Comprehensive Metabolomic Profiling of Common Bean (Phaseolus vulgaris L.) Reveals Biomarkers Involved in Viral Disease Detection and Monitoring
, Clabe Wekesa 3, Francis N. Muyekho 4, Hassan Karakacha Were 4 and Patrick Okoth 1
Round 1
Reviewer 1 Report
Review the manuscript, and send for English editing.
Based on the review on this manuscript, I encourage the authors to address the following points:
1. Line 19, 54, 212, 372 on the document, the author should put a full stop at the end of sentences.
2. Line 27, the author need not to start a sentence with a number, they should use words first.
3. Line 121-123, the sentences are confusing, rephrase.
4. Check line 169 and fix.
5. Line 186, the author needs to recheck their in-text references for minor mistakes. This should be done throughout the document.
6. Line 255, rephrase the sentence as it does not read well.
7. Line 230, the sentence comes out of nowhere without a meaning to the above interpretation. There is no proper interpretation of the figure (Fig 4).
8. Line 238 and 244, are the authors discussing differentially expressed metabolites or genes? Revisit the title.
9. Line 244 and 245, there is a repetition of words, with the other sentence incomplete. Hence, English editing is required.
10. Line 260, the authors did not take time to interpret the hormone analysis data, and they need to go back to the data to describe their figures properly.
11. Line 287-287 is confusing. Is this sentence highlighting the results observed in this study, or acts as a supporting statement? Rephrase.
12. Line 294-295, rephrase the sentence.
13. Line 349-362 insinuates the outcomes of the current study without a supporting references that reported similar results. The author needs to show how they came with a suggestions such as this in their study. There should be work that reported similar results as those in this study.
14. Line 370-372, see comment no 13. What kind of role are the authors suggesting here with respect to downregulations? Who observed similar results as these?
15. Line 392, 407- 411 the authors should report their findings in past tense.
16. Line 410-411: The consistent increase of SA plays an essential role in plant responses to stress across diverse environments, what does this mean?
17. Line 416-418, the sentence is confusing, rephrase. It is not clear what you want to report about the unaffected levels of JA. Try to align the standard levels with the morphology and physiological data to extract the reason why JA was not affected by the conditions in the plants.
18. The title for the tables and figures on the results and discussion sections should be self-explanatory, and not be like a supporting sentence. Eg, Figure 2 should be something like this: Illustration of the upregulated and downregulated pathways, accompanied by pathway enrichment, with 214 on the Y-axis and the four counties examined on the X-axis.
19. Line 487 and 489, the references are inconsistent. The journal names are written in full in 487, while abbreviated in 489. Check all your references for consistency. It is suggested that you use the same referencing style, and recheck manually before submission again.
Overall, the research was well performed, however, it lacks proper interpretation and discussion to support the findings. Some of the figures are not well interpreted and there is a lot of information that can be shared from the data. In the discussion, the authors suggest the outcomes or conclusions without references. The authors need to revisit these sections.
I recommend a resubmission of the manuscript, with major reviews and English editing.
Author Response
Please see the attachment.
Author Response File: 
Author Response.docx
Reviewer 2 Report
This paper presents the metabolomic response of a common bean cultivar after being infected with two viruses that affect this crop in several regions worldwide. The comprehensive metabolomic profile of the common bean can be useful to reveal biomarkers involved in the detection and monitoring of viral diseases and other stresses. These results can contribute to detect metabolic pathways that are activated in response to stress, which can be useful for genetic improvement of the crop as well as to detect crop management strategies.
Introduction: Improve the writing aspects of lines 48, 55, 58 and 92. Improve the writing of the last paragraph to improve the statement of the hypothesis and the objective of the research.
Methodology: Report details such as agroclimatic conditions of the study locations, experimental design, statistical analysis, characteristics of the cultivar used in the study. Results: Focus the results on the differential response of infected plants compared to non-infected ones.
Discussion: Focus the discussion on the specific response to the viruses that were the subject of this research.
Comments for author File: 
Comments.pdf
Author Response
Please see the attachment.
Author Response File: Author Response.docx
Reviewer 3 Report
The manuscript reported the comparative metabolite profiling of common bean planted in different areas which treated with virus. The manuscript contain interesting information. However, I have several comments and suggestions.
1. The title seems not really fit with the content. I would like to suggest for a revision because it is specifically using two viruses BCMV and BCMNV.
2. The abstract also need a revision because the results regarding the phytohormones is not included but extensively discussed.
3. Methods section need revision because it is not clear. I would like to suggest to include subsection, For instance : a. plant material and design experiment b. metabolite profiling (Sample preparation, LC-MS and data analysis).
Please also elaborate why the authors separated the phytohormone analysis ? LC- MS 9030 Shimadzu also could perform this kind of analysis.
4. Results section need revision. Table 2 and the statistical analysis is not conducted properly. For example, Abscisic acid (ABA) in Bungoma is not significant compared to the control in table 2. But in Figure 7. The data clearly shown that it should be significant. I would like to recommend that the data should be necessary to have a check performed by statistician.
5. Discussion section also need a revision, since it discussed the result. Also, please discussed the metabolite abundance with the defence mechanism related to BCMV and BCMNV.
6. Conclusion section is not answering the objective or the title of the manuscript. Such as what is the most prominent metabolite profiles (biomarkers) related to BCMV and BCMNV.
I also have specific comments regarding the manuscript.
1. Line 19 . Please add full stop
2. Line 41. Please revise the reference (in number)
3. Line 55. Please use italic (Phaseolus vulgaris)
4. Line 111. Please also include more detail regarding the plant material and design experiment section
5. Line 122. Please revise and elaborate what is “. Inoculation, the”
6. Figure 1. Please include bar scale
7. Line 139. The author used targeted metabolomics but what is the metabolite target and the reference of metabolite used ? I did not see this targeted metabolite profiling results in the manuscript. Please include in the material and method section.
8. Line 186. Redundant reference Heyer et al.
9. Figure 3. Provide higher resolution picture. The test is not readable.
10. Figure 4. Please provide the list of DEG for supplementary material
11. Figure 4. The X axis threshold for -log10 pvalue is not clear. The authors only shown FDR treshold.
12. Figure 6. Please put in the supplementary.
13. Line 263. Please provide the figure mentioned (low expression levels of SA and ABA)
14. Figure 7. Y axis abbreviation should be explained in legend.
15. Table 2. Please check the statistical analysis again. It is not matched with Figure 7 results.
16. Please provide the raw data Table 2 and Fig 7 in the supplementary.
17. Line 391. Phytohormones/ targeted metabolomics. Is it a subsection ? Please revise.
18. Line 453. Implications and future directions. This section is not common please consider to merge in the discussion or conclusion section.
19. Line 473. Conclusion section. Please revise as my suggestion in the general comments .
Author Response
Please see the attachment.
Author Response File: Author Response.docx
Round 2
Reviewer 1 Report
The manuscript still needs to go through English editing, as there are still some sentences that does not make sense.
There is a repetition of your references throughout the whole list, rework the references accordingly. Use a refencing software.
Line 78-80, the sentence does not make sense, it needs rephrasing.
Line 210-212 could be incorporated into the results section before table 1, as the figure explains the same trends as Table 1. Provided more interpretation is included from Figure 2.
Figure 2, the y-axis is confusing. Is the numbers on represented as number of genes per pathway, or fold change? Interpret the figure title in detail, if its not explained in the text.
Line 227, why is Figure 3B cited before 3A?
Line 230, the letter A is missing.
The authors still did not interpret the data of the volcano plots. Why did they show the volcano plots? what do they explain in terms of the data? There is a lot of data that can be extracted from the volcano plots: Eg, No of downreg and upreg metabolites within and between the counties; fold change differences, non-significant metabolites, what does this data mean in detecting diseases?
Line 237-238, the authors are citing Figure 5, is it A or B? If its A, why is Figure 5B not cited in the study?
Line 242, the authors still talk about differentially expressed genes, is there any data on DEGs that is missing here?
Line 242 and 243 is a repetition of words.
Figure 6A and B are not cited in this study.
Rephrase the title of Figure 7, it still doesn't make sense and all over the place.
Line 383, are there two references or not?
There is a repetition of your references throughout the whole list, rework the references accordingly. Use a refencing software.
Author Response
Line 78-80, the sentence does not make sense, it needs rephrasing.
AUTHORS' RESPONSE TO THE REVIEWER'S ISSUES AND CONCERNS
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REVIEWERS CONCERNS |
AUTHORS REBUTTAL |
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Line 78-80, the sentence does not make sense, it needs rephrasing.
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The authors have amended the sentence to be more precise to read ‘Investigating the untargeted metabolome profiles of common beans affected by viral diseases can enhance our understanding of the plant's stress response mechanisms and overall plant health.’ See lines 78-80 |
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Line 210-212 could be incorporated into the results section before table 1, as the figure explains the same trends as Table 1. Provided more interpretation is included from Figure 2.
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We concurred with the advice and subsequently moved the results just before Table 1 see lines 214-215 |
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Figure 2, the y-axis is confusing. Is the numbers on represented as number of genes per pathway, or fold change? Interpret the figure title in detail, if its not explained in the text.
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The authors have corrected the Figure legend to read ‘The upregulated and downregulated pathways, along with the number of metabolites per pathway, are shown on the Y-axis, with the four counties studied represented on the X-axis’ to remove the ambiguity see Figure lines 220-221 |
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Line 227, why is Figure 3B cited before 3A?
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We have corrected and cited Figure 3A first before Figure 3B as observed in lines 223 and 226 |
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Line 230, the letter A is missing.
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We have inserted the letter A see line 247 |
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The authors still did not interpret the data of the volcano plots. Why did they show the volcano plots? what do they explain in terms of the data? There is a lot of data that can be extracted from the volcano plots: Eg, No of downreg and upreg metabolites within and between the counties; fold change differences, non-significant metabolites, what does this data mean in detecting diseases?
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The authors appreciate the reviewer's observation, which enriches the results and overall output of the paper, and subsequently interpreted the volcano plots as shown in lines 233-246. As a result, the authors enhanced the discussion by incorporating these findings into the discussion and conclusion, as seen in lines 437-464 and 545-546, respectively |
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Line 237-238, the authors are citing Figure 5, is it A or B? If its A, why is Figure 5B not cited in the study?
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The authors considered this observation from the reviewer and have cited the figure in the text in line 264 |
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Line 242, the authors still talk about differentially expressed genes, is there any data on DEGs that is missing here?
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The authors noted this concern and have gone ahead to correct the word genes to metabolites see line 259 |
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Line 242 and 243 is a repetition of words.
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The authors have merged the two sentences to read Across the four sites, ten metabolites were commonly up-regulated, including those with the following mapping IDs: 2603, 2843, 3767, 3773, 6251, 8793, 8796, 9995, 10337, and 11308 see line 260-262 |
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Figure 6A and B are not cited in this study. |
The authors have cited the figures as observed by the reviewer see lines 263 |
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Rephrase the title of Figure 7, it still doesn't make sense and all over the place.
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The author have improved the legend of the figure to read Phytohormones extracted from diseased common beans in the Western region of Kenya (Kakamega, Bungoma, Vihiga, and Busia), involved in the plant defense mechanism, are shown on the Y-axis, with their concentrations normalized using the MinMaxScaler function from the sklearn.preprocessing module in Python represented on the X-axis see Figure 7 lines 282-285. |
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Line 383, are there two references or not?
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The authors have deleted the reference see line 400 |
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There is a repetition of your references throughout the whole list, rework the references accordingly. Use a referencing software.
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The authors appreciate this observation and have addressed the repetitions by using the Zotero tool for referencing. |
AUTHORS' RESPONSE TO THE REVIEWER'S ISSUES AND CONCERNS
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REVIEWERS CONCERNS |
AUTHORS REBUTTAL |
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Line 78-80, the sentence does not make sense, it needs rephrasing.
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The authors have amended the sentence to be more precise to read ‘Investigating the untargeted metabolome profiles of common beans affected by viral diseases can enhance our understanding of the plant's stress response mechanisms and overall plant health.’ See lines 78-80 |
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Line 210-212 could be incorporated into the results section before table 1, as the figure explains the same trends as Table 1. Provided more interpretation is included from Figure 2.
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We concurred with the advice and subsequently moved the results just before Table 1 see lines 214-215 |
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Figure 2, the y-axis is confusing. Is the numbers on represented as number of genes per pathway, or fold change? Interpret the figure title in detail, if its not explained in the text.
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The authors have corrected the Figure legend to read ‘The upregulated and downregulated pathways, along with the number of metabolites per pathway, are shown on the Y-axis, with the four counties studied represented on the X-axis’ to remove the ambiguity see Figure lines 220-221 |
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Line 227, why is Figure 3B cited before 3A?
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We have corrected and cited Figure 3A first before Figure 3B as observed in lines 223 and 226 |
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Line 230, the letter A is missing.
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We have inserted the letter A see line 247 |
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The authors still did not interpret the data of the volcano plots. Why did they show the volcano plots? what do they explain in terms of the data? There is a lot of data that can be extracted from the volcano plots: Eg, No of downreg and upreg metabolites within and between the counties; fold change differences, non-significant metabolites, what does this data mean in detecting diseases?
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The authors appreciate the reviewer's observation, which enriches the results and overall output of the paper, and subsequently interpreted the volcano plots as shown in lines 233-246. As a result, the authors enhanced the discussion by incorporating these findings into the discussion and conclusion, as seen in lines 437-464 and 545-546, respectively |
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Line 237-238, the authors are citing Figure 5, is it A or B? If its A, why is Figure 5B not cited in the study?
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The authors considered this observation from the reviewer and have cited the figure in the text in line 264 |
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Line 242, the authors still talk about differentially expressed genes, is there any data on DEGs that is missing here?
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The authors noted this concern and have gone ahead to correct the word genes to metabolites see line 259 |
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Line 242 and 243 is a repetition of words.
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The authors have merged the two sentences to read Across the four sites, ten metabolites were commonly up-regulated, including those with the following mapping IDs: 2603, 2843, 3767, 3773, 6251, 8793, 8796, 9995, 10337, and 11308 see line 260-262 |
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Figure 6A and B are not cited in this study. |
The authors have cited the figures as observed by the reviewer see lines 263 |
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Rephrase the title of Figure 7, it still doesn't make sense and all over the place.
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The author have improved the legend of the figure to read Phytohormones extracted from diseased common beans in the Western region of Kenya (Kakamega, Bungoma, Vihiga, and Busia), involved in the plant defense mechanism, are shown on the Y-axis, with their concentrations normalized using the MinMaxScaler function from the sklearn.preprocessing module in Python represented on the X-axis see Figure 7 lines 282-285. |
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Line 383, are there two references or not?
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The authors have deleted the reference see line 400 |
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There is a repetition of your references throughout the whole list, rework the references accordingly. Use a referencing software.
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The authors appreciate this observation and have addressed the repetitions by using the Zotero tool for referencing. |
AUTHORS' RESPONSE TO THE REVIEWER'S ISSUES AND CONCERNS
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REVIEWERS CONCERNS |
AUTHORS REBUTTAL |
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Line 78-80, the sentence does not make sense, it needs rephrasing.
|
The authors have amended the sentence to be more precise to read ‘Investigating the untargeted metabolome profiles of common beans affected by viral diseases can enhance our understanding of the plant's stress response mechanisms and overall plant health.’ See lines 78-80 |
|
|
Line 210-212 could be incorporated into the results section before table 1, as the figure explains the same trends as Table 1. Provided more interpretation is included from Figure 2.
|
We concurred with the advice and subsequently moved the results just before Table 1 see lines 214-215 |
|
|
Figure 2, the y-axis is confusing. Is the numbers on represented as number of genes per pathway, or fold change? Interpret the figure title in detail, if its not explained in the text.
|
The authors have corrected the Figure legend to read ‘The upregulated and downregulated pathways, along with the number of metabolites per pathway, are shown on the Y-axis, with the four counties studied represented on the X-axis’ to remove the ambiguity see Figure lines 220-221 |
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|
Line 227, why is Figure 3B cited before 3A?
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We have corrected and cited Figure 3A first before Figure 3B as observed in lines 223 and 226 |
|
|
Line 230, the letter A is missing.
|
We have inserted the letter A see line 247 |
|
|
The authors still did not interpret the data of the volcano plots. Why did they show the volcano plots? what do they explain in terms of the data? There is a lot of data that can be extracted from the volcano plots: Eg, No of downreg and upreg metabolites within and between the counties; fold change differences, non-significant metabolites, what does this data mean in detecting diseases?
|
The authors appreciate the reviewer's observation, which enriches the results and overall output of the paper, and subsequently interpreted the volcano plots as shown in lines 233-246. As a result, the authors enhanced the discussion by incorporating these findings into the discussion and conclusion, as seen in lines 437-464 and 545-546, respectively |
|
|
Line 237-238, the authors are citing Figure 5, is it A or B? If its A, why is Figure 5B not cited in the study?
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The authors considered this observation from the reviewer and have cited the figure in the text in line 264 |
|
|
Line 242, the authors still talk about differentially expressed genes, is there any data on DEGs that is missing here?
|
The authors noted this concern and have gone ahead to correct the word genes to metabolites see line 259 |
|
|
Line 242 and 243 is a repetition of words.
|
The authors have merged the two sentences to read Across the four sites, ten metabolites were commonly up-regulated, including those with the following mapping IDs: 2603, 2843, 3767, 3773, 6251, 8793, 8796, 9995, 10337, and 11308 see line 260-262 |
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Figure 6A and B are not cited in this study. |
The authors have cited the figures as observed by the reviewer see lines 263 |
|
|
Rephrase the title of Figure 7, it still doesn't make sense and all over the place.
|
The author have improved the legend of the figure to read Phytohormones extracted from diseased common beans in the Western region of Kenya (Kakamega, Bungoma, Vihiga, and Busia), involved in the plant defense mechanism, are shown on the Y-axis, with their concentrations normalized using the MinMaxScaler function from the sklearn.preprocessing module in Python represented on the X-axis see Figure 7 lines 282-285. |
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Line 383, are there two references or not?
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The authors have deleted the reference see line 400 |
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There is a repetition of your references throughout the whole list, rework the references accordingly. Use a referencing software.
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The authors appreciate this observation and have addressed the repetitions by using the Zotero tool for referencing. |
AUTHORS' RESPONSE TO THE REVIEWER'S ISSUES AND CONCERNS
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|
REVIEWERS CONCERNS |
AUTHORS REBUTTAL |
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Line 78-80, the sentence does not make sense, it needs rephrasing.
|
The authors have amended the sentence to be more precise to read ‘Investigating the untargeted metabolome profiles of common beans affected by viral diseases can enhance our understanding of the plant's stress response mechanisms and overall plant health.’ See lines 78-80 |
|
|
Line 210-212 could be incorporated into the results section before table 1, as the figure explains the same trends as Table 1. Provided more interpretation is included from Figure 2.
|
We concurred with the advice and subsequently moved the results just before Table 1 see lines 214-215 |
|
|
Figure 2, the y-axis is confusing. Is the numbers on represented as number of genes per pathway, or fold change? Interpret the figure title in detail, if its not explained in the text.
|
The authors have corrected the Figure legend to read ‘The upregulated and downregulated pathways, along with the number of metabolites per pathway, are shown on the Y-axis, with the four counties studied represented on the X-axis’ to remove the ambiguity see Figure lines 220-221 |
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|
Line 227, why is Figure 3B cited before 3A?
|
We have corrected and cited Figure 3A first before Figure 3B as observed in lines 223 and 226 |
|
|
Line 230, the letter A is missing.
|
We have inserted the letter A see line 247 |
|
|
The authors still did not interpret the data of the volcano plots. Why did they show the volcano plots? what do they explain in terms of the data? There is a lot of data that can be extracted from the volcano plots: Eg, No of downreg and upreg metabolites within and between the counties; fold change differences, non-significant metabolites, what does this data mean in detecting diseases?
|
The authors appreciate the reviewer's observation, which enriches the results and overall output of the paper, and subsequently interpreted the volcano plots as shown in lines 233-246. As a result, the authors enhanced the discussion by incorporating these findings into the discussion and conclusion, as seen in lines 437-464 and 545-546, respectively |
|
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Line 237-238, the authors are citing Figure 5, is it A or B? If its A, why is Figure 5B not cited in the study?
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The authors considered this observation from the reviewer and have cited the figure in the text in line 264 |
|
|
Line 242, the authors still talk about differentially expressed genes, is there any data on DEGs that is missing here?
|
The authors noted this concern and have gone ahead to correct the word genes to metabolites see line 259 |
|
|
Line 242 and 243 is a repetition of words.
|
The authors have merged the two sentences to read Across the four sites, ten metabolites were commonly up-regulated, including those with the following mapping IDs: 2603, 2843, 3767, 3773, 6251, 8793, 8796, 9995, 10337, and 11308 see line 260-262 |
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Figure 6A and B are not cited in this study. |
The authors have cited the figures as observed by the reviewer see lines 263 |
|
|
Rephrase the title of Figure 7, it still doesn't make sense and all over the place.
|
The author have improved the legend of the figure to read Phytohormones extracted from diseased common beans in the Western region of Kenya (Kakamega, Bungoma, Vihiga, and Busia), involved in the plant defense mechanism, are shown on the Y-axis, with their concentrations normalized using the MinMaxScaler function from the sklearn.preprocessing module in Python represented on the X-axis see Figure 7 lines 282-285. |
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Line 383, are there two references or not?
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The authors have deleted the reference see line 400 |
|
|
There is a repetition of your references throughout the whole list, rework the references accordingly. Use a referencing software.
|
The authors appreciate this observation and have addressed the repetitions by using the Zotero tool for referencing. |
AUTHORS' RESPONSE TO THE REVIEWER'S ISSUES AND CONCERNS
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|
REVIEWERS CONCERNS |
AUTHORS REBUTTAL |
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Line 78-80, the sentence does not make sense, it needs rephrasing.
|
The authors have amended the sentence to be more precise to read ‘Investigating the untargeted metabolome profiles of common beans affected by viral diseases can enhance our understanding of the plant's stress response mechanisms and overall plant health.’ See lines 78-80 |
|
|
Line 210-212 could be incorporated into the results section before table 1, as the figure explains the same trends as Table 1. Provided more interpretation is included from Figure 2.
|
We concurred with the advice and subsequently moved the results just before Table 1 see lines 214-215 |
|
|
Figure 2, the y-axis is confusing. Is the numbers on represented as number of genes per pathway, or fold change? Interpret the figure title in detail, if its not explained in the text.
|
The authors have corrected the Figure legend to read ‘The upregulated and downregulated pathways, along with the number of metabolites per pathway, are shown on the Y-axis, with the four counties studied represented on the X-axis’ to remove the ambiguity see Figure lines 220-221 |
|
|
Line 227, why is Figure 3B cited before 3A?
|
We have corrected and cited Figure 3A first before Figure 3B as observed in lines 223 and 226 |
|
|
Line 230, the letter A is missing.
|
We have inserted the letter A see line 247 |
|
|
The authors still did not interpret the data of the volcano plots. Why did they show the volcano plots? what do they explain in terms of the data? There is a lot of data that can be extracted from the volcano plots: Eg, No of downreg and upreg metabolites within and between the counties; fold change differences, non-significant metabolites, what does this data mean in detecting diseases?
|
The authors appreciate the reviewer's observation, which enriches the results and overall output of the paper, and subsequently interpreted the volcano plots as shown in lines 233-246. As a result, the authors enhanced the discussion by incorporating these findings into the discussion and conclusion, as seen in lines 437-464 and 545-546, respectively |
|
|
Line 237-238, the authors are citing Figure 5, is it A or B? If its A, why is Figure 5B not cited in the study?
|
The authors considered this observation from the reviewer and have cited the figure in the text in line 264 |
|
|
Line 242, the authors still talk about differentially expressed genes, is there any data on DEGs that is missing here?
|
The authors noted this concern and have gone ahead to correct the word genes to metabolites see line 259 |
|
|
Line 242 and 243 is a repetition of words.
|
The authors have merged the two sentences to read Across the four sites, ten metabolites were commonly up-regulated, including those with the following mapping IDs: 2603, 2843, 3767, 3773, 6251, 8793, 8796, 9995, 10337, and 11308 see line 260-262 |
|
|
Figure 6A and B are not cited in this study. |
The authors have cited the figures as observed by the reviewer see lines 263 |
|
|
Rephrase the title of Figure 7, it still doesn't make sense and all over the place.
|
The author have improved the legend of the figure to read Phytohormones extracted from diseased common beans in the Western region of Kenya (Kakamega, Bungoma, Vihiga, and Busia), involved in the plant defense mechanism, are shown on the Y-axis, with their concentrations normalized using the MinMaxScaler function from the sklearn.preprocessing module in Python represented on the X-axis see Figure 7 lines 282-285. |
|
|
Line 383, are there two references or not?
|
The authors have deleted the reference see line 400 |
|
|
There is a repetition of your references throughout the whole list, rework the references accordingly. Use a referencing software.
|
The authors appreciate this observation and have addressed the repetitions by using the Zotero tool for referencing. |
AUTHORS' RESPONSE TO THE REVIEWER'S ISSUES AND CONCERNS
|
|
REVIEWERS CONCERNS |
AUTHORS REBUTTAL |
|
|
Line 78-80, the sentence does not make sense, it needs rephrasing.
|
The authors have amended the sentence to be more precise to read ‘Investigating the untargeted metabolome profiles of common beans affected by viral diseases can enhance our understanding of the plant's stress response mechanisms and overall plant health.’ See lines 78-80 |
|
|
Line 210-212 could be incorporated into the results section before table 1, as the figure explains the same trends as Table 1. Provided more interpretation is included from Figure 2.
|
We concurred with the advice and subsequently moved the results just before Table 1 see lines 214-215 |
|
|
Figure 2, the y-axis is confusing. Is the numbers on represented as number of genes per pathway, or fold change? Interpret the figure title in detail, if its not explained in the text.
|
The authors have corrected the Figure legend to read ‘The upregulated and downregulated pathways, along with the number of metabolites per pathway, are shown on the Y-axis, with the four counties studied represented on the X-axis’ to remove the ambiguity see Figure lines 220-221 |
|
|
Line 227, why is Figure 3B cited before 3A?
|
We have corrected and cited Figure 3A first before Figure 3B as observed in lines 223 and 226 |
|
|
Line 230, the letter A is missing.
|
We have inserted the letter A see line 247 |
|
|
The authors still did not interpret the data of the volcano plots. Why did they show the volcano plots? what do they explain in terms of the data? There is a lot of data that can be extracted from the volcano plots: Eg, No of downreg and upreg metabolites within and between the counties; fold change differences, non-significant metabolites, what does this data mean in detecting diseases?
|
The authors appreciate the reviewer's observation, which enriches the results and overall output of the paper, and subsequently interpreted the volcano plots as shown in lines 233-246. As a result, the authors enhanced the discussion by incorporating these findings into the discussion and conclusion, as seen in lines 437-464 and 545-546, respectively |
|
|
Line 237-238, the authors are citing Figure 5, is it A or B? If its A, why is Figure 5B not cited in the study?
|
The authors considered this observation from the reviewer and have cited the figure in the text in line 264 |
|
|
Line 242, the authors still talk about differentially expressed genes, is there any data on DEGs that is missing here?
|
The authors noted this concern and have gone ahead to correct the word genes to metabolites see line 259 |
|
|
Line 242 and 243 is a repetition of words.
|
The authors have merged the two sentences to read Across the four sites, ten metabolites were commonly up-regulated, including those with the following mapping IDs: 2603, 2843, 3767, 3773, 6251, 8793, 8796, 9995, 10337, and 11308 see line 260-262 |
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Figure 6A and B are not cited in this study. |
The authors have cited the figures as observed by the reviewer see lines 263 |
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Rephrase the title of Figure 7, it still doesn't make sense and all over the place.
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The author have improved the legend of the figure to read Phytohormones extracted from diseased common beans in the Western region of Kenya (Kakamega, Bungoma, Vihiga, and Busia), involved in the plant defense mechanism, are shown on the Y-axis, with their concentrations normalized using the MinMaxScaler function from the sklearn.preprocessing module in Python represented on the X-axis see Figure 7 lines 282-285. |
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Line 383, are there two references or not?
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The authors have deleted the reference see line 400 |
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There is a repetition of your references throughout the whole list, rework the references accordingly. Use a referencing software.
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The authors appreciate this observation and have addressed the repetitions by using the Zotero tool for referencing. |
AUTHORS' RESPONSE TO THE REVIEWER'S ISSUES AND CONCERNS
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REVIEWERS CONCERNS |
AUTHORS REBUTTAL |
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Line 78-80, the sentence does not make sense, it needs rephrasing.
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The authors have amended the sentence to be more precise to read ‘Investigating the untargeted metabolome profiles of common beans affected by viral diseases can enhance our understanding of the plant's stress response mechanisms and overall plant health.’ See lines 78-80 |
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Line 210-212 could be incorporated into the results section before table 1, as the figure explains the same trends as Table 1. Provided more interpretation is included from Figure 2.
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We concurred with the advice and subsequently moved the results just before Table 1 see lines 214-215 |
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Figure 2, the y-axis is confusing. Is the numbers on represented as number of genes per pathway, or fold change? Interpret the figure title in detail, if its not explained in the text.
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The authors have corrected the Figure legend to read ‘The upregulated and downregulated pathways, along with the number of metabolites per pathway, are shown on the Y-axis, with the four counties studied represented on the X-axis’ to remove the ambiguity see Figure lines 220-221 |
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Line 227, why is Figure 3B cited before 3A?
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We have corrected and cited Figure 3A first before Figure 3B as observed in lines 223 and 226 |
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Line 230, the letter A is missing.
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We have inserted the letter A see line 247 |
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The authors still did not interpret the data of the volcano plots. Why did they show the volcano plots? what do they explain in terms of the data? There is a lot of data that can be extracted from the volcano plots: Eg, No of downreg and upreg metabolites within and between the counties; fold change differences, non-significant metabolites, what does this data mean in detecting diseases?
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The authors appreciate the reviewer's observation, which enriches the results and overall output of the paper, and subsequently interpreted the volcano plots as shown in lines 233-246. As a result, the authors enhanced the discussion by incorporating these findings into the discussion and conclusion, as seen in lines 437-464 and 545-546, respectively |
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Line 237-238, the authors are citing Figure 5, is it A or B? If its A, why is Figure 5B not cited in the study?
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The authors considered this observation from the reviewer and have cited the figure in the text in line 264 |
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Line 242, the authors still talk about differentially expressed genes, is there any data on DEGs that is missing here?
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The authors noted this concern and have gone ahead to correct the word genes to metabolites see line 259 |
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Line 242 and 243 is a repetition of words.
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The authors have merged the two sentences to read Across the four sites, ten metabolites were commonly up-regulated, including those with the following mapping IDs: 2603, 2843, 3767, 3773, 6251, 8793, 8796, 9995, 10337, and 11308 see line 260-262 |
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Figure 6A and B are not cited in this study. |
The authors have cited the figures as observed by the reviewer see lines 263 |
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Rephrase the title of Figure 7, it still doesn't make sense and all over the place.
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The author have improved the legend of the figure to read Phytohormones extracted from diseased common beans in the Western region of Kenya (Kakamega, Bungoma, Vihiga, and Busia), involved in the plant defense mechanism, are shown on the Y-axis, with their concentrations normalized using the MinMaxScaler function from the sklearn.preprocessing module in Python represented on the X-axis see Figure 7 lines 282-285. |
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Line 383, are there two references or not?
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The authors have deleted the reference see line 400 |
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There is a repetition of your references throughout the whole list, rework the references accordingly. Use a referencing software.
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The authors appreciate this observation and have addressed the repetitions by using the Zotero tool for referencing. |
Reviewer 2 Report
There are still minor details regarding the statement of the research objective. An objective is stated in the summary that does not match the one stated in the introduction. In turn, two objectives are stated in the introduction. In addition, the experimental design must be reviewed. After reviewing these details, the manuscript can be published.
Notes are made in the manuscripts regarding changes in the objective, so that the objective stated in the abstract agrees with the one stated in the introduction.
Comments for author File: Comments.pdf
Author Response
AUTHORS' RESPONSE TO THE REVIEWER'S ISSUES AND CONCERNS
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AUTHORS REBUTTAL |
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Line 93-94 The objective does not match the one in the abstract |
The authors have harmonized the objective with the one in the abstract to read ‘This study aimed to identify potential biomarkers for BCMV and BCMNV viral diseases by analyzing small molecule metabolites in diseased common bean systems and exploring the associated metabolic pathways’ see lines 93-95 |
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Line 98-102: Two objectives are being raised. Improve the approach to the research objective |
The authors have improved the objective to read(Allwood et al., 2021). By integration of these approaches, the objective was to encompass a comprehensive range of metabolites, particularly emphasizing the identification of novel entities. See lines 99-101 |
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Line 105-107: In addition to the coordinates it is necessary to know the soil, rainfall and temperature of the region |
The authors have added more information to the methodology by adding a statement to read Temperatures in Western Kenya range from 14°C to 18°C minimum to 30°C to 36°C maximum year-round, with the heaviest rainfall in April and lowest in January, averaging between 1,740 mm and 1,940 mm annually, while the soils, mainly acrisols (utisols) and ferralsols (oxisols), are highly weathered and suffer from widespread nitrogen and phosphorus deficiencies see lines 109-113 |
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Line 108 If RCBD was used how many replications |
The authored have improved the statement by adding three replications in line 114 |
AUTHORS' RESPONSE TO THE REVIEWER'S ISSUES AND CONCERNS
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REVIEWERS CONCERNS |
AUTHORS REBUTTAL |
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Line 93-94 The objective does not match the one in the abstract |
The authors have harmonized the objective with the one in the abstract to read ‘This study aimed to identify potential biomarkers for BCMV and BCMNV viral diseases by analyzing small molecule metabolites in diseased common bean systems and exploring the associated metabolic pathways’ see lines 93-95 |
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Line 98-102: Two objectives are being raised. Improve the approach to the research objective |
The authors have improved the objective to read(Allwood et al., 2021). By integration of these approaches, the objective was to encompass a comprehensive range of metabolites, particularly emphasizing the identification of novel entities. See lines 99-101 |
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Line 105-107: In addition to the coordinates it is necessary to know the soil, rainfall and temperature of the region |
The authors have added more information to the methodology by adding a statement to read Temperatures in Western Kenya range from 14°C to 18°C minimum to 30°C to 36°C maximum year-round, with the heaviest rainfall in April and lowest in January, averaging between 1,740 mm and 1,940 mm annually, while the soils, mainly acrisols (utisols) and ferralsols (oxisols), are highly weathered and suffer from widespread nitrogen and phosphorus deficiencies see lines 109-113 |
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Line 108 If RCBD was used how many replications |
The authored have improved the statement by adding three replications in line 114 |
AUTHORS' RESPONSE TO THE REVIEWER'S ISSUES AND CONCERNS
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REVIEWERS CONCERNS |
AUTHORS REBUTTAL |
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Line 93-94 The objective does not match the one in the abstract |
The authors have harmonized the objective with the one in the abstract to read ‘This study aimed to identify potential biomarkers for BCMV and BCMNV viral diseases by analyzing small molecule metabolites in diseased common bean systems and exploring the associated metabolic pathways’ see lines 93-95 |
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Line 98-102: Two objectives are being raised. Improve the approach to the research objective |
The authors have improved the objective to read(Allwood et al., 2021). By integration of these approaches, the objective was to encompass a comprehensive range of metabolites, particularly emphasizing the identification of novel entities. See lines 99-101 |
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Line 105-107: In addition to the coordinates it is necessary to know the soil, rainfall and temperature of the region |
The authors have added more information to the methodology by adding a statement to read Temperatures in Western Kenya range from 14°C to 18°C minimum to 30°C to 36°C maximum year-round, with the heaviest rainfall in April and lowest in January, averaging between 1,740 mm and 1,940 mm annually, while the soils, mainly acrisols (utisols) and ferralsols (oxisols), are highly weathered and suffer from widespread nitrogen and phosphorus deficiencies see lines 109-113 |
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Line 108 If RCBD was used how many replications |
The authored have improved the statement by adding three replications in line 114 |
AUTHORS' RESPONSE TO THE REVIEWER'S ISSUES AND CONCERNS
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REVIEWERS CONCERNS |
AUTHORS REBUTTAL |
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Line 93-94 The objective does not match the one in the abstract |
The authors have harmonized the objective with the one in the abstract to read ‘This study aimed to identify potential biomarkers for BCMV and BCMNV viral diseases by analyzing small molecule metabolites in diseased common bean systems and exploring the associated metabolic pathways’ see lines 93-95 |
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Line 98-102: Two objectives are being raised. Improve the approach to the research objective |
The authors have improved the objective to read(Allwood et al., 2021). By integration of these approaches, the objective was to encompass a comprehensive range of metabolites, particularly emphasizing the identification of novel entities. See lines 99-101 |
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Line 105-107: In addition to the coordinates it is necessary to know the soil, rainfall and temperature of the region |
The authors have added more information to the methodology by adding a statement to read Temperatures in Western Kenya range from 14°C to 18°C minimum to 30°C to 36°C maximum year-round, with the heaviest rainfall in April and lowest in January, averaging between 1,740 mm and 1,940 mm annually, while the soils, mainly acrisols (utisols) and ferralsols (oxisols), are highly weathered and suffer from widespread nitrogen and phosphorus deficiencies see lines 109-113 |
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Line 108 If RCBD was used how many replications |
The authored have improved the statement by adding three replications in line 114 |
AUTHORS' RESPONSE TO THE REVIEWER'S ISSUES AND CONCERNS
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REVIEWERS CONCERNS |
AUTHORS REBUTTAL |
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Line 93-94 The objective does not match the one in the abstract |
The authors have harmonized the objective with the one in the abstract to read ‘This study aimed to identify potential biomarkers for BCMV and BCMNV viral diseases by analyzing small molecule metabolites in diseased common bean systems and exploring the associated metabolic pathways’ see lines 93-95 |
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Line 98-102: Two objectives are being raised. Improve the approach to the research objective |
The authors have improved the objective to read(Allwood et al., 2021). By integration of these approaches, the objective was to encompass a comprehensive range of metabolites, particularly emphasizing the identification of novel entities. See lines 99-101 |
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Line 105-107: In addition to the coordinates it is necessary to know the soil, rainfall and temperature of the region |
The authors have added more information to the methodology by adding a statement to read Temperatures in Western Kenya range from 14°C to 18°C minimum to 30°C to 36°C maximum year-round, with the heaviest rainfall in April and lowest in January, averaging between 1,740 mm and 1,940 mm annually, while the soils, mainly acrisols (utisols) and ferralsols (oxisols), are highly weathered and suffer from widespread nitrogen and phosphorus deficiencies see lines 109-113 |
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Line 108 If RCBD was used how many replications |
The authored have improved the statement by adding three replications in line 114 |
Reviewer 3 Report
The manuscript is improved after revision.
All of my comments and suggestions were addressed.
Author Response
The reviewer raised no concern to respond to. However we appreciate his comments that have greatly improved the manuscript
