Genetic Diversity and Population Structure of Bursaphelenchus xylophilus in Central China Based on SNP Markers
Round 1
Reviewer 1 Report
The study delivers valuable insights into the genetic structure of the pine wilt disease (PWD) causative agent, Bursaphelenchus xylophilus, in Central China. The authors examined the genetic information of PWD populations in Hubei, Hunan, and Henan provinces and compared them with strains from Guangdong and Jiangsu provinces. The discoveries shed light on the genetic relationships, transmission pathways, and potential sources of PWD in the region.
1. Please modify the abstract and more specifically introductory lines
2. “After DNA extraction, molecular identification based on the SCAR marker was performed to ensure detection accuracy” data can be included in this study.
3. “When a sufficient sample size was obtained”. What actually is the sufficient sample size
4. Please correct lines 95-96
5. Improve the quality of figures
6. Expand figure caption 4 by adding the necessary information.
7. It will be better to highlight the practical implication of this study
8. Phylogenetic stress should be improved by reconstructing and providing adequate information along with accession ids on each branch.
minor changes required.
Author Response
Dear Reviewer 1:
On behalf of my co-authors, we thank you very much for giving us an opportunity to revise our manuscript, we really appreciate editor and reviewers for their positive and constructive comments and suggestions on our manuscript entitled “Genetic Diversity and Population Structure of Bursaphelenchus xylophilus in Central China based on SNP Markers”. We have evaluated all comments carefully and have made revisions by using the track changes mode in our revised manuscript. We do hope the revised version of our paper would solve all concerns made by you.
The responses to your questions and suggestions are as follows:
- C1: Please modify the abstract and more specifically introductory lines
Response 1: Thank you very much for your suggestions. We have carefully examined the sentences in the manuscript and improved some of them.
- C2: “After DNA extraction, molecular identification based on the SCAR marker was performed to ensure detection accuracy” data can be included in this study.
Response 2: Thank you very much for your suggestion. Molecular identification of PWNs was performed using an automatic identification instrument based on SCAR markers. The CT threshold value of the qPCR was set to 30 for automatic identification of PWN. However, we only focused on outcome judgment and did not record specific CT values. We will note this later. Thank you again for your advice.
- C3: “When a sufficient sample size was obtained”. What actually is the sufficient sample size
Response 3: We used Botrytis cinerea for reproductive culture of pine wood nematodes. When all the B. cinerea have been fed, the pine wood nematodes will fill the entire medium, at which point the number is at its maximum enough to be preserved. After cultivation, the number will generally reach tens of thousands or even hundreds of thousands. We have revised the manuscript to isolate pine wood nematodes after 5-7 days of culture and after feeding B. cinerea.
- C4: Please correct lines 95-96
Response 4: Thank you very much for your suggestions. We have confirmed and revised this sentence on lines 104-106.
- C5: Improve the quality of figures
Response 5: Thank you very much for your suggestions. We will adjust the sharpness of the pictures in the manuscript.
- C6: Expand figure caption 4 by adding the necessary information.
Response 6: Thank you very much for your suggestions. We redrew the picture and added details. The note id is shown in Figure 4.
- C7: It will be better to highlight the practical implication of this study
Response 7: Thank you very much for your suggestions. We have highlighted the practical significance of this study in the conclusions section. See Line 270: During the 41 years of PWN invasion, many different geographical strains were formed in the genetic structure of PWN populations in China. Based on the genetic differences, we investigated the genetic structure of PWN populations in different endemic areas of China, which provided a theoretical basis for exploring the reproduction route, population genetic structure, and formulating quarantine strategies of PWN.
- C8: Phylogenetic stress should be improved by reconstructing and providing adequate information along with accession ids on each branch.
Response 8: Thank you very much for your suggestions. We redrew the picture and added details. The note id is shown in Figure 4.
Author Response File: 
Author Response.docx
Reviewer 2 Report
Please address these comments:
line 50: write the full name for RAPD at first mention line 54: write the full name for SNP at first mention line 58: 7 pawn strains line 63: this section is confusing. Please reword it: "Population results in eastern China showed that there was some correlation between each group and geographical origin" what do you mean by population results? What method did they use? You often use PWN or PWNs, for example, on line 69: it should be PWN, and whenever applicable, change PWNs to PWN strains. At the end of your introduction, please provide more than one reason to justify the study. Line 83: mentions what SCAR stands for. Do this for any first mention of the abbreviations please. Line 84: It is better to say : were established in the laboratory on Botrytis cinerea growing on potato dextrose agar (reference?) Line 86: Bermann funnel method (reference?) Line 92. Which Qubit:1 or 2? Line 93: What do you mean by qualified DNA? What are your criteria for good nematode DNA? 94: Can you please explain why you call it resequencing? Figure 1 and figure 2: make the fonts in the figures bigger and put the legend name for each figure.i.e Strain name Figure 2: make jitters less dispersed -> geom_jitter(width = 0.2) line 153: could be -> were line 154: group 2 consisted of line 157: among the PWN populations Figure 3: make the fonts in the figure bigger and put the legend name for each figure.i.e Strain name Line 184: Previous studies have demonstrated that environmental factors can induce founder effects and genetic drift, resulting in diminished or lost genetic diversity and population genetic differentiation among species undergoing migration and dispersal. Line 187: mention what AFLP stands for.
Needs minor edits. Please looks at the comments.
Author Response
Dear Reviewer 2:
On behalf of my co-authors, we thank you very much for giving us an opportunity to revise our manuscript, we really appreciate the editor and reviewers for their positive and constructive comments and suggestions on our manuscript entitled “Genetic Diversity and Population Structure of Bursaphelenchus xylophilus in Central China based on SNP Markers”. We have evaluated all comments carefully and have made revisions by using the track changes mode in our revised manuscript. We do hope the revised version of our paper would solve all concerns made by you.
The responses to your questions and suggestions are as follows:
line 50: write the full name for RAPD at first mention line 54: write the full name for SNP at first mention
Response: Thank you very much for your suggestions. We added the full name of RAPD and SNP in line 53 and line 57: Random Amplified Polymorphic DNA and Single Nucleotide Polymorphisms.
line 58: 7 pawn strains
Response: We are sorry for the error, but we have revised the seventh line of the manuscript. “7 pwn strains”
line 63: this section is confusing. Please reword it: "Population results in eastern China showed that there was some correlation between each group and geographical origin" what do you mean by population results? What method did they use?
Response: Wang Qingtong et al. analyzed the population genetic structure of pine wood nematodes in East China and divided them into three groups by principal component analysis. Then the geographical distribution of different groups of strains was analyzed, and it was found that there was a certain relationship between the three groups and the geographical region.
You often use PWN or PWNs, for example, on line 69: it should be PWN, and whenever applicable, change PWNs to PWN strains.
Response: Thank you very much for your suggestions. We have changed PWNs to PWN strains in this manuscript.
At the end of your introduction, please provide more than one reason to justify the study.
Response: Understanding the population structure of PWN by studying their genetic differences is beneficial to the analysis of genetic diversity and is also a necessary step for tracing the origin of PWN. During the 41 years of the invasion of PWN in China, cross-invasion occurred continuously.
Line 83: mentions what SCAR stands for. Do this for any first mention of the abbreviations please.
Response: Thank you very much for your suggestions. We added the full name of SCAR in line 91: sequence characterized amplified regions.
Line 84: It is better to say : were established in the laboratory on Botrytis cinerea growing on potato dextrose agar (reference?)
Response: Thank you very much for your suggestions. We have revised it and added references in line 94 of the manuscript.
Line 86: Bermann funnel method (reference?)
Response: Thank you very much for your suggestions. We have added references in line 97 of the manuscript.
Line 92. Which Qubit:1 or 2?
Response: Sorry for the trouble caused to you, we have confirmed and revised the model of the instrument as Nano-drop 2000/2000C in the manuscript.
Line 93: What do you mean by qualified DNA? What are your criteria for good nematode DNA?
Response: Qualified DNA should have a concentration greater than 100, an A260/A280 ratio of about 1.8, and an A260/A230 ratio greater than 2.0.
Line 94: Can you please explain why you call it resequencing?
Response: Since the genome sequence of pine wood nematode has been published, sequencing the genome of different individuals of a species with a known genome sequence is called resequencing.
Figure 1 and figure 2: make the fonts in the figures bigger and put the legend name for each figure.i.e Strain name Figure 2: make jitters less dispersed -> geom_jitter(width = 0.2)
Response: Thank you very much for your suggestions. We redrew and adjusted the coordinates and legend in Figures 1 and 2 and modified the jitters’ width in Figure 2. We focused on the overall genetic structure of the three provinces. Add a legend name for each figure, which is not very clear for the analysis. We used the tabulated data to analyze the differences between each worm strain and expressed the genetic differences of each strain by constructing a phylogenetic tree.
line 153: could be -> were
Response: Thank you very much for your suggestions. We have changed "could be" to "were" on line 166.
line 154: group 2 consisted of
Response: Thank you very much for your suggestions. We have changed "comprised" to " consisted of " on line 167.
line 157: among the PWN populations Figure 3: make the fonts in the figure bigger and put the legend name for each figure.i.e Strain name
Response: Thank you very much for your suggestions. We redrew and adjusted the coordinates and legend in Figure 3. We focused on the overall genetic structure of the three provinces. Add a legend name for each figure, which is not very clear for the analysis. We expressed the genetic differences of each strain by constructing a phylogenetic tree.
Line 184: Previous studies have demonstrated that environmental factors can induce founder effects and genetic drift, resulting in diminished or lost genetic diversity and population genetic differentiation among species undergoing migration and dispersal.
Response: Thank you very much for your suggestions. We have revised this sentence in the manuscript.
Line 187: mention what AFLP stands for.
Response: Thank you very much for your suggestions. We added the full name of AFLP in line 205: Amplified fragment length polymorphism.
Author Response File: Author Response.docx
Round 2
Reviewer 1 Report
The authors have addressed my critical comments and made the necessary revisions to the manuscript. In my opinion, the manuscript may be accepted.
