Comparative and Phylogenetic Analyses of the Complete Chloroplast Genomes of Four Ottelia Species
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsI checked your manuscript and described comments below.
Actinidia deliciosa is an important fruit native to China and eaten all over the world.
Ottelia is an aquatic plant that grows naturally in Asia, Africa, and Australia.
This paper provides a very good comparative genomic analysis of Ottelia chloroplasts.
I think you should consider the following points.
1. Regarding "3.2. Sequencing and Assembling of Chloroplast Genome", I think it would be better to list the GenBank accession IDs used for analysis.
2. "3.3. Chloroplast Genome Structural Analysis" uses MEGA-X, and "3.5. Phylogenomic Reconstruction" uses MEGA-6, but these are older versions of software. Analysis should be performed with the latest MEGA-11.
3. Ref. 12, Ref. 15, and Ref. 18 should be written in more details.
I don't think this paper has new various major mistakes or grammatical problems.
Author Response
- Regarding "3.2. Sequencing and Assembling of Chloroplast Genome", I think it would be better to list the GenBank accession IDs used for analysis.
Response: We have listed all the GenBank accession IDs in this manuscript in Table S3 to facilitate easier access to this information.
- "3.3. Chloroplast Genome Structural Analysis" uses MEGA-X, and "3.5. Phylogenomic Reconstruction" uses MEGA-6, but these are older versions of software. Analysis should be performed with the latest MEGA-11.
Response: Thanks for the suggestion. 3.3. RSCU was assessed using Codonw version 1.4.4. Sorry for the carelessness and we have corrected it in the revised version. And for phylogenomic reconstruction, we performed it with the latest MEGA-11 as you suggested and the result is the same. We have modified the M & M section.
- Ref. 12, Ref. 15, and Ref. 18 should be written in more details.
Response: We have added the details of three refs.
Reviewer 2 Report
Comments and Suggestions for AuthorsThe article "Comparative and Phylogenetic Analysis of the Complete Chloroplast Genomes of Four Ottelia Species" by Jianmin Tang et al. presented a comprehensive analysis of the cp genomes of five newly sequenced samples from four Ottelia species. They performed detailed characterization of the organization and arrangement of the Ottelia cp genomes and identified highly divergent regions. Based on that data, they investigated evolutionary relationships within the Ottelia species.
Main remark: A more profound discussion is needed! Delving deeper into the obtained results is crucial, as they hold significant implications for our understanding of the Ottelia species. A more extensive discussion will help us fully comprehend the evolutionary relationships within Ottelia species and the potential of the regions for DNA barcoding identified in this study.
Some small remarks:
Line 35 - O. mesenterium must be in Italic.
Line 294 – Manufacturer of the DNA extraction kit?
Lines 169-170 – The text is not well formatted.
Author Response
Main remark: A more profound discussion is needed! Delving deeper into the obtained results is crucial, as they hold significant implications for our understanding of the Ottelia species. A more extensive discussion will help us fully comprehend the evolutionary relationships within Ottelia species and the potential of the regions for DNA barcoding identified in this study.
Response: Thank you for your insightful remark. We appreciate the emphasis on the importance of a deeper discussion of our results. In response to your suggestion, we have significantly expanded the discussion, especially the potential of the identified regions for DNA barcoding.
Some small remarks:
Line 35 - O. mesenterium must be in Italic.
Response: we have italicized the names of the taxa and loci throughout the text in the revised version.
Line 294 – Manufacturer of the DNA extraction kit?
Response: thanks for the suggestion. We have corrected it in the revised version.
Lines 169-170 – The text is not well formatted.
Response: we have formatted the text in the revised version.
Reviewer 3 Report
Comments and Suggestions for AuthorsThis paper is acceptable. Still, some corrections are necessary.
The phylogenetic analysis is weak, as in the most similar studies. This is simply because of the sampling. Therefore, I suggest adding the word "preliminary" to the legend of Figure 5 (lines 286-287) and elsewhere in the text.
Running ModelTest (or similar software) may not be necessary if authors have already decided to use RAxML (GTR Model and its derivatives are the default RAxML setting). Please correct the related section in "Materials and Methods" (lines 341 - 354).
"Conclusions" (as written) sound odd and must be wholly re-established. I encourage authors to avoid conclusions from the phylogenetic analysis due to the latter's weakness.
Minor
The names of the taxa and loci must be italicized throughout the text.
English is acceptable, but one more polishing is worth to add.
English is acceptable, but one more polishing is worth to add.
Author Response
- The phylogenetic analysis is weak, as in the most similar studies. This is simply because of the sampling. Therefore, I suggest adding the word "preliminary" to the legend of Figure 5 (lines 286-287) and elsewhere in the text.
Response: Thank you very much for the suggestion. We have added the word “preliminary” to the legend and in the text. We believe this change makes the article more objective.
- Running ModelTest (or similar software) may not be necessary if authors have already decided to use RAxML (GTR Model and its derivatives are the default RAxML setting). Please correct the related section in "Materials and Methods" (lines 341 - 354).
Response: We have improved M & M according to your suggestion.
- "Conclusions" (as written) sound odd and must be wholly re-established. I encourage authors to avoid conclusions from the phylogenetic analysis due to the latter's weakness.
Response: We have revised our conclusions to avoid overemphasizing the results from the phylogenetic analysis.
- The names of the taxa and loci must be italicized throughout the text.
Response: we have italicized the names of the taxa and loci throughout the text in the revised version.
- English is acceptable, but one more polishing is worth to add.
Response: we have polished the English using MDPI editing services.
Round 2
Reviewer 2 Report
Comments and Suggestions for AuthorsThe article Comparative and Phylogenetic Analysis of the Complete Chloroplast Genomes of Four Ottelia Species by Jianmin Tang and coauthors is suitable for publication in the journal Horticulturae in its present form. The authors have considered my recommendations and notes, and now the article looks more scientifically valuable and interesting to the readers.
