Characterization and Phylogenetic Analyses of the Complete Chloroplast Genome Sequence in Arachis Species

Round 1

Reviewer 1 Report

The manuscript presents interesting and valuable results on the phylogenetic relationships and genomic information of wild and cultivated groundnut chloroplasts. In this study, 14 complete Arachis chloroplast genomes were sequenced and analysed alongside 110 chloroplast sequences retrieved from the NCBI databases. While a thorough literature review of chloroplast genome sequencing in Arachis and other species has been conducted, much of the information has been presented without thorough analysis, limiting the depth of some research findings. Therefore, considerable effort is needed to review and supplement the discussion of the results. It is crucial to discuss the two groups highlighted in the phylogenetic tree.

NA

Author Response

Dear Editor and Reviewers:

Thank you for your letter and for the reviewers’ comments concerning our manuscript “Characterization and Phylogenetic Analyses of the Complete Chloroplast Genome Sequence in Arachis Species” Based on these comments and suggestions, we have made careful modification on the original manuscript. All changes made to the text are in red so that they may be easily identified and the responds to the reviewer’s comments are as flowing:

The manuscript presents interesting and valuable results on the phylogenetic relationships and genomic information of wild and cultivated groundnut chloroplasts. In this study, 14 complete Arachis chloroplast genomes were sequenced and analysed alongside 110 chloroplast sequences retrieved from the NCBI databases. While a thorough literature review of chloroplast genome sequencing in Arachis and other species has been conducted, much of the information has been presented without thorough analysis, limiting the depth of some research findings. Therefore, considerable effort is needed to review and supplement the discussion of the results. It is crucial to discuss the two groups highlighted in the phylogenetic tree.

Response: We have revised and supplemented the discussion of the results in Discussion part.

Reviewer 2 Report

The manuscript gives valuable information about Arachis species chloroplast genome, although several previously published papers discussed similar topics as in this research. It would be very valuable if authors could define better and accentuate novelty of this research. The novelty and originality of the research is not evident.

The English language should be significantly improved. Improved language will contribute notably in understanding and following the research done.

The introduction part is good formulated except its last paragraph. Could you, please, go through it and rewrite in a manner to be more concise?

Material and methods section lacks crucial information about laboratory analyses that were done in order to get bioinformatics data. The Next Generation Sequencing procedure is not explained sufficiently well. There are only data about library construction but nothing about following steps is the procedure. I am suggesting adding more detailed description of this part, so the results could be reproducible based on the details given in the methods section.

Results section should be written more concise, my impression is that there are too much numbering, maybe the authors could present more results in a form of table, and then to highlight the  most important or somehow interesting ones in the text. The table titles should be better formulated and also all the parameters in table Header should be properly explained below the table.

Discussion should be expanded with more information from other similar research on the same and different species. Moreover, discussion should be written more concise.

Almost 50% of the references are older than 20 years and according to journal proposition, majority of them should be most recently written. Could you please, improve this section. Also, technical corrections according to journal propositions are needed, too.

The manuscript gives valuable information about Arachis species chloroplast genome, although several previously published papers discussed similar topics as in this research. It would be very valuable if authors could define better and accentuate novelty of this research. The novelty and originality of the research is not evident.

The English language should be significantly improved. Improved language will contribute notably in understanding and following the research done.

The introduction part is good formulated except its last paragraph. Could you, please, go through it and rewrite in a manner to be more concise?

Material and methods section lacks crucial information about laboratory analyses that were done in order to get bioinformatics data. The Next Generation Sequencing procedure is not explained sufficiently well. There are only data about library construction but nothing about following steps is the procedure. I am suggesting adding more detailed description of this part, so the results could be reproducible based on the details given in the methods section.

Results section should be written more concise, my impression is that there are too much numbering, maybe the authors could present more results in a form of table, and then to highlight the  most important or somehow interesting ones in the text. The table titles should be better formulated and also all the parameters in table Header should be properly explained below the table.

Discussion should be expanded with more information from other similar research on the same and different species. Moreover, discussion should be written more concise.

Almost 50% of the references are older than 20 years and according to journal proposition, majority of them should be most recently written. Could you please, improve this section. Also, technical corrections according to journal propositions are needed, too.

The English should be significantly improved.

Author Response

Dear Editor and Reviewers:

Thank you for your letter and for the reviewers’ comments concerning our manuscript “Characterization and Phylogenetic Analyses of the Complete Chloroplast Genome Sequence in Arachis Species” Based on these comments and suggestions, we have made careful modification on the original manuscript. All changes made to the text are in red so that they may be easily identified and the responds to the reviewer’s comments are as flowing:

1.The manuscript gives valuable information about Arachis species chloroplast genome, although several previously published papers discussed similar topics as in this research. It would be very valuable if authors could define better and accentuate novelty of this research. The novelty and originality of the research is not evident.

Response: In this study, 14 complete Arachis chloroplast genomes were sequenced and analysed together with 110 chloroplast sequences retrieved from the NCBI databases, representing by far the largest number of chloroplast sequences from Arachis species in this study. We have revised and supplemented the discussion of the results in the Discussion section.

2.The English language should be significantly improved. Improved language will contribute notably in understanding and following the research done.

Response: We've improved on the language.

3.The introduction part is good formulated except its last paragraph. Could you, please, go through it and rewrite in a manner to be more concise?

Response: We have rewrite accordingly with last paragraph P2:L64-79

4.Material and methods section lacks crucial information about laboratory analyses that were done in order to get bioinformatics data. The Next Generation Sequencing procedure is not explained sufficiently well. There are only data about library construction but nothing about following steps is the procedure. I am suggesting adding more detailed description of this part, so the results could be reproducible based on the details given in the methods section.

Response: We have added accordingly in Material and methods section P11 :L272-278

5.Results section should be written more concise, my impression is that there are too much numbering, maybe the authors could present more results in a form of table, and then to highlight the most important or somehow interesting ones in the text. The table titles should be better formulated and also all the parameters in table Header should be properly explained below the table.

Response: We have revised accordingly, especially in “Phylogenetic Analysis” P4 :L101-116.

6.Discussion should be expanded with more information from other similar research on the same and different species. Moreover, discussion should be written more concise.

Almost 50% of the references are older than 20 years and according to journal proposition, majority of them should be most recently written. Could you please, improve this section. Also, technical corrections according to journal propositions are needed, too.

Response: We have revised accordingly, P9-10.

Reviewer 3 Report

Please find attached my comments.

Comments for author File: Comments.pdf

Minor editing of English language is required.

Author Response

Dear Editor and Reviewers:

Thank you for your letter and for the reviewers’ comments concerning our manuscript “Characterization and Phylogenetic Analyses of the Complete Chloroplast Genome Sequence in Arachis Species” Based on these comments and suggestions, we have made careful modification on the original manuscript. All changes made to the text are in red so that they may be easily identified and the responds to the reviewer’s comments are as flowing:

• It will be more informative to include a list of Arachis species with published chloroplast genomes used for phylogenetic cluster analysis (to be included as a supplementary file, or in the materials and methods section; authors are free to choose).

Response: We have supplemented all sequence data of Arachis species with published chloroplast genomes in S-file

• Kindly furnish a high-resolution image for Figure 1, as the legend accompanying it is not clear.

Response: We have revised high-resolution image for Figure 1 accordingly

• Consider appending a table subsequent to Figure 1, detailing the functions of genes identified from the chloroplast genome of Arachis species (with gene category, group, and functions, also, annotate genes containing introns and duplicated genes).

Response: gene category group, and functions was list in Table 3, duplicated genes was list in Table3 and S-Table3  

• “Table 2. Basic characteristics of the 14 Arachis chloroplast genomes that have been acquired”, Table 2, is not completed as several important information are missing, authors must consider adding for each species the nucleotide composition of the whole genome, Large Single-Copy region (LSC), Small Single-Copy region (SSC), Inverted Repeat region (IR), tRNA, rRNA, Intron, Intergenic space.

Response: We have added accordingly in Table 2.

• Consider writing all scientific names in Italics.

Response: We have added accordingly

• Authors must expand on the limitation of the current study and add perspectives, and future research directions to their conclusion section. The paper in its overall is good, implementing the requested changes will enhance the suitability of this work to the journal, and enhance its chances to be accepted.

Response: The genus Arachis consists of 81 species with a wide variety of genome types, including AA, BB, AABB, CC, DD, EE, EEXX, FF, HH, KK, PR, RR1, RR2, TT and TTEE. Since not all Arachis genome types were included in this study, it is limited to understanding the origin and evolution of cultivated peanuts. Future work should attempt to collect germplasm resources of a variety of genome types from different geographic regions to provide a better understanding of the taxonomic status of the different Arachis species and the evolutionary relationships between them.

We have revised and supplemented the discussion of the results in Discussion part.

Round 2

Reviewer 2 Report

The authors adopted majority of suggestions and the manuscript is now more concise and comprise valuable information for scientific community. Additional suggestions are following:

Introduction

Lines 70 -73: too much chloroplast genome resources have been expanded and the evolutionary relationships provided rich genetic information for the improvement of peanut and also help us to better 72 understand the origin relationships between wild and cultivated species.

The stated sentence is still not clear, it should be improved, English should be corrected.

Results

Lines 101 – 104 A total of 110 complete chloroplast genomes in Arachis from 19 different varieties were used to construct a phylogenetic tree (14 from present study and 96 from NCBI) using the maximum likelihood method (Fig. 2; Table S4), which was divided into two groups (Group I and Group II) containing 39 and 71 chloroplast genomes of Arachis were included.

This sentence should be also improved, English should be corrected. The correction is suggested.

Lines 105-106 Group I contained cultivated species with AABB and A. duranensis species with 105 AA are the two predominant genome types.

The correction is suggested (marked with red color).

I suggested that all the parameters in table Headers should be properly explained below the table, but I can not find the explanation of the LSC (bp), SSC (bp), IR (bp) for Table 2. Similar, for Table3, what are M1a vs. M2a, for example, I could not find the explanation anywhere in the text. Please, check all the tables once again and add needed information.

Comments for author File: Comments.pdf

English could be improved

Author Response

Dear Editor and Reviewers:

Thank you for your letter and for the reviewers’ comments concerning our manuscript “Characterization and Phylogenetic Analyses of the Complete Chloroplast Genome Sequence in Arachis Species” Based on these comments and suggestions, we have made careful modification on the original manuscript. All changes made to the text are in green so that they may be easily identified and the responds to the reviewer’s comments are as flowing:

Introduction

Lines 70 -73: too much chloroplast genome resources have been expanded and the evolutionary relationships provided rich genetic information for the improvement of peanut and also help us to better understand the origin relationships between wild and cultivated species. The stated sentence is still not clear, it should be improved, English should be corrected. 

Response: We have revised accordingly as flowing:

The reported chloroplast genome offered a wealth of genetic information for the improvement of peanut and also contributed to a better understanding of the evolutionary relationships between wild and cultivated plants.

Results

Lines 101 – 104 A total of 110 complete chloroplast genomes in Arachis from 19 different varieties were used to construct a phylogenetic tree (14 from present study and 96 from NCBI) using the maximum likelihood method (Fig. 2; Table S4), which was divided into two groups (Group I and Group II) containing 39 and 71 chloroplast genomes of Arachis were included. This sentence should be also improved, English should be corrected. The correction is suggested.

 Response: We have revised accordingly as flowing:

A total of 110 complete chloroplast genomes from 19 different Arachis varieties were utilized to construct a phylogenetic tree using the maximum likelihood method (Fig. 2; Table S4). The phylogenetic tree comprised 14 genomes obtained in this study and an additional 96 genomes obtained from NCBI. The resulting phylogenetic tree showed two major groups, Group I and Group II, which encompassed a total of 39 and 71 Arachis chloroplast genomes, respectively.

Lines 105-106 Group I contained cultivated species with AABB and A. duranensis species with 105 AA are the two predominant genome types.  The correction is suggested (marked with red color). I suggested that all the parameters in table Headers should be properly explained below the table, but I can not find the explanation of the LSC (bp), SSC (bp), IR (bp) for Table 2. Similar, for Table3, what are M1a vs. M2a, for example, I could not find the explanation anywhere in the text. Please, check all the tables once again and add needed information.

Response: Lines 105-106 We have revised accordingly: The cultivated peanuts with genome type of AABB and the species with genome type of AA (A. duranensis) are mainly distributed in Group I;

We have written the explanation of the LSC (bp), SSC (bp), IR (bp) for Table 2 in Discussion part Line180-185;

For Table3, M1a vs. M2a means M1 and M2 amino acid sequence comparison, we have unified format as M1 vs. M2.