Identifying Molecular Markers for Ficus erecta Thunb. Based on Complete Plastome Sequences of Korean Figs (Ficus L., Moraceae)

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The paper "Identifying Molecular Markers for the Medicinal Species Ficus erecta Based on Complete Plastome Sequences of Korean Figs (Ficus L. Moraceae)" investigates the plastome sequences of Korean fig species, focusing on developing molecular markers for Ficus erecta. Using next-generation sequencing and PCR techniques, the study characterizes complete plastomes of various fig varieties, identifies single nucleotide polymorphisms (SNPs), and develops specific molecular markers for F. erecta. While the study presents valuable insights into the plastome sequences of Korean figs and the development of molecular markers for F. erecta, it falls short in providing a comprehensive analysis of whole plastome-based molecular diagnostic characters. The phylogenetic analysis also requires further validation and clarity. The paper would benefit significantly from incorporating a broader molecular diagnostic approach and a more robust validation of the phylogenetic relationships it proposes.

 

Major issue:

The presented paper lacks any whole plastome-based molecular diagnostic characters analysis, instead focusing on target SNP for one species. I would encourage authors to perform some superbarcoding based analysis and estimate MDCs (molecular diagnostic characters for each taxon). It can be easily done using FASTAChar or other software.

 

Minor issues:

Paragraph “Phylogenetic relationships with related taxa”

Statement  All three analyses validated the monophyly of Moraceae tribes 8

(Moreae, Dorstenieae, Castilleae, and Ficeae)” can be validated by an analyzed dataset since tribes Castilleae and Moreae are represented by single specimens.

Statement “The phylogenetic trees further corroborate that F. erecta and F. erecta var. sieboldii, as well as F. pumila and F. sarmentosa var. thunbergii, are grouped within the same species.” have to be rewritten, analysis rather indicate that F. pumila and F. sarmentosa are paraphyletic. I wouldn't claim “the same species”.

 

Author Response

We really appreciate the time and effort that you have provided your valuable comments on this manuscript. Please find the detailed responses in attached files and the corresponding revisions/corrections highlighted/in track changes in the re-submitted files (in red colors). We have also requested the editor to send you the revised manuscript.

Best regards,

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

This study is one of very many annotating the chloroplast genomes of Korean figs: F. erecta, F. erecta var. sieboldii, F. sarmentosa var. nipponica, and F. sarmentosa var. thunbergii.

The work is done exactly like other similar articles and includes relevant problems.

 

Why do you need to study SSR loci in the chloroplast genome?

: "The plastome of F. erecta contains 96 SSRs 19 and 44 long repeats, predominantly located in non-coding regions." 

 

An SSR locus only makes sense for a chromosomal genome, and only if that marker is polymorphic. Second, poly-A,T,C,G are not SSR loci. Therefore, I recommend that everything about SSRs be removed from the article.

Authors need to bring originality to their research, not copy-paste identical papers. Annotation of genomes like chloroplasts, and mitochondria is not something important and required for publication. The value of a scientific paper is new and original. 

 

It is somehow briefly written here, without references to original articles:

49 "PCR-based molecular markers, including random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), microsatellites, and single nucleotide polymorphisms (SNPs), simplify genetic analysis by using primer pairs to specifically target and amplify DNA regions, thus eliminating the need for probe hybridisation [12]."

- Remove the reference to the article [12], this is not the right level and not the right authors to cite. Authors need to be very careful about the sources they cite. This is a good reason to Reject an article. Therefore, cite the original article to "RAPD", to "AFLP" and SNP. 

 

88 We downloaded 30 complete plastome sequences.

- provide the site where the "30 complete plastome sequences" were obtained. 

- Delete the section completely and the results: SSR and Long Repeat Sequence Analysis

 

Table 2. Features of the LSC, SSC, and IR of the plastomes in this study.

- remove the column GenBank accession No.

Author Response

We really appreciate the time and effort that you have provided your valuable comments on this manuscript. Please find the detailed responses in attached files and the corresponding revisions/corrections highlighted/in track changes in the re-submitted files (in blue colors). We have also requested the editor to send you the revised manuscript.

Best regards,

Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

Comments and Suggestions for Authors

The authors have made some corrections based on my comments. But to give a reasoned justification of such work, was not received. The authors also have also left the SSR analysis in the paper, as in similar papers like this one. 

I wanted to hear from the authors why similar papers are done that are exactly similar as twins. Referring to the articles the authors used to prepare their paper is not an argument.  

For species identification, this analysis is completely unnecessary and will not be used. The least perspective is the use of probable conditional SSR loci in the plastid genome. Let the authors show where and when such analysis was performed as a professional service. 

Author Response

Thank you once again for the time and effort you have invested in providing valuable feedback on this manuscript. Please find the detailed responses below and the corresponding revisions/corrections highlighted/in track changes in the re-submitted files. Regarding your comments, we have removed all parts of SSRs and long repeats in the manuscript and included more details with green color words.

Author Response File: Author Response.pdf