Complete Chloroplast Genome Sequence of Rosa lucieae and Its Characteristics

Round 1

Reviewer 1 Report

The work "Complete Chloroplast Genome Sequence of Rosa lucieae and Its Characteristics" presented to me for review is of low value. A very similar work describing, among others, the Rosa lucieae chloroplast genome was published earlier in 2019 (Comparative Analysis of the Complete Chloroplast Genome Sequences of Three Closely Related East-Asian Wild Roses (Rosa sect. Synstylae; Rosaceae) - Genes 2019, 10, 23 ; doi: 10.3390 / genes10010023) and contains most of the analyzes described here.

Additionally, there are many errors and inaccuracies in the work itself, e.g .:

- Tab. 2 indicate 2 copies of ycf1 but in Fig. 1 there is only 1 copy, the same is described in line 220,

- in line 211 "licieae" must be replaced with "lucieae"

-in Fig. 4 there in no analyzed R. lucieae (156 504bp). Instead, there is another genome

of 156 555bp that is not presented in Tab. 1. In addition, in IRb there is ycf1 which is truncated form of original ycf1 presented in JSA border.

- in line 233 Rosa / Geum „sequences” should be replaced with "cp genome sequences" (the same in line 265)

- in Fig. 6 there is no analyzed line with accession no. OK938394 (the same in Fig. A1 and A2).

Discussion and conclusion sections rather poor.

Author Response

Dear reviewer：

It is a great honor that our article has been reviewed by you. According to your questions, we have replied.

Please see the attachment.

If there is anything wrong, please criticize and correct. We are looking forward to your review again.

Kind regards,
Weixiang Shen

Author Response File: Author Response.docx

Reviewer 2 Report

The sequencing, comparison, sliding window analysis and phylogenetic analysis of the Rosa lucieae cp genome were performed by Jeon and Kim (10.3390/genes10010023). What are the differences in your work?

13 chloroplast genomes were used to analyze the sliding window, 28 genomes were used for positive selection analysis and 27 genomes were used for phylogenetic selection.  It would be correct to take the same number of sequences.

Positive selection is considered when the dN/dS ratio is greater than 1. Table 3 is unclear.

Line 346-348 “The phylogenetic tree shows that R. lucieae 346 (MG727864) is closely related to R. maximowicziana, which is consistent with the research results of Zhao et al. [25] and Gao et al. [24].”  The sequence MG727864 was obtained in another work. The OK938394 cp genome sequenced by you does not fall into this clade. The sentence is confused. And perhaps requires a more detailed discussion.

It is necessary to discuss better the results on hypervariable regions, IR expansion and contraction, SSR types, etc. based on more recent studies of chloroplast genomes, not limited to the genus Rose or related species. This is necessary to show general biological patterns and differences.

Author Response

Dear reviewer：

It is a great honor that our article has been reviewed by you. According to your questions, we have replied.

Please see the attachment.

If there is anything wrong, please criticize and correct. We are looking forward to your review again.

Kind regards,
Weixiang Shen

Author Response File: Author Response.docx

Reviewer 3 Report

In the submitted manuscript the authors presented the complete chloroplast genome of Rosa lucieae and its analysis. This is not the first plastid genome, which has been sequenced for this species. In GenBank, there are at least three other sequences of complete chloroplast genome of Rosa lucieae: MN689791, MH355580, and MG727864. However, in the presented manuscript, the authors conducted more deep analysis of the plastid genome of Rosa lucieae and compared it with genomes of related Rosa species.

The study includes the following parts:

I.                For Rosa lucieae:

-          Rosa lucieae chloroplast genome assembly and gene annotation.

-          The base composition of 53 CDSs in the chloroplast genome of R. lucieae and the codon content and termination codons of 20 amino acids from 53 coding genes.

II.              For 13 chloroplast genomes of Rosa (including the genome of R. lucieae)

-          Repeat Sequence and SSR Analysis

-          Contraction and Expansion of IRs

-          Sliding window analyses and determine the nucleotide diversity (Pi) of 13 chloroplast genome sequences closely related to R. lucieae

III.            For 28 plastid genome sequences of Rosa (incl. R. lucieae)

-        Positive selection analysis

-        Phylogenetic analysis.

The most valuable results obtained in the presented article:

-        Identification of SSRs in Rosa plastid genome (may serve as genetic markers)

-        Identification of highly differentiated regions (may serve as genetic markers)

-        Genes under positive selection

-        Phylogenetic reconstruction that does not correspond to the traditional taxonomy of the studied group.

The study was conducted using appropriate modern methods. The results obtained improve our understanding of the structure and characteristics of the plastid genome in the Rosa group under study.

However, several points in the work need to be corrected and improved.

Major items:

1.   In the introduction, the authors should provide references to previous studies of the complete plastid genome of Rosa lucieae (Cui et al. (2020) doi: 10.1080/23802359.2019.1700198; Jeon & Kim (2019) doi:10.3390/genes10010023)

2.   Taking into account that this is not the first study of the plastid genome of R. lucieae, the authors should better formulate the goals of this study.

3.   The non-monophyletic pattern of Rosa luceae in phylogenetic reconstruction is not described in the results and is not discussed. I think, this should be added.

 

4.   Phylogenetic reconstruction that does not correspond to the traditional taxonomy of Rosa group under study is not discussed. 

Minor items:

1.     Please, check the correctness of the Latin names and the names of the authors of the taxa.

2.     Legends on the figures should be improved.

3.     Abbreviations should be explained either in the text or in the figure captions.

For details, see highlighted text and sticky notes in the pdf file.

Comments for author File: Comments.pdf

Author Response

Dear reviewer：

It is a great honor that our article has been reviewed by you. According to your questions, we have replied.

Please see the attachment.

If there is anything wrong, please criticize and correct. We are looking forward to your review again.

Kind regards,
Weixiang Shen

Author Response File: Author Response.docx

Round 2

Reviewer 2 Report

The authors have responded to the comments and the article can be accepted for publication.

Author Response

Dear reviewer:

Thank you very much for your time to review the manuscript. Your valuable opinions and suggestions are of great guiding significance to our current and future research.

Kind regards,

Weixiang Shen