope of the article is limited.

Response 17: Thank you for your comment. The discussion has been revised, and relevant references have been added.

 

Author Response File: Author Response.docx