The Complete Plastid Genome Sequences of the Belian (Eusideroxylon zwageri): Comparative Analysis and Phylogenetic Relationships with Other Magnoliids
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsThe current manuscript is interesting but there is some minor revision in the manuscript which should be revised before acceptance.
· This research entitled “The complete plastid genome sequences of the Belian (Eusider-oxylon zwageri): comparative analysis and phylogenetic relationships with other magnoliids” has good academic significance. The topic addressed has good scientific depth.
· The abstract line number 19 in our article rephrases the sentence and writes the complete reference.
· Abstract written in scientific and clear meaning.
· Introduction write should be related to your title, please Lauraceae, Eusideroxylon explain clearly, and write the significance of the study.
· Material and methods which are used in the research were clear and explanatory. A few References are missing and incorrect in this portion of the study, please check it.
· Sentence number 47 rephrase and write quadripartite structure.
· The phylogenetic tree should be writing the figure caption the left data shows the Ml tree and the second shows the Bi tree.
· Figure 6. Comparison of the boundary patterns of the large single-copy (LSC) region, small single- copy (SSC) region, and inverted repeat (IR) regions among the three Belian chloroplast genomes, please add some Belian genomes species related family.
· Spacing mistakes and spelling in paragraphs must be rectified.
· Results of the research work are well. If possible properly explain the table and figures caption.
· Discussion must be connected with results parts.
1. Umar Zeb, Azizullah Azizullah, Xiukang Wang, Sajid Fiaz, Hanif Khan. (2021). Comparative genome sequence and phylogenetic analysis of chloroplast for evolutionary relationship among Pinus species. Saudi Journal of Biological Sciences. https://doi.org/10.1371/ journal.
2. Umar Zeb, Azizullah Azizullah, Sajid fiaz. (2021). Novel insights into Pinus species plastids genome through phylogenetic relationships and repeat sequence analysis. PLOS ONE. https://doi.org/10.1371/ journal.pone.0262040
Please cite this paper and follow the abstract and conclusion of this article.
Kindly follow the instructions as mentioned in the Manuscript.
After a thorough evaluation of the manuscript. I recommend it fe improve English language
Author Response
Dear reviewer,
Please find our revised manuscript uploaded to MDPI website. We greatly appreciate your comments and for the opportunity to revise our manuscript. Overall, the manuscript has improved and we have made some changes. You can find two word files in our submitted folder, one is highlighted and the other is modified.
Kind regards.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsDear Authors,
I trust this email finds you well. I have had the pleasure of reviewing your manuscript titled "The complete plastid genome sequences of Belian (Eusideroxylon zwageri): comparative analysis and phylogenetic relationships with other magnoliids." I appreciate the valuable insights your study provides into the Belian chloroplast genome and its significance for taxonomic identification, phylogenetic studies, and the conservation of genetic resources.
However, I have some queries and suggestions that I believe will enhance the clarity and completeness of your manuscript. Kindly address these points in your revision:
Query 1:
In Figure 1, instead of a distribution map of the species, I suggest providing a map focusing solely on the sampling sites. Additionally, consider using different colors to indicate sampling sites from Ariati et al. (2023). Also, include plant species reference photos from your three accessions.
Query 2:
While you've discussed the importance, distribution, and conservation needs of the species, there is a lack of information about its unique characteristics. Despite being monotypic, consider mentioning the distinctive features of the species.
Query 3:
Provide details about the quality of Illumina Sequencing reads. Include information on trimming or quality control programs, the quantity of data obtained, how much data was used for the assembly, and its coverage. Clarify if the short-insert (500 bp) library is a single-end or paired-end library and mention the kit used for library preparation from Illumina.
Query 4:
Explain why there is a difference in the chloroplast genomes of Belian between MF939381 and (LAU00162 & LAU00163). Compare the results with the plant reference pictures to verify if it is the same species or a variety of Belian.
Query 5:
In the phylogenetic tree, observe that there is no difference in IR boundaries, and coding genes are the same for all three accessions of Belian. However, there is a difference in the plastid genome size (157,535 to 157,577 bp) and SSR repeats of Belian from different accessions. Explain this discrepancy.
Query 6:
Discuss the mutations observed in the Belian chloroplast genomes, particularly between Belian I and Belian III. Clarify if Belian I and III are the same species and justify the 143 nucleotide variations between them.
Query 7:
Specify whether Belian I is from your previous study or from the study of Ariati et al. (2023).
Query 8:
Provide information on the trimming/quality control program used, the total amount of data received from Illumina reads, the average length of pair-end reads, and the mean, median, and range for the depth of coverage of the plastomes.
Query 9:
Indicate which model of molecular evolution was used in your maximum likelihood ML Tree (e.g., Jukes-Cantor or Tamura-Nei).
Query 10:
Clarify the main aim of the present study, especially in comparing two accessions of Belian and their relation to Ariati et al., 2023. Clearly differentiate between Belian I, II, and III, and provide a detailed discussion on the comparison between them.
I appreciate your attention to these matters and look forward to reviewing the revised manuscript
Author Response
Dear reviewer,
Please find our revised manuscript uploaded to MDPI website. We greatly appreciate your comments and for the opportunity to revise our manuscript. Overall, the manuscript has improved and we have made some changes. You can find two word files in our submitted folder, one is highlighted and the other is modified.
Kind regards.
Author Response File: Author Response.pdf
Reviewer 3 Report
Comments and Suggestions for AuthorsThank you for the opportunity to review this fine work. Although I am not qualified to comment on the molecular technology, perhaps a little non-molecular input will help. A focal component of the effort is GeneBank acc. MF939351, which in Ariati et al. fell oddly into Myristicaceae, not Lauraceae as is traditional, and as the present authors have contended with extensive data. The odd outcome with MF939351 was of apparent marginal interest to Ariati et al. who suggested that the specimen was "probably misidentified," in need of verification. They by no means contended that Eusideroxylon belongs in Myristicaceae, instead, setting it aside as probable fluke not at the heart of their work. Although it is implicit in the paper under review (lines 75, 269) that MF939351 is consistent with Eusideroxylon, making misidentification unlikely, the present paper should address the suspected misidentification overtly. And should confirm reidentification of the herbarium voucher, preferably by a separate Lauraceae specialist. Or at the least,, the present authors should discuss the MF939351consistency with Eusideroxylon making direct reference to the suggestion by Ariati et al. My point is the important suggestion of misidentified materials is presently unacknowledged by the rebutting authors except by implicit indirect references in two sentences. Lines 389 and 390 strike me as a needlessly speculative yet accusing An outside reader could rightly or wrongly suspect a grudge.
For readers with taxonomic, forestry, or ecological orientations, more non-molecular context would help. Has anyone other than Ariati et al suggested Myristicaceae? (No?) Have taxonomists in recent history all placed Eusideroxylon in Lauraceae? (I think so). How does Eusideroxylon compare morphologically with the families in question? (Fits Lauraceae nicely I think) Are there relevant non-molecular studies? (Yes, such as Kimoto et al. 2006 Bot J. Linn. Soc. 150:187-201). Any work on wood anatomy? Floral structure? Etc. I would not suggest a massive non-molecular review, but at least a brief orientation to relevant context. As written, the "Lauraceae" vs. "Myristicaceae" questions stands starkly isolated. Hope these comments are useful. Looking forward to seeing the paper finalized.
Author Response
Dear reviewer,
Please find our revised manuscript uploaded to MDPI website. We greatly appreciate your comments and for the opportunity to revise our manuscript. Overall, the manuscript has improved and we have made some changes. You can find two word files in our submitted folder, one is highlighted and the other is modified.
Kind regards.
Author Response File: Author Response.pdf
Round 2
Reviewer 2 Report
Comments and Suggestions for AuthorsDear Authors,
It was a pleasure to read the revised manuscript entitled “Two plastid genome sequences of the Belian (Eusideroxylon zwageri): comparative analysis and phylogenetic relationships with other magnoliids”.
Thanks to all authors for considering my suggestions on this manuscript. I hope the authors have gone through all the comments and changes made to correct them in the revised manuscript. I am satisfied with the authors' responses.
Thank you
