Genome-Wide Resequencing Reveals Genetic Relationships between Main Gardenia jasminoides Ellis Cultivars
Round 1
Reviewer 1 Report
Review “Genome-wide Resequencing Reveals Genetic Relationship of 2 Main Gardenia Jasminoides Cultivars” by Li et al.
Nineteen strains of Gardenia jasminoides originating from China were subjected to genome resequencing. The study involved mapping the genomes against a reference genome to detect inDel sites and SNP sites, as well as calculating variations in heterozygosity ratios. Additionally, a phylogenetic tree was constructed, revealing that the 19 strains could be categorized into four distinct groups. Furthermore, genetic structure and principal component analysis were conducted, yielding similar conclusions.
The authors present a substantial amount of data that contributes to our understanding of the breeding history of Gardenia Jasminoides Cultivars, which holds significant value for future investigations on this economically important species in China. However, I have identified significant limitations in the way the data is presented and analyzed. Consequently, these limitations affect the authors' ability to draw conclusive findings by the end of their study.
Comments:
Line 20, and throughout the article. The authors employed interchangeable terminology such as varieties, species, and strains. It is essential to clarify the specific meanings attributed to these terms in their study.
Line 38, “It has the functions of clearing fire and overcoming restlessness; clearing heat and promoting diuresis; cooling blood and detoxifying; detumescence and relieving pain.” Perhaps it would be helpful to provide a more comprehensible explanation of these terms in the context of traditional Chinese medicine.
Line 72, “There were 17 cultivars of G. jasminoides and two related species in total (Deng et al., 2018, 2020) (Table 1).” Could you please provide specific details about what the two related species you are referring to? From Table 1, I could only locate one of the other species mentioned, which is Gardenia stenophylla.
Line 77, “the Tiangen novel plant genome extraction kit.” Please reference the kit in the usual manner as typically done for scientific publications, i.e., cited the city and country of origin.
Lines 77-81, “After DNA samples were qualified by Nanodrop and agarose gel electrophoresis, the second generation sequencing library was constructed by genomic DNA fragmentation, end repair, A adding, adaptor adding, fragment selection, PCR amplification and product purification.” To enhance clarity regarding the procedures, it would be beneficial to split the text into separate sentences. Additionally, when referencing previous work, please provide proper citations or describe any modifications made to the procedure. Furthermore, remember to cite the specific kits utilized for the described steps.
Line 95, “IQ-TREE software (maximum likelihood method)” Please ensure that you cite the IQ-TREE software and its corresponding publication accurately and in accordance with the appropriate citation style.
Lines 115-116, “Of the Indel sites, the number of heterozygous sites ranged from 167,512 (Y_40) to 471,006 (Y_4).” The authors should aim to communicate with a wider scientific audience by providing explanations and definitions for the terms used in their analysis. It is crucial to clearly describe how the indel sites, heterozygous sites, and other relevant metrics were counted.
Lines 152-156, Please provide a description of your results that goes beyond simply stating what they are, and also explain their significance and implications.
Line 165, “Figure 4. The UPGMA phylogenetic tree for the samples of G. jasminoides constructed.” In the presented phylogenetic tree, it appears that the UPGMA method was utilized, which is a Neighbor Joining approach rather than the maximum likelihood method mentioned in both the Results and Materials and Methods sections. It is important to note this discrepancy between the reported methodology and the actual type of tree displayed.
Line 171, “PCA was used to obtain the dendrogram of 19 strains of G. jasminoides (Figure 5).” A dendrogram, by definition, visually represents the hierarchical relationships between objects. However, in Figure 5, there was no dendrogram or tree presented. It is crucial to ensure that the correct figure is displayed and corresponds to the intended representation.
Lines 196-226, second paragraph of discussion. To begin with, the available information regarding the reconstruction of the phylogenetic tree is limited. It remains unclear which dataset was used for constructing the tree, and there is confusion regarding the methodology employed (described as maximum likelihood but displaying a distance tree). Additionally, the tree presented appears to be unrooted, without any mention of tree polarization. Without evidence supporting Y_2 as the ancestor, an unrooted tree does not allow for determining the order of clade branching or the sequence of branching.
see above
Author Response
- Line 20, and throughout the article. The authors employed interchangeable terminology such as varieties, species, and strains. It is essential to clarify the specific meanings attributed to these terms in their study.
Response 1: We have calibrated and unified the terminology throughout the article (line 19, 110-111, and throughout the article).
- Line 38, “It has the functions of clearing fire and overcoming restlessness; clearing heat and promoting diuresis; cooling blood and detoxifying; detumescence and relieving pain.” Perhaps it would be helpful to provide a more comprehensible explanation of these terms in the context of traditional Chinese medicine.
Response 2: We have added explanations in the article (line 41-43).
- Line 72, “There were 17 cultivars of G. jasminoides and two related species in total (Deng et al., 2018, 2020) (Table 1).” Could you please provide specific details about what the two related species you are referring to? From Table 1, I could only locate one of the other species mentioned, which is Gardenia stenophylla.
Response 3: The two species is G. jasminoides and G. stenophylla. There were 19 samples of the Gardenia were sequenced, including G. jasminoides and 17 cultivars of G. jasminoides and one outgroup of G. stenophylla in the article. From Table 1, one of the other species mentioned, which is G. jasminoides(No. Y_29). We have added explanations in the article (line 110-111)
- Line 77, “the Tiangen novel plant genome extraction kit.” Please reference the kit in the usual manner as typically done for scientific publications, i.e., cited the city and country of origin.
Response 4: We have added it (line 116).
- Lines 77-81, “After DNA samples were qualified by Nanodrop and agarose gel electrophoresis, the second generation sequencing library was constructed by genomic DNA fragmentation, end repair, A adding, adaptor adding, fragment selection, PCR amplification and product purification.” To enhance clarity regarding the procedures, it would be beneficial to split the text into separate sentences. Additionally, when referencing previous work, please provide proper citations or describe any modifications made to the procedure. Furthermore, remember to cite the specific kits utilized for the described steps.
Response 5: We have splitted the text into separate sentences and cited the specific kits(line 117-122).
- Line 95, “IQ-TREE software (maximum likelihood method)” Please ensure that you cite the IQ-TREE software and its corresponding publication accurately and in accordance with the appropriate citation style.
Response 6: We have added it (line 140).
- Lines 115-116, “Of the Indel sites, the number of heterozygous sites ranged from 167,512 (Y_40) to 471,006 (Y_4).” The authors should aim to communicate with a wider scientific audience by providing explanations and definitions for the terms used in their analysis. It is crucial to clearly describe how the indel sites, heterozygous sites, and other relevant metrics were counted.
Response 7: We have added the explanation and description(line 132-137, 177-178).
- Lines 152-156, Please provide a description of your results that goes beyond simply stating what they are, and also explain their significance and implications.
Response 8: We have added analysis and explanation content in the article (line 214-225).
- Line 165, “Figure 4. The UPGMA phylogenetic tree for the samples of G. jasminoides constructed.” In the presented phylogenetic tree, it appears that the UPGMA method was utilized, which is a Neighbor Joining approach rather than the maximum likelihood method mentioned in both the Results and Materials and Methods sections. It is important to note this discrepancy between the reported methodology and the actual type of tree displayed.
Response 9: We have verified and revised it (line 236).
- Line 171, “PCA was used to obtain the dendrogram of 19 strains of G. jasminoides (Figure 5).” A dendrogram, by definition, visually represents the hierarchical relationships between objects. However, in Figure 5, there was no dendrogram or tree presented. It is crucial to ensure that the correct figure is displayed and corresponds to the intended representation.
Response 10: We have verified and revised it (line 242).
- Lines 196-226, second paragraph of discussion. To begin with, the available information regarding the reconstruction of the phylogenetic tree is limited. It remains unclear which dataset was used for constructing the tree, and there is confusion regarding the methodology employed (described as maximum likelihood but displaying a distance tree). Additionally, the tree presented appears to be unrooted, without any mention of tree polarization. Without evidence supporting Y_2 as the ancestor, an unrooted tree does not allow for determining the order of clade branching or the sequence of branching.
Response 11: We have verified and revised it. We are certain that it is a maximum likelihood tree (line 236). And, We constructed a rooted tree with G. stenophylla as an outgroup(line 235).
Author Response File: 
Author Response.docx
Reviewer 2 Report
1. Quality of figure not good enough so please replace with high quality figure.
2. Please add few description of related species used for the studies.
3. Figure 3. The Population structure of G. jasminoides.: add few description to make more easy understandable
4. What kind of further utilization of current resequencing will be used.
Author Response
- Quality of figure not good enough so please replace with high quality figure.
Response 1: We have replaced the high quality figures (line 209, 235).
- Please add few description of related species used for the studies.
Response 2: We have added some descriptions of related species (line 31-37).
- Figure 3. The Population structure of G. jasminoides.: add few description to make more easy understandable
Response 3: We have added some descriptions in the article (line 210-212).
- What kind of further utilization of current resequencing will be used.
Response 4: We have elaborated and added the content in the article (line 110-105).
Author Response File: Author Response.docx
Reviewer 3 Report
The manuscript is good written in silico based study. The importance of the results as well as application possibilities based on your bioinformatic data must be introduced and discussed more deeply. Similar, some possible hypothesis for further research that resulted from your findings will improve this manuscript, too.
In introduction - actual knowledge about genome, geentics as well as polymorphism, etc. ... of G. jasminoides is missing, this must be added.
Manuscript is written well, no specific English language editing is needed.
Author Response
- The manuscript is good written in silico based study. The importance of the results as well as application possibilities based on your bioinformatic data must be introduced and discussed more deeply. Similar, some possible hypothesis for further research that resulted from your findings will improve this manuscript, too.
Response 1: We have elaborated and added the content in the article (line 110-105, line 265-307)
- In introduction - actual knowledge about genome, geentics as well as polymorphism, etc. ... of jasminoidesis missing, this must be added.
Response 2: We have added actual knowledge about genome, geentics as well as polymorphism, etc. ... of G. jasminoides (line 55-88).
Author Response File: Author Response.docx
Reviewer 4 Report
- The scientific name of the plant should be complete and accompanied by the author's name
- The discussion is weak and should be compared with previous similar studies
What were the conditions of the cultivated samples? What was the basis of their selection?
Author Response
- The scientific name of the plant should be complete and accompanied by the author's name.
Response 1: We have completed the name (line 3, 11, 27, Table 1).
- The discussion is weak and should be compared with previous similar studies.
Response 2:We have enriched the discussion (line 265-307).
- What were the conditions of the cultivated samples? What was the basis of their selection?
Response 3: Compared with other plants such as peony, osmanthus, rose, etc., there are relatively few cultivars of G. jasminoides. In this study, the cultivars include the traditional ornamental cultivar G. jasminoides ‘Fortuneana’, and the cultivars such as G. jasminoides ‘Longicarpa’, G. jasminoides ‘Grandiflora’ and G. jasminoides ‘Jinfu Shuizhi’ used for pigment cultivation in China. And it includes G. jasminoides ‘Hehua’, G. jasminoides ‘Variegata’, G. jasminoides ‘Radicans’, G. jasminoides ‘Albomarginata’ and other cultivars from Japan, South Korea and the Netherlands, as well as G. jasminoides ‘Xiangxue’, G. jasminoides ‘Yinzhan’, G. jasminoides ‘Zongheng’and other new cultivars in China in recent years. Our research object covers almost all the existing cultivars. Therefore, our conclusions are pioneering. And we have added actual knowledge about the cultivated samples (line 55-69).
Author Response File: Author Response.docx
Round 2
Reviewer 2 Report
Authors implemented all the suggestions
Reviewer 3 Report
Thank you for your work and reasearch as well as for accepting my suggestions.
