Comparative Analysis of Codon Usage Patterns in Chloroplast Genomes of Cherries
Round 1
Reviewer 1 Report
This manuscript analyzed the condon composition of 58 shared CDSs extracted from 36 chloroplast genomes of subg. Cerasus species. The analyses on Neutrality plot, ENC plot and PR2 plot based on GC content and ENC value show that the codon usage bias is mainly caused by natural selection. The manuscript is well written and easy to follow, but there are a few areas that can be improved as listed below:
1. in the method section, all the methods were very briefly touched without explaining biological reasons behind them. Some numerical metrics are lack of details. For example, how RSCU, ENC, CAI are calculated? why calculating these values? what the values indicate in terms of codon usage and natural selection.
2. diagrams are not very informative and not legible. For example, in Figure 1, there is no indication on what x and y axes mean. Figure 3 is not legible. Resolution needs to be improved. It is not clear what the authors are trying to draw as conclusion from Figures 2 and 3, as the distribution of each genome in Figure 2 and 3 look highly similar. The message from Figure 4 is not clearly explained as well. It sounds like that it visualizes principle components, but lack of information in the text.
3. The clustering analysis differs from the phylogenetic tree significantly. What is the possible reason behind it? How is it related to the topic of this work?
There are some minor edits that are annotated on the pdf file as attached.
Comments for author File: 
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Author Response
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Author Response File: 
Author Response.docx
Reviewer 2 Report
The manuscript is interesting to understand the plant evolution considering the chlorpolast condon usagen. They chosen the cherries to be their mode. The presented the different codon presence and usage, and the authors compared the different codon usage.
The manuscript need major changes
1) abstract - it needs to be improved - there ae many ideias and it is difficulto to understand the focus of the manuscript
2) Introduction - it needs to be improved - it is difficult to understand why the focus is cherries for clhoroplast used, it is missing information and maybe the order the paragraphs may be changed
3) Methods, all the tools used are excellent to their aim, but they may be describe some items better
4) Results - it is ok, but figure legends may be developed, to help the reader understand the figures, explain X and Y aix, what colors represents. Figure 3 needs to improve it is difficult to analyze, figure 7 and 8 may be put together as (a) and (b)
5) Discussion - need to be improved, the results need to be deeply discussed and which are the possible implications, whats the reason for this research, and the next steps. It is missing something.
Author Response
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Author Response File: Author Response.docx
Reviewer 3 Report
The relative abundance of codon use is frequently described in the analysis of genomes and provides valuable phylogenetics and functional information. The comparative analysis of codon usage in 36 species of Prunus subg. Cerasus must be acknowledged but has limited interest in a broad context. In addition, the manuscript has formal and scientific deficiencies that further decrease its interest. Authors should carefully correct the English of the manuscript, avoid rhetoric, and, about all, provide experimental and informatic details that are essential in scientific publications.
1. The manuscript should detail how DNA was extracted from 12 subgroup Cerasus species, and how it was processed and sequenced.
2. Table 1 and all figures require legends, and details of the of the source of data and informatic approaches.
3. The absence of ndhB gene in P. conadenia is intriguing and need additional explanations. What about other ndh genes?
4. Comparison with codon usage in chloroplast DNA of distant plants is required to evaluate the relevance of the manuscript. What about the divergence time among Prunus species?
5. A relative high number of primary transcripts of chloroplast encoded genes are C to U edited. Authors should consider possible bias due to RNA editing and of repeated genes.
Author Response
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Author Response File: Author Response.docx
Round 2
Reviewer 1 Report
The authors have addressed all of my comments. I'm happy with the revisions.
Figures 2, 3, 4 are still not legible. Subfigures are too small. Resolutions in these figures need to be improved before publishing.
Author Response
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Author Response File: Author Response.docx
Reviewer 2 Report
The authors mande changes that improve the manuscript. But in my view others modification would be important to be made.
1) Introduction - some paragraphs may be changes de order. I would not begin the introduction with "Besides biological methionine ...."
2) Legends were not improved.
for example line 175 Figure 1. The kernel density curve of GC1, GC2 and GC3. What else we need to see, axis X, axis Y, it needs to describe more for all figure legends
3) English revision for example line 60 "Currently, however, little is known"
line 289 "We also learned that in addition ...."
Author Response
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Author Response File: Author Response.docx
Reviewer 3 Report
The revised version has added required data and corrections. It, essentially, overcomes my criticism to the former one.
Author Response
We appreciate your comments very much.
