A High-Quality Genome Assembly of the Mitochondrial Genome of the Oil-Tea Tree Camellia gigantocarpa (Theaceae)
Round 1
Reviewer 1 Report
This study presents for the first time the sequencing and analysis of the structure of the mitochondrial genome of C. gigantocarpa. Using Hi Fi and Hi-C sequencing, the authors coped with the difficult task of assembling the mitochondrial genome. The manuscript contains the necessary methodological actions typical for this type of research.
Nevertheless, there are certain comments.
Major
Need to expand results and discussion about gene content. Conduct a comparative analysis of their structure and diversity. Indicate what mutational events occur and how they can possibly affect.
Minor
Provide data on the level of coverage and the number of reads.
Line 124: “ML” It is necessary to decipher when it occurs for the first time.
Line: 136-141: The gene composition does not match those in Figures 2 and 3. Please provide all the genes once you have started doing this.
Line 159: Please avoid starting a sentence with numbers.
Line 163-164: SSR values do not coincide with those indicated in Table 2. Please check it.
Line 179: Please avoid starting a sentence with numbers.
Line 363-385: Please format the literature according to the requirements of the journal.
The GenBank access number is not active.
Author Response
Response to Reviewer 1 Comments
Need to expand results and discussion about gene content
Response 1: Many thanks for this valuable suggestion. In the revised manuscript, we expanded the description of gene content in Results and Discussion in line 134-143 and line 237-238.
Conduct a comparative analysis of their structure and diversity. Indicate what mutational events occur and how they can possibly affect.
Response 2: Thanks for reviewer’s constructive suggestions. We calculated the similarity of the protein coding genes between C. gigantocarpa and C. sinensis (99.8%), C. gigantocarpa and A. thaliana (95.2%). To show that, compared with their high rate of rearrangements in mitochondrial genome, the coding region were high conserved. In the revised manuscript, we add these data in line 183-202.
Provide data on the level of coverage and the number of reads.
Response 3: Thank you for the comments to help improve the quality of the paper. In the revised manuscript, we add“Finally, the complete mitochondrial genome of C. gigantocarpa were used 71,338 HiFi reads with approximately 1070X coverage.” at line 88-89.
Line 124: “ML” It is necessary to decipher when it occurs for the first time.
Response 4: Many thanks for your valuable suggestion. We made corrections at line 129.
Line: 136-141: The gene composition does not match those in Figures 2 and 3. Please provide all the genes once you have started doing this.
Response 5: Thank you for point this out. 稍微解释一句We have made corrections at line 133-146.
Line 159: Please avoid starting a sentence with numbers.
Line 179: Please avoid starting a sentence with numbers.
Response 6: Many thanks for the valuable suggestion. In the revised manuscript, we improved this at line 159-160 and line 179-180.
Line 163-164: SSR values do not coincide with those indicated in Table 2. Please check it.
Response 7: We thank the referee for his careful reading. We have made corrections on line 162-166.
Line 363-385: Please format the literature according to the requirements of the journal.
Response 9: Thank you for pointing it out, all references are now corrected.
The GenBank access number is not active.
Response 10: Thank you for pointing it out. We upload the mitochondrial genome of Camellia gigantocarpa on August 19, and we received GenBank accession number on August 22. I have sent an email to consult the progress. If you request the mitochondrial genome, we will send you via email.
Author Response File: 
Author Response.docx
Reviewer 2 Report
REVIEW
of the article “A High-Quality Genome Assembly of the Mitochondrial Genome of Camellia gigantocarpa (one of oil-tea tree)”
submitted to the DIVERSITY journal, Special issue Genetic Diversity and Conservation of Economic Plants, belonging to the Section Plant Diversity
This article describes new information on mitochondrial genome structure for the oil-tea tree genus Camellia. The authors attempted to characterize and analyze the obtained molecular data from phylogenetic point of view. The manuscript may be potentially interesting, but its focus, some methodological flaws, and its English should be strengthened before re-submission.
Please consider my comments listed below, which may help you improve the manuscript. Moreover, I am attaching a pdf version with many additional corrections.
Title
I would suggest a slight change to the title (highlighted in yellow):
A High-Quality Genome Assembly of the Mitochondrial Genome of the Oil-tea Tree Camellia gigantocarpa (Theaceae)
ABSTRACT
1. There is a logical inconsistency: Line 8 contradicts to Line 16. Is C. sinensis an oil tea tree or not? If yes (and it is, as far as I know), then you cannot claim that the new mitogenome is the first for this group of plants.
2. In addition, I found a lot of lexical negligences (see my comments in the attached pdf). The abstract needs more attention. This is a very important representative part of your article.
INTRODUCTION
Again, pay attention to your phrase “the first mitochondrial genome sequence published for oil-tea
tree” (Line 49).
I hope my comments in pdf can help you to improve the text (Lines: 23, 45-47, and 54-57).
MATERIALS AND METHODS
Plant Materials and Genome Sequencing
Corrections suggested for your text in Lines: 60-63, 65, 69, 70, 73-74.
Genome Assembly
1. The first sentence looses a verb.
Maybe this variant: “The genome assembly was followed the method described by Kovar et al. [17]”.
2. Please specify which genome was used as a reference? (Line 78).
3. There are comments for the Lines 77, 80, 82, 83, and 87.
Genome Annotation and Visualization
1. Corrections are in Lines 90 and 95.
2. Line 94: change to italic – de novo
Synteny Analysis
Corrections are in Lines 110, 112, 113, 114.
Phylogenetic Analysis
Corrections are in Lines 120-121.
RESULTS
1. The first part of the section (Lines 128-137) describes methods and should be moved to the appropriate section of the manuscript.
2. The sentence (Line 128) is lexically incorrect.
3. The mitogenome content description is unclear, since arithmetic doesn't add up. A clearer description of the composition of genes and the number of their copies is required (Lines 138-141).
4. Figure 2 (Line 148) is unreadable.
5. Line 158: Again about methods.
6. Corrections suggested for Lines 184 and 187.
7. Line 188: Move the information to Methods.
8. Corrections suggested for Lines 206-207, 212.
DISCUSSION
1. Line 222-223: a verb (predicate) is absent.
2. Line 225: answer the question in pdf.
3. Using of the term “chromosome” for mitochondrial genome is incorrect.
4. Mistakes were found in Lines 117, 228, 229, 239, 242, and 248.
Comments for author File: 
Comments.pdf
Author Response
Response to Reviewer 2 Comments
Title
I would suggest a slight change to the title (highlighted in yellow):
A High-Quality Genome Assembly of the Mitochondrial Genome of the Oil-tea Tree Camellia gigantocarpa (Theaceae)
Response: Thank you so much for your consideration and kind help. In the revised manuscript, we changed it.
ABSTRACT
- There is a logical inconsistency: Line 8 contradicts to Line 16. Is C. sinensis an oil tea tree or not? If yes (and it is, as far as I know), then you cannot claim that the new mitogenome is the first for this group of plants.
Response: Thank you for your careful work. C. sinensis is a species of “tea tree” used to make tea, which leaves are rich in catechin and caffein. While C. gigantocarpa is an oil crop belong to “oil-tea tree”, which can extract camellia oil (rich in unsaturated fatty acids and secondary metabolites beneficial to human health) from its seeds. C. sinensis belong to Sect. Thea and C. gigantocarpa belong to Sect. Furfuracea in genus Camellia (see following figure, high light in red box, wu., The Plant Journal 2022). I agree that the “oil-tea tree” is a very misleading name. To avoid misleading, we add the common name of C. sinensis in line 14 in the revised manuscript.
Wu, Q.; Tong, W.; Zhao, H.; Ge, R.; Li, R.; Huang, J.; Li, F.; Wang, Y.; Mallano, A.I.; Deng, W.; Wang, W.; Wan, X.; Zhang, Z.; Xia, E. Comparative transcriptomic analysis unveils the deep phylogeny and secondary metabolite evolution of 116 Camellia plants. The Plant Journal 2022, 111, 406-421.
- In addition, I found a lot of lexical negligences (see my comments in the attached pdf). The abstract needs more attention. This is a very important representative part of your article.
Response: Thank you so much again for your excellent feedback on our paper. Based on your helpful suggestions, we have improved the abstract and the Introduction at line 7-19, 23, and 46-48.
INTRODUCTION
Again, pay attention to your phrase “the first mitochondrial genome sequence published for oil-tea tree” (Line 49).
Response: Thank you for your careful work. we add the common name (tea tree) of C. sinensis in line 48 in the revised manuscript.
I hope my comments in pdf can help you to improve the text (Lines: 23, 45-47, and 54-57).
Response: Thank you so much for your excellent feedback on our paper. Done!
MATERIALS AND METHODS
Plant Materials and Genome Sequencing
Corrections suggested for your text in Lines: 60-63, 65, 69, 70, 73-74.
Response: Thanks for the correction, all suggested corrections have been incorporated in the revised manuscript.
Genome Assembly
- The first sentence looses a verb. Maybe this variant: “The genome assembly was followed the method described by Kovar et al. [17]”.
Response: Thanks for the correction, Done!
- Please specify which genome was used as a reference? (Line 78).
Response: Many thanks for your valuable suggestion. We use 15 plant mitochondrial genome as reference in this work. In the revised manuscript, we list them all at line 74-77.
- There are comments for the Lines 77, 80, 82, 83, and 87.
Response: Thanks for the correction, Done!
Genome Annotation and Visualization
- Corrections are in Lines 90 and 95.
Response: Thanks for the correction, Done!
- Line 94: change to italic – de novo
Response: Thanks for the correction, Done!
Synteny Analysis
Corrections are in Lines 110, 112, 113, 114.
Response: Thanks for the correction, Done!
Phylogenetic Analysis
Corrections are in Lines 120-121.
Response: Thanks for the correction, Done!
RESULTS
- The first part of the section (Lines 128-137) describes methods and should be moved to the appropriate section of the manuscript.
Response: Many thanks for your valuable suggestion. In the revised manuscript, we move all the methods describes in result to M&Ms.
- The sentence (Line 128) is lexically incorrect.
Response: Many thanks for your valuable suggestion. In the revised manuscript, we have changed this sentence into “The mitochondrial genome assembly was started according to the pipeline of Kovar et al [17]”, and move it to M&Ms.
- The mitogenome content description is unclear, since arithmetic doesn't add up. A clearer description of the composition of genes and the number of their copies is required (Lines 138-141).
Response: Thank you for your careful work. In the previous version, we did not add the copy number of the multi-copy gene which caused misleading. We have made corrections of the mitogenome content to “44 protein-coding genes” at line 130-143.
- Figure 2 (Line 148) is unreadable.
Response: Many thanks for your valuable suggestion. We redraw Figure 2.
- Line 158: Again about methods.
Response: Thanks for the correction, Done!
- Corrections suggested for Lines 184 and 187.
Response: Thanks for the correction, Done!
- Line 188: Move the information to Methods.
Response: Thanks for the correction, Done!
- Corrections suggested for Lines 206-207, 212.
Response: Thanks for the correction, Done!
DISCUSSION
- Line 222-223: a verb (predicate) is absent.
Response: Thank you for your careful work. In the revised manuscript, we have changed this sentence into “Here, we used a combination of sequencing technologies, …”
- Line 225: answer the question in pdf.
Response: Thank you for your careful work. The workflows not only for Camelia spp., but also for all the plant mitochondrial genome with large size and highly repetitive sequences. In the revised manuscript, we have changed this sentence into “… and present workflows for the accurate and complete assembly the large and complex plant mitochondrial genome with highly repetitive sequences (Figure 1).” at line 230-232
- Using of the term “chromosome” for mitochondrial genome is incorrect.
Response: We would highly appreciate valuable comments. In the revised manuscript, we rewrote these sections. Now we used “mitochondrial genome” and “sequences” instead of “chromosome”.
- Mistakes were found in Lines 117, 228, 229, 239, 242, and 248.
Response: Thanks for the correction, Done!
Author Response File: Author Response.docx
Round 2
Reviewer 1 Report
The authors have made the necessary corrections. And I believe that the article can be accepted for publication.
Author Response
Response to Reviewer 1 Comments
The authors have made the necessary corrections. And I believe that the article can be accepted for publication.
Response: Thanks again for your approval of our work.
Reviewer 2 Report
Authors improved a lot, but still not enough.
In Abstract, I would suggest to re-write one sentence: To date, no data on the mitochondrial genome of the oil-tea tree, in contrast to the tea-tree C. sinensis, which belongs to the same genus.
Then in the further there is no need to use the full word Camellia in species names. Leave only where one genus name is used.
Figure 2 is still difficult to read. The figure should be larger.
Author Response
Response to Reviewer 2 Comments
In Abstract, I would suggest to re-write one sentence: To date, no data on the mitochondrial genome of the oil-tea tree, in contrast to the tea-tree C. sinensis, which belongs to the same genus.
Response 1: Thank you so much again for your excellent feedback on our paper. Based on your helpful suggestions, we have improved the abstract at line 8-9, which are marked with yellow color.
Then in the further there is no need to use the full word Camellia in species names. Leave only where one genus name is used.
Response 2: Thank you for your careful work. Done!
Figure 2 is still difficult to read. The figure should be larger.
Response 3: Many thanks for your valuable suggestion, we improved Figure 2 again, I hope this time the figure can show genes clearly.
