Employing Genome-Wide SNP Discovery to Characterize the Genetic Diversity in Cinnamomum camphora Using Genotyping by Sequencing
Round 1
Reviewer 1 Report
The manuscript by Gong et al,. is on the application of the GBS method to genotype 171 accessions of Cinnamomum camphora, identify robust dataset of SNPs to be used for population structure analysis and investigation on genetic variation.
The design of the study is simple but appropriate. The question posed by the authors is clear and the methods that have been used are adequate. The manuscript is well written although I found the use of punctuation a bit arbitrary. I suggest some compulsory revisions to improve the overall quality of the manuscript.
Major:
To respect the principles of open science and data FAIRability, authors MUST submit the reads they got to a public repository (e.g. SRA). In addition, they MUST make the raw vcf file available. These are two necessary conditions for me to express a favorable opinion on publication.
Is not clear to me which tool was used for SNP calling. Samtools or Stacks? There is some confusion about this point.
How did you get the reference genome? which tool was used? what parameters?
Minor:
The use of “STRUCTURE” is misleading. I suggest to replace it with “population structure analysis” throughout the text. STRUCTURE is a software!
I would replace “clean data” with “high quality data” throughout the text. “Clean” sounds very conversational.
Line 48: Please, replace “Today” with “Nowadays” or “At present”.
Line 48: Please, replace “fragmented” with “scattered”.
Lines 51-52: genetic variation is a material??? Please, rephrase.
Line 76: Please, remove “next generation sequencing” inside the round brackets.
Lines 91-92: Please, remove “of C. camphora”.
Lines 144-145: PLINK is not a population structure analysis tool. Please, correct it.
Figure 2: Please, include bootstrap supporting values in the tree.
You analysed k values from 2 to 4. I would like to know the statistic that indicates which is the best value of K that is the number of subpopulations that make up the total population. You missed this info.
I suggest to include results from Treemix (https://bitbucket.org/nygcresearch/treemix/wiki/Home) to estimate the historical relationships among populations.
Your interpretation of FST values is quite strange. According to Wright 1978:
FST= 0.05 to 0.15 means “moderate differentiation”
FST = 0.15 to 0.25 means “great genetic differentiation”
FST > 0.25 means “ very great genetic differentiation”
Please, justify the discrepancy of interpretation with respect to the general rule.
Author Response
Dear Reviewer,
Thank you very much for your comments and suggestions.
As suggested, we have revised the manuscript according to the comments and suggestions of the reviewers and editors and responded, point by point, to the comments listed below.
Please let me know if you have any question!
With kindest regards,
Yours Sincerely
Yongda Zhong
Author Response File: 
Author Response.docx
Reviewer 2 Report
The study by Gong et al. (Employing Genome-wide SNP Discovery to Characterize the Genetic Diversity in Cinnamomum camphora Using Genotyping by Sequencing) reports the investigation of genetic diversity pattern in Cinnamomum camphora by employing genotyping by SNP. For this, they collected a total of 171 samples of C. camphora from 39 natural populations from its whole range of distribution in China and one Japanese population. This study provided improved understanding of the genetic diversity and genetic structure of C. camphora in East Asia.
In general the manuscript is well-written and provides valuable information to this research field. I recommend the publication of the manuscript after some minor issues given below are addressed.
Please reconsider and fix the last sentence of the Abstract.
Line 47-50 please fix the species name.
Some statements are too long. Please shorten or divide them. It is hard to follow.
Line 49-51 Please rewrite this part.
I noticed many grammatical errors. Please reconsider all manuscript.
Author Response
Dear Reviewer,
Thank you very much for your comments and suggestions.
As suggested, we have revised the manuscript according to the comments and suggestions of the reviewers and editors and responded, point by point, to the comments listed below.
Please let me know if you have any question!
With kindest regards,
Yours Sincerely
Yongda Zhong
Author Response File: Author Response.docx
Reviewer 3 Report
The studies are concerned with Cinnamomum camphora, which is a slightly threatened species due to its high importance as a source of spice, timber, and gardening, and has high economic, ornamental, and ecological value. C. camphora is mainly distributed in subtropical China and in central and southern Japan.
The paper presents good background literature research, followed by a carefully elaborated and performed methodological design. It is worth mentioning the innovative/novel character of the study there up to now are only a few reports on the genetic diversity and population structure of C.
camphora. The utilisation of the simple sequence repeat (SSR) primers to study the genetic diversity and genetic differentiation of woody plants are referenced last 15th years due to the problem of recognition of complicated genome of plant material.
Nevertheless, the authors used very widely available genetic tools to characterize the genetic diversity in Cinnamomum camphora as well as the current and historical references.
It is very important due to the fact that the genome of C. camphora has not been genotyped yet, and the genetic diversity and genetic structure of the C. camphora population are still unclear. But, current data of authors on the basis of their research enables the elaboration of the preservation strategy of the species.
The section Materials and Methods were presented very clear to enable other scientists to follow the results and continue recognition of other genetic doubts. It is worth noticing that the authors wanted to care about the purity and integrity of the DNA quality for further analysis.
At the species level, the average values of Ho and He of C. camphora were 0.365 and 0.352, respectively (Table 2). The analysis of genetic diversity in each region showed that the population from Japan had the highest level of genetic heterozygosity (Ho = 0.504, He= 0.442), followed by Western China (Ho = 0.333, He = 0.333) and Central China (Ho = 0.322, He = 0.327), and the genetic diversity in eastern China was the lowest (Ho = 0.302, He = 0.306). As a scientist, I wonder why these genetic parameters are lower than similar ones in Japan? Maybe (?) due to geographical trend selection (?) or intensive utilisation of the species? It is a little bit a pity that the comparative sample used during the studies was very low in the 4 genotypes, but I understand the troubles to access the material. From the methodological point of view to access the DNA/SNP identification, as well as GBS library construction it is enough.
The conclusions were derived from the obtained results during the performed studies and concluded on the basis of the carefully selected scientific literature data.
The paper was written very carefully. So, my decision is accepting in present form.
Author Response
Dear Reviewer,
Thank you very much for your comments and suggestions.
With kindest regards,
Yours Sincerely
Yongda Zhong
