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It is evident that you have made a significant effort to improve the language of the manuscript. Although there are still minor issues with the English, these no longer detract significantly from the reader's understanding of the project. This version was reviewed by myself rather than going out to reviewers again, as all issues around the science had previously been addressed. This manuscript is now ready for publication.
[# PeerJ Staff Note - this decision was reviewed and approved by Paula Soares, a PeerJ Section Editor covering this Section #]
**PeerJ Staff Note:** Although the Academic and Section Editors are happy to accept your article as being scientifically sound, a final check of the manuscript shows that it would benefit from further English editing. Therefore, please identify necessary edits and address these while in proof stage.
While you have made changes related to the previous review, the language and standard of written English of the manuscript remain an issue. I have added some suggestions for you; unfortunately our system won't allow me to attach the Word file with track changes, so I have attached a pdf. However I would suggest having a fluent English speaker also review the manuscript; if there is no-one you know that can do this for you, there are academic services that will review manuscripts.
**Language Note:** The Academic Editor has identified that the English language must be improved. PeerJ can provide language editing services - please contact us at copyediting@peerj.com for pricing (be sure to provide your manuscript number and title). Alternatively, you should make your own arrangements to improve the language quality and provide details in your response letter. – PeerJ Staff
Both reviewers have made largely the same comments, often around language, proofreading, and clarity of the manuscript. All of these comments will improve the quality of the manuscript, as will adding information about the limitations and impact of the study, as suggested by reviewer 1. I agree with reviewer 2 that if you have a colleague who is a fluent English speaker that can proofread this for you, that would help improve the clarity of the manuscript.
[# PeerJ Staff Note: Please ensure that all review and editorial comments are addressed in a response letter and any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate. #]
[# PeerJ Staff Note: The Academic Editor has identified that the English language must be improved. PeerJ can provide language editing services - please contact us at copyediting@peerj.com for pricing (be sure to provide your manuscript number and title) #]
The article effectively provides a comprehensive background on Gardenia jasminoides, highlighting its significance in genetic analysis through whole-genome resequencing. The research objectives of the study are also clearly outlined.
Some comments on basic reporting of the paper:
1) The use of certain technical terms may pose a challenge for non-experts. To enhance clarity, it is recommended to provide the full form of acronyms wherever possible. For example, acronyms FCVS, FDR
2) The article contains several typos and grammatical errors. It is crucial to thoroughly proofread the text and correct these issues to enhance clarity and maintain professionalism. For example, Line 146 and Line 149 require attention, and the Q30 value is missing in Line 149. Additionally, Lines 157 to 161 need revision for clarity.
3) There are inconsistencies between the numbers mentioned in the text and the actual data presented in the study. It is essential to ensure that the numbers mentioned align with the data provided. For instance, Line 148-149 should match the Q20 and Q30 values in Table 1. Line 152 should also correspond to the 1x, 5x, and 10% values in Table S1.
4) Some sections contain duplicate information, where similar content is repeated in different sentences. It is advisable to revise and condense such instances to avoid unnecessary repetition. For example, Lines 157-161 and Results Section 3.4 and 3.5 are the same.
5) Figures 3a, 3b, 4a, and 4b would benefit from better quality images. Ensuring clear and high-resolution images will enhance the readers' understanding and interpretation of the data.
6) Some result claims lack proper references to the corresponding data in figures and tables. It is important to provide appropriate citations for the data presented.
No comments
The article provides an overview on study's findings on the genetic diversity of Gardenia jasminoides, including SNP, InDel, CNV, and SV mutations. It also explores the variation genes related to medicinal substances in gardenia fruit. However, there are several areas where improvements can be made to enhance clarity and readability.
Some comments:
1) The results & discussion sections contains long and complex sentences, which can make it difficult for readers to follow the information. Breaking down these sentences into shorter, more concise statements would improve readability and comprehension.
2) Please highlight some of the limitations/challenges of the study & how it might have impacted the results.
3) It would be valuable to highlight the potential impact of this study on genetic breeding efforts in the times to come.
4) The conclusion is brief and does not effectively summarize the key findings and implications of the study. It would be beneficial to provide a more comprehensive conclusion that highlights the main results and their significance in the context of the broader field of research.
This manuscript provides an extensive look into the genomic diversity between wild and cultivated varieties of the medicinal plant Gardenia jasminoides. One wild and one cultivated sample were sequenced on an Illumina HiSeq and the sequencing reads were aligned to a G. jasminoides reference genome. Single-nucleotide polymorphisms, indels and both structural and copy number variation were investigated between each sample and the reference genome; any genes where this was identified were compared to the KEGG, COG and GO databases for functional annotations.
The introduction is thorough and provides good context to the research. Below is a list of comments to address:
• English language should be improved so the article is clearer to an international audience. I recommended asking a colleague who is proficient in English to proof-read the manuscript.
• Line 43 – ‘Gardenia’ should be italicised.
• Line 73 – when describing abbreviations, it is not necessary to repeat the phrase within the parentheses.
• Line 77 – please explain what ‘FCVS’ means.
• Line 85/86 – please add some more detail describing how the functional genes evolved.
• Line 89/90 – please add further detail to contradictions in the results of previous work.
• Line 92/93 – you describe in the abstract and methods aligning one wild type and one cultivated variety, but here two wild type genomes are mentioned. Please clarify this.
• Figure one can be removed as it only contains three numbers, this can easily be reported in the main text.
• Figure two legend needs to be more detailed and proof-read, as currently is not very clear.
• Figure five should be moved to the supplementary material.
• Table one and two – ‘Sample’ is spelled incorrectly, and underscores need to be removed from column headers.
• Table two legend refers to ‘reference genomes’ although only one reference genome has been used.
• Supplementary figure two – axis text needs to be increased in size.
• Supplementary figure three – different colours need to be used for the two samples.
• Supplementary table one - ‘Sample’ is spelled incorrectly, and underscores need to be removed from column headers.
• Supplementary tables – legends need to be more detailed. Where abbreviations are used for column headers make sure the full word is described underneath the table.
This is an original manuscript within the scope of the journal. The authors clearly describe the problem and how the samples they have sequenced, and analysis performed works to close that knowledge gap. There are no major issues but here is a list of minor comments which need to be addressed:
• Line 102/103 – please described how sample FD is an improved variety as this is not obvious from the text.
• Line 110-112 – please clarify what ‘> 10% paired-end reads with bases’ refers to. Please clarify what ‘sequencing connectors’ refers to, does this mean adapter sequences?
• Please include version numbers for all software used, such as for GATK and Manta.
• Line 120/121 – it is clear why SNPs within 5 bp of an indel were removed but please clarify what within 10 bp of the adjacent Indel refers to.
• ‘Clean Reads’ does not need to be capitalised.
Validity of the findings:
The conclusion is concise and clearly states the benefits of the research. The authors highlight the role their work plays in future gene-based breeding of G. jasminoides. Below is a list of minor comments for the results and discussion.
• Line 146 – the size of the reference genome is described as 635.6 Mb whereas the assembly on NCBI is 534.9 Mb.
• Line 148 – 39 Mb should be changed to 39 million clean reads.
• Line 148/149 – Q30 is not mentioned.
• Line 158 – please use commas to make the numbers more easily readable.
• Line 171/172 – use ‘Indels’ instead of ‘insertions and deletions’ to make ‘respectively’ less ambiguous.
• Line 173 – please include numbers or statistics instead or just referring to ‘more than’.
• Line 197 – please clarify what ‘variation genes’ refers to.
• Line 224 – please clarify what ‘mutant gene’ refers to. Synonymous or non-synonymous or indels?
• Line 236 – ‘YP1 annotated 58 genes’, please clarify whether this refers to mutant genes.
• Section 3.5 appears largely identical to 3.4. Please check this.
• Line 281 – ‘clean datas’ should be changed to reads.
• Line 281 – Two wild type species are referred to when only one was sequenced.
• Line 282 – average depth was described as 10x in the results, please clarify.
• Line 302 – please include what Ti/Tv refers to as this is the first time it
No comment
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