Comparative Phylogenetic Analysis of Ancient Korean Tea "Hadong Cheon-Nyeon Cha (Camellia sinensis var. sinensis)" Using Complete Chloroplast Genome Sequences

Response to Reviewer 1 Comments

1. Summary

Responses to the Reviewers’ Comments

20 January, 2024

Dear reviewers and editorial staffs in Current Issues in Molecular Biology.

We are sincerely grateful for your thorough consideration and scrutiny of our manuscript, “Comparative Phylogenetic Analysis of Ancient Korean Tea ‘Hadong Cheon-Nyeon Cha (Camellia sinensis var. sinensis)’ Using Complete Chloroplast Genome Sequences”, control number cimb-2831979. Through the accurate comments made by the reviewers, we better understand the critical issues in this paper. We have revised the manuscript according to the Reviewer’s suggestions. We hope that our revised manuscript will be considered and accepted for publication in the Current Issues in Molecular Biology. We acknowledge that the scientific quality of our manuscript was improved by the scrutinizing efforts of the reviewers and editors.

The changes within the revised manuscript were highlighted (underlined and in red). Point-by-point responses to the reviewers’ comments are provided below.

2. Questions for General Evaluation

Reviewer’s Evaluation

Response and Revisions

Does the introduction provide sufficient background and include all relevant references?

Yes

We appreciate the reviewer’s evaluation.

Are all the cited references relevant to the research?

Yes

We appreciate the reviewer’s evaluation.

Is the research design appropriate?

Yes

We appreciate the reviewer’s evaluation.

Are the methods adequately described?

Yes

We appreciate the reviewer’s evaluation.

Are the results clearly presented?

Yes

We appreciate the reviewer’s evaluation.

Are the conclusions supported by the results?

Yes

We appreciate the reviewer’s evaluation.

3. Point-by-point response to Comments and Suggestions for Authors

Comments 1:

The research paper "Comparative Phylogenetic Analysis of Ancient Korean Tea 'Hadong Cheon-Nyeon Cha (Camellia sinensis var. sinensis)’ Using Complete Chloroplast Genome Sequences" provides a valuable resource for understanding ancient tea plants' chloroplast structure, variation information, and phylogenetic relationships in Korea. This is a base for e for the further improvement of leaf traits and plant types in ancient tea plants in Korea. The research was well designed and performed and the results are convincing.

Response 1:

We appreciate the reviewer’s comment. Thank you for the reviewer's compliment and encouragement of our study.

Comments 2:

I have two minor notes

1. the first sentence needs editing "Tea (Camellia sinensis (L.) O. Kuntze) is one of the most popular beverages worldwide"

Tea is the beverage which is an extract from the plant's leaves.

"Tea (extract from the leaves of tea plant Camellia sinensis (L.) O. Kuntze) is one of the most popular beverages worldwide"

Response 2:

We appreciate the reviewer’s comment. We agree with the reviewer’s note. “Tea is the beverage which is an extract from the tea plant’s leaves”, this is absolutely true. We updated text in the manuscript (page 1, paragraph 1, line 1). Thank you for pointing this out.

Comments 3:

2. The discussion needs editing aiming for clarification regarding the objects of comparison. Otherwise, the reader must guess what the authors meant. It obviously concerns other species in the genus Camellia and other subspecies but it should be detailed in the text.

Response 3:

The authors really thank for your comments and concerns. We think it's a very good point, and we agree with the reviewer's opinion. When making genetic comparisons or conjectures, it is crucial to compare different species within the same genus. However, please understand that our research is focused on the origin and evolution of 'Hadong Cheon-Nyeon Cha (HCNC)’ through the genomic analysis of seven species of green tea, including 'Hadong Cheon-Nyeon Cha (HCNC)’, rather than the relationships with other species or subspecies within the Camellia genus. We have made some adjustments to the Discussion based on your feedback (page 12, paragraph 1-3, line 297-300).

4. Response to Comments on the Quality of English Language

Point 1: None

Response 1:

5. Additional clarifications

We look forward to hearing from you in due time regarding our submission and to respond to any further questions and comments you may have.

Sincerely,

Dong-Kyung Yoon, Ph.D.,

Postdoctoral Researcher, Department of Southern Area Crop Science, National Institute of Crop Science (NICS), Rural Development Administration (RDA), 50424 Miryang, Korea.

Tel: (+82) 55-350-1273, H/P: (+82) 10-6678-1450, E-mail: [email protected]

Response to Reviewer 2 Comments

1. Summary

Responses to the Reviewers’ Comments

20 January, 2024

Dear reviewers and editorial staffs in Current Issues in Molecular Biology.

We are sincerely grateful for your thorough consideration and scrutiny of our manuscript, “Comparative Phylogenetic Analysis of Ancient Korean Tea ‘Hadong Cheon-Nyeon Cha (Camellia sinensis var. sinensis)’ Using Complete Chloroplast Genome Sequences”, control number cimb-2831979. Through the accurate comments made by the reviewers, we better understand the critical issues in this paper. We have revised the manuscript according to the Reviewer’s suggestions. We hope that our revised manuscript will be considered and accepted for publication in the Current Issues in Molecular Biology. We acknowledge that the scientific quality of our manuscript was improved by the scrutinizing efforts of the reviewers and editors.

The changes within the revised manuscript were highlighted (underlined and in red). Point-by-point responses to the reviewers’ comments are provided below.

2. Questions for General Evaluation

Reviewer’s Evaluation

Response and Revisions

Does the introduction provide sufficient background and include all relevant references?

Yes

We appreciate the reviewer’s evaluation.

Are all the cited references relevant to the research?

Yes

We appreciate the reviewer’s evaluation.

Is the research design appropriate?

Can be improved

We thank the reviewer for pointing this out. We have revised.

Are the methods adequately described?

Yes

We appreciate the reviewer’s evaluation.

Are the results clearly presented?

Yes

We appreciate the reviewer’s evaluation.

Are the conclusions supported by the results?

Can be improved

We thank the reviewer for pointing this out. We have revised.

3. Point-by-point response to Comments and Suggestions for Authors

Comments 1:

The study focuses on the analysis of the complete chloroplast genomes of seven Camellia sinensis var. sinensis cultivars, including the ancient Korean tea 'Hadong Cheon-nyeon Cha' (HCNC), known as Korea's oldest tea tree. The study's meticulous sequencing and assembly of multiple chloroplast genomes provide valuable data for gaining insights into the genetic composition of various tea cultivars. This research contributes significantly to our understanding of genetic diversity and evolution in Korean tea plants, especially the ancient HCNC.

Response 1:

We appreciate the reviewer’s comment. Thank you for the reviewer's compliment and encouragement of our study.

Comments 2:

The objectives of the study are clear and the idea is intriguing. I don't have any major comments to make. However, I am concerned about the existence of several previously published complete chloroplast genomes. After checking the NCBI database, I found roughly 15 papers that have already been published on this topic. In these papers, the authors downloaded complete chloroplast genomes and conducted phylogenetic analyses, as seen in Figure 8 of your manuscript. Nevertheless, the authors provide only a brief discussion in this manuscript and fail to offer a clear perspective on the origin of Korea's oldest tea tree. Therefore, I kindly request that you revise the manuscript to provide a more distinct view of the origin and evolution of Korea's oldest tea tree.

Response 2:

The authors really thank for your comments and concerns. We think it's a very good point, and we agree with the reviewer's opinion. When making genetic comparisons or conjectures, it is crucial to compare different species within the same genus. However, please understand that our research is focused on the origin and evolution of 'Hadong Cheon-nyeon Cha (HCNC)’ through the genomic analysis of seven species of green tea, including 'Hadong Cheon-nyeon Cha (HCNC)’, rather than the relationships with other species or subspecies within the Camellia genus. We have made some adjustments to the Discussion based on your feedback (page 12, paragraph 1-3, line 297-300).

Comments 3:

Overall, the English writing, grammar, and syntax in the manuscript meet the high standards typical of scientific writing in the UK. The paper is well-structured, with clearly delineated sections for the introduction, methods, results, and conclusions. The logical flow from one section to the next aids in reader comprehension. However, there are instances where the manuscript employs long and complex sentences, particularly in the methods and results sections. Simplifying these sentences could improve clarity and readability.

Response 3:

Thanks for your comment. The authors all agree with your opinions. Since this paper is in the field of Data informatics using de novo assembly technology, it has a lot of technical terminology and may feel complicated due to the nature of the field (for reference, we present several other papers on similar topics). However, readers who encounter this paper are likely to have a high level of understanding and interest in it. We kindly ask for your understanding.

1.      Rawal, H.C., Borchetia, S., Bera, B. et al. Comparative analysis of chloroplast genomes indicated different origin for Indian tea (Camellia assamica cv TV1) as compared to Chinese tea. Sci Rep 11, 110 (2021). https://doi.org/10.1038/s41598-020-80431-w

2.      Chen Q, Chen C, Wang B, Wang Z, Xu W, Huang Y and Sun Q (2022) Complete chloroplast genomes of 11 Sabia samples: Genomic features, comparative analysis, and phylogenetic relationship. Front. Plant Sci. 13:1052920. doi: https://doi.org/10.3389/fpls.2022.1052920

3.      Lu, Q.-X.; Chang, X.; Gao, J.; Wu, X.; Wu, J.; Qi, Z.-C.; Wang, R.-H.; Yan, X.-L.; Li, P. Evolutionary Comparison of the Complete Chloroplast Genomes in Convallaria Species and Phylogenetic Study of Asparagaceae. Genes 2022, 13, 1724. https://doi.org/10.3390/genes13101724

4. Response to Comments on the Quality of English Language

Point 1: Minor editing of English language required

Response 1:

We appreciate the reviewer’s comment. We got English corrected as the reviewer’s opinion for a more clear expression.

5. Additional clarifications

We look forward to hearing from you in due time regarding our submission and to respond to any further questions and comments you may have.

Sincerely,

Dong-Kyung Yoon, Ph.D.,

Postdoctoral Researcher, Department of Southern Area Crop Science, National Institute of Crop Science (NICS), Rural Development Administration (RDA), 50424 Miryang, Korea.

Tel: (+82) 55-350-1273, H/P: (+82) 10-6678-1450, E-mail: [email protected]