Transcriptome Analyses Reveal the Mechanism of Changes in the Sugar Constituents of Jujube Fruits under Saline–Alkali Stress
Round 1
Reviewer 1 Report
The current study report interesting findings on jujube fruit sugar transcriptome. Following points need to be addressed before its publication.
English revisions are needed for more precision and for comprehensive presentation: As in abstract: L 16-18: Rephrase, repetition L 22-25: Rephrase. Similarly, the whole manuscript should be revised.
Introduction, should incorporate previous transcriptome studies related to this study and similarly genes comparison of this study with previous studies specially those are related to sugar metabolism.
In which repository the RNA-Seq data was deposited? Provide RNA Seq data submission number.
Figures text is not clear. Particularly, Figure 3, 4, 5 and 6.
In figure 3B, PCA can be more elaborative if sign annotation is clear as in Figure 1, it’s easier to grab the salinity level and DAF. In PCA grouping is difficult to understand.
Regarding DEG, information regarding DEGs among LS and HS are not highlighted. It would be interested to know this difference and also to know whether these are different or common as are among CK and HS? Similar deviation is present n figure 2, sucrose and total sugar content at 110 DAF. How would you explain it?
For qPCR, only glucose metabolism related genes were selected? Any particular reason of not adding others as for sucrose or fructose metabolism genes? While you are reporting that sucrose metabolism is of utmost important for this plant.
For genes that have similar level of expression at CK and HS and different (higher or lower LOC 107422414, LOC107435337 ) at LS, how would you explain this difference. As instead of gradual increase or decrease from CK to HS, LS level deviates.
English editing is needed as only in abstract, repetition of concept is present at two locations.
Author Response
Response to Reviewer 1:
Many thanks for the reviewer’s wonderful summary and comments on our manuscript. Accordingly, we have made changes upon the comments and substantially improved the manuscript. All changes were marked in red, and we hope this reviewer will be satisfactory with this revision.
- English revisions are needed for more precision and for comprehensive presentation: As in abstract: L 16-18: Rephrase, repetition L 22-25: Rephrase. Similarly, the whole manuscript should be revised.
Response: Thanks for your wonderful suggestion. We have revised the text to address your concerns and hope that it is now clearer(Lines 18-20, Lines 23-28).
- Introduction, should incorporate previous transcriptome studies related to this study and similarly genes comparison of this study with previous studies specially those are related to sugar metabolism.
Response: We thank the reviewer for pointing this out. We added studies related to the transcriptome and sugar metabolism(Lines 80-93).
- In which repository the RNA-Seq data was deposited? Provide RNA Seq data submission number.
Response: The RNA-Seq data were deposited at the NCBI, and RNA Seq data number is SUB13756193.
- Figures text is not clear. Particularly, Figure 3, 4, 5 and 6.
In figure 3B, PCA can be more elaborative if sign annotation is clear as in Figure 1, it’s easier to grab the salinity level and DAF. In PCA grouping is difficult to understand.
Response: Thanks for your wonderful suggestion. Figure 3,4,5 and 6 are remade to make the symbol annotation clearer.
- Regarding DEG, information regarding DEGs among LS and HS are not highlighted. It would be interested to know this difference and also to know whether these are different or common as are among CK and HS? Similar deviation is present n figure 2, sucrose and total sugar content at 110 DAF. How would you explain it?
Response: Thanks for your wonderful suggestion. We have not previously focused on the differential information for LS and HS. Following your suggestion, we have added this content. The results indicate that DEG in LS and HS gradually increased with fruit development, and the regulation a different rules between CK and LS，as do HS(Lines 218-222).
- For qPCR, only glucose metabolism related genes were selected? Any particular reason of not adding others as for sucroseor fructose metabolism genes? While you are reporting that sucrose metabolism is of utmost important for this plant.
Response: It was my mistake. It should be ‘12 sucrose metabolism-related genes were randomly selected for quantitative reverse transcription-polymerase chain reaction (qRT-PCR) validation’. We have modified the response in the text(Lines 297-299).
- For genes that have similar level of expression at CK and HS and different (higher or lower LOC 107422414, LOC107435337 ) at LS, how would you explain this difference. As instead of gradual increase or decrease from CK to HS, LS level deviates.
Response: Thank you very much for raising this question. This question is interesting, and for the interpretation of this question, it is possible that mild salinity stress promotes or suppresses the expression of some genes, thus increasing or decreasing the synthesis of some substances. With the increase of stress, the regulation of genes changed, and the synthesis of related substances also changed, as the changes of glucose, fructose and sucrose in the different salinity stress treatments.
We would like to thank the referee again for taking the time to review our manuscript.
Author Response File: 
Author Response.doc
Reviewer 2 Report
Wang et al., present transcriptome analysis of how jujube fruit responds under Saline-alkali stress. The authors argue that mild stress improved the sugar content while the higher stress significantly decreased the accumulated sugar. The study is conducted well, but the structure of the MS needs some changes before it is suitable for publication
Line 35- Introduction first line needs rephrasing
Figure 1- All abbreviations and their full form should be mentioned in the legend for this figure and all others. Also all abbreviations should be written full when they first appear in the text for example in the result section.
Line 158- “fruit samples were available among treatments” - not clear what was available here. This should be clearly explained.
Line 165- what is collocation analysis?
Figure 3A Panel is not all clear. Authors need to provide a high resolution figure for this panel. Also the resolution of all other figures need to be checked too. Most figures are not all easy to read. Also figures need to have better explained legends. All abbreviations should be listed and explained in full.
Line 196- what is corepresentation network
Figure 4- Panel C is not readable at all. Authors need to provide better figures.
Line 241-253: It is not clear what authors are trying to convey in this part of coexpression network analysis. Can the authors simplify the text and convey clearly why and how this analysis was done and why this is important for this study.
Line 261- Section 2.7 is about qRT-PCr validation of the RNA-seq data. Can the authors explain if the qRT-PCR validation was done with the independent RNA samples or the same as used for RNA-seq. Because if the samples were the same, it is very likely the correlation would be high.
Line 273- Discuss is too vague. The authors need to rewrite discussion and focus more on their results and compare it to what is known from previous studies. Several part of discussion is repetitive from the introduction section.
Methods section should include all relevant full form. Table 2 should be moved to the supplemental table.
All the English of the manuscript needs some proof reading.
The quality of English at some places needs some consideration. The use of some words for eg, excavate need attention.
Author Response
Response to Reviewer2:
Many thanks for the reviewer’s wonderful summary and comments on our manuscript. Accordingly, we have made changes upon the comments and substantially improved the manuscript. All changes were marked in red, and we hope this reviewer will be satisfactory with this revision.
- Line 35- Introduction first line needs rephrasing
Response: Thanks for your wonderful suggestion. We have done this change (Line 37).
- Figure 1- All abbreviations and their full form should be mentioned in the legend for this figure and all others. Also all abbreviations should be written full when they first appear in the text for example in the result section.
Response: We apologize if the original figure 1 did not show clearly, we have modified the chart and hope to see what is in the chart clearly now(Line 130, 132,139, 152, 168).
- Line 158- “fruit samples were available among treatments” - not clear what was available here. This should be clearly explained.
Response: It indicating that the data of fruit samples were dependable among treatments.
- Line 165- what is collocation analysis?
Response: We have made the change. The new sentence reads as follows. ‘A total of 31,718 genes were obtained after analysis with data filtering and quality control’(Line 194-195).
- Figure 3A Panel is not all clear. Authors need to provide a high resolution figure for this panel. Also the resolution of all other figures need to be checked too. Most figures are not all easy to read. Also figures need to have better explained legends. All abbreviations should be listed and explained in full.
Response: We apologize if the original figure 3A Panel did not show clearly, we have modified the chart and hope to see what is in the chart clearly now.
- Figure 4- Panel C is not readable at all. Authors need to provide better figures.
Response: We apologize if the original figure 4- Panel C did not show clearly, we have modified the chart and hope to see what is in the chart clearly now.
- Line 241-253: It is not clear what authors are trying to convey in this part of coexpression network analysis. Can the authors simplify the text and convey clearly why and how this analysis was done and why this is important for this study.
Response: Thank you very much for raising this question. We have revised the text and hope that it is now clearer. What we want to say is that hub genes controlling sucrose content by co-expression network analysis are clustered into a class, and the hub genes controlling sucrose clustered increased with the fruit develops and saline–alkali stress. (Line 269-275).
- Line 261- Section 2.7 is about qRT-PCr validation of the RNA-seq data. Can the authors explain if the qRT-PCR validation was done with the independent RNA samples or the same as used for RNA-seq. Because if the samples were the same, it is very likely the correlation would be high.
Response: Thank you very much for raising this question. qRT-PCR validation was done with the same sample as used for RNA-seq.
- Line 273- Discuss is too vague. The authors need to rewrite discussion and focus more on their results and compare it to what is known from previous studies. Several part of discussion is repetitive from the introduction section.
Response: Thanks for your wonderful suggestion. We have revised the text and hope that it is now clearer(Line 315-406).
- Methods section should include all relevant full form. Table 2 should be moved to the supplemental table.
Response: We thank the reviewer for pointing this out. We agree with the reviewer and have revised.
- All the English of the manuscript needs some proof reading.
Response: Thanks for your wonderful suggestion. We conducted a comprehensive English proofreading.
We would like to thank the referee again for taking the time to review our manuscript.
Author Response File: Author Response.doc
Round 2
Reviewer 1 Report
Dear Authors,
You have improved the several section of manuscript. Still two important aspects that need to be addressed are:
Improvement of figures: quality should be improved. Legends and axis are not legible.
Thorough improvement of language.
Bests
Thorough improvement of language is still needed.
Author Response
Response to Reviewer 1 (Round 2):
We are pleased to submit the revised draft of our manuscript. We appreciate the time and effort dedicated by the editorial staff and reviewers. The comments provided were valuable and helped us refine our paper. As such, we have made several revisions to the manuscript based on the suggestions given. We hope this reviewer will be satisfactory with this revision.
Below are our point-by-point responses to the reviewers’ comments.
- Improvement of figures: quality should be improved. Legends and axis are not legible.
Response: Thank you very much for raising this question. We apologize if the original figure did not show clearly, we have modified the chart and hope to see what is in the chart clearly now(Line 306).
- Thorough improvement of language.
Response: Thanks for your wonderful suggestion. We conducted a comprehensive English proofreading.
We would like to thank the referee again for taking the time to review our manuscript.
