Complete Chloroplast Genome Structural Characterization and Comparative Analysis of Viburnum japonicum (Adoxaceae)
Round 1
Reviewer 1 Report
The presented research is both intriguing and serves as a valuable complement to the earlier study conducted by Cho et al. in 2018. In my assessment, the current state of the manuscript precludes its immediate suitability for publication, necessitating a series of revisions.
I kindly advise addressing several editorial shortcomings in the manuscript. Notably, species names should be appropriately formatted in italics throughout the text.
Within the dedicated section elucidating the materials and methods employed, it is essential to adhere to the conventions of scholar writing, which typically eschews the third-person perspective in scientific articles.
I noted the absence of bibliographic references for sections 2.1, 2.3, and 2.4.
I encourage providing specific details regarding the quantity of DNA extracted, specifying the unit of measurement (ng) and elucidating the method employed to ascertain both DNA quality and quantity.
Results should not be included in the methodology section (line 64).
It is worth noting that adaptor sequences were not subjected to analysis.
The number of nucleotide repeats analyzed should be included in the text.
In terms of enhancing the study's credibility, I propose to expand the phylogenetic analysis, possibly by incorporating Bayesian Inference, which would be an addition that could reverberate throughout the entirety of the study's framework.
It should be noted that Chapter 3 does not conform to the conventional structure of a discussion.
Figure 2 is unclear.
Table 2: Why are some gene names bolded? (Please add an explanation in the table description).
Line 148 should be corrected by adding an "s" to "SSR" – resulting in "SSRs loci."
Figure 4 does not adhere to the principle of self-explanation in its description. It is recommended to provide further clarification within the legend. Notably, the legend includes the symbol 'C,' despite its absence from the corresponding graph.
For clarity's sake, it is suggested that Figure 5 be relocated to the supplementary material. Furthermore, the substitution of "Ter" with "STOP" is advised to facilitate a more lucid representation. Additionally, the enhancement of table clarity, delineating which codons correspond to specific amino acids, is recommended.
Figure S3 requires a comprehensive description to fulfill the criterion of self-explanatory clarity.
Figures 6 and 7 require enhancing the resolution. Moreover, Figure 7 is illegible.
A notable limitation is observed within the discussion, characterized by its brevity and lack of substantive elaboration. To augment its scholarly rigor, I recommend referencing among others the results of RSCU and SSR analyses in comparison with existing literature data.
Author Response
Response to Reviewer 1 Comments
Point 1: I kindly advise addressing several editorial shortcomings in the manuscript. Notably, species names should be appropriately formatted in italics throughout the text.
Response 1: The Latin names of all plants were individually italicized.
Point 2: Within the dedicated section elucidating the materials and methods employed, it is essential to adhere to the conventions of scholar writing, which typically eschews the third-person perspective in scientific articles.
Response 2: Thank you for you kind reminding, we used passive voice for modification in the “materials and methods” sections.
Point 3: I noted the absence of bibliographic references for sections 2.1, 2.3, and 2.4.
Response 3: We have added references to the mentioned sections.
Point 4: I encourage providing specific details regarding the quantity of DNA extracted, specifying the unit of measurement (ng) and elucidating the method employed to ascertain both DNA quality and quantity.
Response 4: The aforementioned details have been added to Section 3.1.
Point 5: Results should not be included in the methodology section (line 64).
Response 5: Agreed, and then we have moved the results in section 3.1.
Point 6: It is worth noting that adaptor sequences were not subjected to analysis.
Response 6: Can you specify the adapter sequence and in which part of the article it is?
Point 7: The number of nucleotide repeats analyzed should be included in the text.
Response 7: Can you specify which part of the article is being analyzed for the number of nucleotide repeats?
Point 8: In terms of enhancing the study's credibility, I propose to expand the phylogenetic analysis, possibly by incorporating Bayesian Inference, which would be an addition that could reverberate throughout the entirety of the study's framework.
Response 8: We appreciate your valuable suggestions on our research. You suggested incorporating Bayesian analysis in the section on phylogenetic results, which is indeed an effective tree-building method. However, we chose to use maximum likelihood method for phylogenetic analysis due to its scientific rationale and advantages. Compared to Bayesian analysis, the ML method has several advantages: 1) Efficiency: ML method only requires maximizing the objective function without complex posterior probability calculations. This makes maximum likelihood method more efficient when dealing with large datasets. 2) Statistical properties: ML method has properties such as consistency, asymptotic unbiasedness, and efficiency. These properties enable ML method to provide consistent estimation results and allow inference through classical statistical theory. 3) Model selection: ML method allows for comparison between different models by comparing their likelihood ratios. This helps us make more accurate inferences about phylogenetic relationships. Although Bayesian analysis has its unique advantages in phylogenetic inference, we believe that using only ML method is reasonable in our study and can accurately reflect our research objectives and dataset characteristics. In our study, we have extensively utilized the advantages of the ML method in our study and have thoroughly described the adopted methods and data processing procedures. Naturally, for future research, we will consider using other methods such as Bayesian analysis for further analysis to validate and enrich our results.
Point 9: It should be noted that Chapter 3 does not conform to the conventional structure of a discussion.
Response 9: Agreed, and we added a paragraph to the discussion section.
Point 10: Figure 2 is unclear.
Response 10: Figure 2 has been replaced with a higher quality image.
Point 11: Table 2: Why are some gene names bolded? (Please add an explanation in the table description).
Response 11: The bold gene name was initially intended for statistically duplicated genes, as already indicated with an asterisk (*) in the note. Consequently, the bold formatting is removed.
Point 12: Line 148 should be corrected by adding an "s" to "SSR" – resulting in "SSRs loci."
Response 12: Agreed, and we made the addition accordingly.
Point 13: Figure 4 does not adhere to the principle of self-explanation in its description. It is recommended to provide further clarification within the legend. Notably, the legend includes the symbol 'C,' despite its absence from the corresponding graph.
Response 13: As we described in Section 3.2, the SSR of V. japonicum contains three repeat types: F, P, and R, while type C is absent.
Point 14: For clarity's sake, it is suggested that Figure 5 be relocated to the supplementary material. Furthermore, the substitution of "Ter" with "STOP" is advised to facilitate a more lucid representation. Additionally, the enhancement of table clarity, delineating which codons correspond to specific amino acids, is recommended.
Response 14: Thank you for your suggestions. However, due to the improved clarity of the picture in Figure 5, we deemed it necessary to include it in the text. The term "Termination codon" was utilized in Table 3.
Point 15: Figure S3 requires a comprehensive description to fulfill the criterion of self-explanatory clarity.
Response 15: In Section 3.1, we made necessary additions to the description of Figure S3.
Point 16: Figures 6 and 7 require enhancing the resolution. Moreover, Figure 7 is illegible.
Response 16: We enhanced the resolution of both graphs.
Point 17: A notable limitation is observed within the discussion, characterized by its brevity and lack of substantive elaboration. To augment its scholarly rigor, I recommend referencing among others the results of RSCU and SSR analyses in comparison with existing literature data.
Response 17: Agreed, and we have incorporated an analysis regarding RSCU and SSR in the second paragraph of the discussion section.
Reviewer 2 Report
- Line 28: The introduction should be more extended, especially in literature review.
- Line 40: Mention to the results of the former reports.
- Line 60: Change "CTAB methods" to "CTAB method".
- Line 61: Add "6000" to the platform name.
- Line 64: Refer to the filtering parameters.
- Line 63: Why you did not use genome referenced-based analysis? If no, please refer to the genome reference.
- Lines 145, 204, 205 and 206: Italic the species name.
- Line 207: Replace "Gnomic" with "Genomic".
- Line 218: Italic the "ycf1".
- Line 251: Add a dot "." after V. japonicum.
Author Response
Response to Reviewer 2 Comments
Point 1: Line 28: The introduction should be more extended, especially in literature review.
Response 1: In the introduction, we provide additional information and analysis on the relevant literature.
Point 2: Line 40: Mention to the results of the former reports.
Response 2: We mentioned the results and controversy in discussion portion.
Point 3: Line 60: Change "CTAB methods" to "CTAB method".
Response 3: We removed the letter.
Point 4: Line 61: Add "6000" to the platform name.
Response 4: We added 6000 to the platform.
Point 5: Refer to the filtering parameters.
Response 5: We added the content of data filtering in Section 2.2.
Point 6: Line 63: Why you did not use genome referenced-based analysis? If no, please refer to the genome reference.
Response 6: The annotated V. erosum (MN218778) chloroplast genome was used as a reference, and we added this sentence to Section 2.2.
Point 7: Lines 145, 204, 205 and 206: Italic the species name.
Response 7: The Latin names of all species name were individually italicized.
Point 8: Line 207: Replace "Gnomic" with "Genomic".
Response 8: We added letters to ensure the correct spelling of the words.
Point 9: Line 218: Italic the "ycf1".
Response 9: The ycf1 gene is italicized.
Point 10: Line 251: Add a dot "." after V. japonicum.
Response 10: A dot has been added at the specified location.
