Mitogenomics of Three Ziczacella Leafhoppers (Hemiptera: Cicadellidae: Typhlocybinae) from Karst Area, Southwest China, and Their Phylogenetic Implications
Round 1
Reviewer 1 Report
This article presented three new mitogenomes of Cicadellidae species with detailed annotation and comprehensively comparative analyses. The authors surveyed these mitogenomes and their general features, such as AT bias, length variation, and codon usage. Phylogenetic trees using BI and ML methods support three newly sequenced species were closely related to genus Mitjaevia and the monophyly of the four tribes within Typhlocybinae. The manuscript provided information of the Cicadellidae mitogenomes. This article can only be accepted after some major adjustments.
1) The authors should provide which genes were used in phylogenetic analyses. 13 PCGs or 13 PCGS plus 2 RNAs?
2) How many Gb of raw data are measured for each species and the average sequencing depth of these mitogenome should be provided in Materials and Methods.
3) Line 28-37, references in the first paragraph were not shown.
Author Response
Dear reviewer,
Thank you for returning our manuscript entitled “Mitogenomics of Three Ziczacella Leafhoppers (Hemiptera: Cicadellidae: Typhlocybinae) from Karst Area, Southwest China and Their Phylogenetic Implications” with valuable comments and suggestions from you. We have revised the manuscript comprehensively based on these comments and suggestions, and here would like to submit the revised manuscript for publication in Diversity.
We tried my best to improve the manuscript and made some changes in the manuscript. We also responded to all comments point-by-point. The file “manuscript_20230725. docx” is a clean revised manuscript with the changed part blue highlighted. We hope that our revised paper is suitable for publication in Diversity.
Point-by-point responses to the reviewer are listed below this letter. Thank you again for your positive comments and valuable suggestions to improve the quality of our manuscript.
Yours faithfully,
First author, Jinqiu Wang
Corresponding author, Prof. Yuehua Song
Point 1: The authors should provide which genes were used in phylogenetic analyses. 13 PCGs or 13 PCGS plus 2 RNAs?
Response 1: Thanks for your suggestion. We used all complete mitochondrial sequences to estimate the phylogeny analyses, not just 13 PCGs or 13 PCGS plus 2 RNAs. In the revised manuscript, we provided this information in Materials and Methods.
Point 2: How many Gb of raw data are measured for each species and the average sequencing depth of these mitogenome should be provided in Materials and Methods.
Response 2: Thanks for your careful checks. According to the reviewer 's suggestion, we provide these information in Materials and Methods.
Point 3: Line 28-37, references in the first paragraph were not shown.
Response 3: The references of first paragraph are listed in the References at the end of the manuscript. If there are any other modifications we could make, we would like very much to modify them and we really appreciate your help.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
Comments for author File: Comments.pdf
Author Response
Dear reviewer,
Thank you for returning our manuscript entitled “Mitogenomics of Three Ziczacella Leafhoppers (Hemiptera: Cicadellidae: Typhlocybinae) from Karst Area, Southwest China and Their Phylogenetic Implications” with valuable comments and suggestions from you. We have revised the manuscript comprehensively based on these comments and suggestions, and here would like to submit the revised manuscript for publication in Diversity.
We tried our best to improve the manuscript and made some changes in the manuscript. We also responded to all comments point-by-point. The file “manuscript_20230725. docx” is a clean revised manuscript with the changed part blue highlighted. We hope that our revised paper is suitable for publication in Diversity.
Point-by-point responses to the reviewer are listed below this letter. If there are any other modifications we could make, we would like very much to modify them and we really appreciate your help.
Yours faithfully,
First author, Jinqiu Wang
Corresponding author, Prof. Yuehua Song
Point 1: Line 35: do not know what “combined species” means. I had never heard that term. Please, clarify or use another term.
Response 1: We intended to show that other species, except for Ziczacella katoi, did not initially belong to the genus of Ziczacella, but were separated from other genera by Anufryev in 1970 based on their head and male genitalic. As an article of mitochondrial genomics, deleting this sentence will not affect the results and discussion of the article. So in the resubmitted manuscript, we delete this sentence.
Point 2: Line 41: replace “relationship” by “relationships”.
Response 2: Thanks for your careful checks. In our resubmitted manuscript, we have corrected the “relationship” into “relationships”. We were really sorry for our careless mistakes.
Point 3: Line 46: “insect mitochondrial genomic DNA” or “insect mitochondrial genome” (and then delete “DNA” inside the parentheses).
Response 3: We have rewritten this part according to the reviewer 's suggestion.
Point 4: Line 59: I think a more detailed explanation of what is known about the phylogenetic relationships of the genus Ziczacella is already known is needed, as well as the motivation for such a study (e.g. economic importance as pest, or whatever).
Response 4: We supplement this part in the text according to the reviewer 's suggestion.
Point 5: Lines 72-75: georreferentiation should be given.
Response 5: Thanks for your suggestion. We have provided the latitude and longitude of the leafhoppers collection site in the text.
Point 6: Line 78: two of each species? Then was DNA extracted from a bulk? That should be clarified.
Response 6: The DNA of the three species was extracted in turn using the kit, and each species required a total of six individuals to extract. Due to the small size of the leafhopper, in order to successfully extract DNA, each species used six leafhoppers.
Point 7: Lines 115-116: How was the evolutionary model selected? Please, give the name of such a software.
Response 7: Thanks for your suggestion. In the revised manuscript, we added software for evolutionary model selection.
Point 8: Lines 169-171: confusing. The same order as in 166-167?
Response 8: The order is the same as the previous sentence. And we have rewritten this sentence so that readers can read it clearly.
Point 9: Lines 260-262: that sounds funny. Maybe the two tribes are one instead? Reword that sentence to give the right information.
Response 9: We have rewritten this part according to the reviewer 's suggestion. In this study, we support merging Zyginellini and Typhlocybini into a single branch and the two tribes should be treated as synonyms.
Point 10: Lines 262-265: Split such a long sentence in two. It is difficult to follow.
Response 10: Thank you very much for your suggestion. We have split this long sentence into two sentences.
Point 11: Line 275: replace “they” for “them”.
Response 11: We have modified this error in the text, “they” is replaced by “them”.
Author Response File: Author Response.pdf
Round 2
Reviewer 1 Report
The authors don't know how to reconstruct phlogenetic trees. You can not use the whole mitochondrial sequences directly. You should use Phylosuite or other softwares to extract PCGs and RNAs, and aligned them using different strategies. Please read and follow the material and methods of some mitogenomic researches carefully and renew the phlogenetic trees.
Generally, the average depth of a mitogenome with 4 Gb clean data is far more than 10X. Please recheck.
Author Response
Dear reviewer,
Thank you for returning our manuscript entitled “Mitogenomics of Three Ziczacella Leafhoppers (Hemiptera: Cicadellidae: Typhlocybinae) from Karst Area, Southwest China and Their Phylogenetic Implications” with valuable comments and suggestions from you. We have revised the manuscript comprehensively based on these comments and suggestions, and here would like to submit the revised manuscript for publication in Diversity.
We tried my best to improve the manuscript and made some changes in the manuscript. We also responded to all comments point-by-point. The file “manuscript_20230807. docx” is a clean revised manuscript with the changed part blue highlighted. We hope that our revised paper is suitable for publication in Diversity.
Point-by-point responses to the reviewer are listed below this letter. Thank you again for your positive comments and valuable suggestions to improve the quality of our manuscript.
Yours faithfully,
First author, Jinqiu Wang
Corresponding author, Prof. Yuehua Song
Point 1: The authors don't know how to reconstruct phlogenetic trees. You can not use the whole mitochondrial sequences directly. You should use Phylosuite or other softwares to extract PCGs and RNAs, and aligned them using different strategies. Please read and follow the material and methods of some mitogenomic researches carefully and renew the phlogenetic trees.
Response 2: We have reconstructed the phylogenetic tree based on 13 PCGs and two rRNAs according to the reviewers ' comments.
Point 2: Generally, the average depth of a mitogenome with 4 Gb clean data is far more than 10X. Please recheck.
Response 2: We have corrected it in the resubmitted manuscript.
Round 3
Reviewer 1 Report
The authors have revised all of my concerns. I recommended Accept for this paper.
