Complete Chloroplast Genome Sequence of Fortunella venosa (Champ. ex Benth.) C.C.Huang (Rutaceae): Comparative Analysis, Phylogenetic Relationships, and Robust Support for Its Status as an Independent Species

Round 1

Reviewer 1 Report

In a peer-reviewed article, the authors present the results of time-consuming painstaking work. Undoubtedly, the work deserves respect, but the manuscript cannot be published in its present form. Major changes to the manuscript are needed. It is required to write a full-fledged part of the "Discussion".

In addition, I have the following comments:

Lines 2-4. It seems to me that the title of the article is formulated poorly. I would recommend changing it. For example, «The use of the first sequenced chloroplast genome of Fortunella venosa (Champ. ex Benth.) C.C.Huang as a tool for Comparative Analysis and Phylogenetic Relationships study in Rutaceae». If the authors insist on their version of the name, then the abbreviations «(Champ. ex Benth.) C.C.Huang» should be added.

Lines 17-18. The sentence “But there are only few reports on the chloroplast (cp) genomes of Fortunella, which limits research on its phylogenomics.” should be deleted or reformulated. Phylogenomics is not limited to chloroplast genomes only. Nuclear genomes are more important. If nuclear genomes are successfully studied, the paucity of reports on chloroplast genomes will not limit the success of phylogenomics.

Lines 32-33. The sentence “These findings will help to make breakthroughs in genomics, genetic engineering and phylogenetic research of this important species.” should be deleted or reformulated. I think that the significance of this work is greatly exaggerated. Chloroplast genomes have been sequenced for a long time and regularly. This work is routine. I have not seen in the article major discoveries that will lead to a breakthrough in the described fields of knowledge.

Part "Results and discussion". This part of the manuscript is poor for discussion. I recommend that authors change the title of this part to "Results" and write a full "Discussion" part.

Lines 205-207. It is necessary to add a few independent links to confirm this data.

Lines 207-208. The sentence “The low GC content and high AT content in the cp genome of F. venosa suggested that its sequence is variable.” should be deleted or reformulated. I have not found evidence of this statement in the manuscript. In general, conclusions based on GC content require a lot of additional research work to confirm. If there is no other evidence, then these conclusions sound like low-grade speculation.

Author Response

Please see the attachment

Author Response File: Author Response.docx

Reviewer 2 Report

Dear authors,   The paper Complete Chloroplast Genome Sequence of Fortunella venosa (Rutaceae): Comparative Analysis, Phylogenetic Relationships and Robust Support for Its Status of Independent Species submitted by Wang et al. presents the complete sequence and phylogenetic analysis of the chloroplast of Fortunella venosa. Overall, the presented rationale, methodology and conclusions are solid and scientifically interesting.   I have only a couple of small comments, which needs to be addressed.   

L58: Please replace “cp” with chloroplast for readability

L176: Why did the authors chose Melia azedarach as an outgroup?

L192: Please state the read length, single-end, paired-end?

L207: Please add a reference for this hypothesis

L217-219: A summary/description sentence or two would be helpful, rather than referring only to the tables. Like what are the four categories? 

L250: Figure 2: What are F, R, P and C. There’s no explanation in the legend

L275 & L277: Please explain Mono, di, tri, tetra, penta and hexa in the figure legends. “Mono” is the only one that starts with a capital letter. Please be consistent.

L330: Differences in IR regions might be just assembly errors?

L340: Please explain Pi value? 

L414: Please explain the number on the branches?

Author Response

Please see the attachment

Author Response File: Author Response.docx

Round 2

Reviewer 1 Report

Dear Authors,

Thank you for your attention to my comments and changes to the manuscript. I see that the manuscript is much better. I am quite satisfied with your answers.

All the best