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Thank you for addressing the remaining concerns of the reviewer and for amending your manuscript accordingly. The revised manuscript is acceptable now.
[# PeerJ Staff Note - this decision was reviewed and approved by Julin Maloof, a PeerJ Section Editor covering this Section #]
Please note that the Section Editor has several issues and queries that need to be addressed:
1) "Comprehensive" should be removed from the title. No study is comprehensive.
2) The title and the abstract overstate the conclusions. Because this is an observational study the analysis here generates hypotheses about how JA may mediate salt sensitivity but does not prove them. The Conclusion section gets this right, the abstract (e.g. line 52) and title do not.
3) Was FPKM or raw counts used as input to DEseq?
4) Please indicate the number of biological replicates in the methods.
5) line 51 in the abstract is hard to understand (too many "throughs") "Taken together, JA-mediated salt-responsive genes expression through transcriptional regulation through transcription factor and post-transcriptional regulation through AS"
6) The K-means clustering (Figure 2) needs to be reconsidered. Why only 2 clusters? It is clear that both clusters have transcripts that are up and down regulated in each condition (that is why there are peaks and troughs for each condition in both plots. Repeat this with a larger K to get meaningful separation.
Please address the remaining concerns of the reviewer and revise the manuscript accordingly.
The author has agreeably amended the manuscript as reviewed previously. The literature has been provided with sufficient recent references to support the study conducted and the language of the manuscript has also been improved.
The suggestions has been agreeably added in the section of experimental design. The methods has been described with sufficient detail along with their proper references cited.
All required data has been provided. The study has been concluded well.
Nil
1) Writing has improved significantly but it needs some more work. For example, in the abstract section, in line 42,” Venn diagram and expression pattern of DEGs indicated that JS further or specifically altered a series of genes 43 expression based on salt treatment, implying the roles of JA in priming salt tolerance”, the phrase”further or specifically” has to be modified. Please go through the article one more time and make sure that it is devoid of any obvious errors.
2) In line 208, “There were 4,286 and 2,896 genes were significantly regulated by salt and JA treatment, respectively…..indicate that those number of genes were differentially regulated when compared to control.
3) Authors state in line 223 that "As shown in table S3, there were 74 genes were upregulated by salt stress, which were compromised by JS treatment. Meanwhile, 28 genes down-regulated by salt stress were upregulated in S_vs_JS analysis, such Fe-Mn superoxide dismutase. Based on the venn diagram there seem to be 49 more genes common between C_vs_S and S_vs_JS. My guess is that the direction of those genes in terms of upregulation of downregulation is common between the two comparisons. Can you comment on those “49” genes?
4) In fig 1D, and 1E, can the authors mark the some of the key genes that are differentially expressed between the two groups. For example, a gene that is upregulated upon Salinity treatment relative to control , which is then downregulated upon JS treatment.
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Please address the concerns pointed out by the reviewers and revise the manuscript accordingly.
[# PeerJ Staff Note: Please ensure that all review and editorial comments are addressed in a response letter and any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate. #]
[# PeerJ Staff Note: The review process has identified that the English language must be improved. PeerJ can provide language editing services - please contact us at copyediting@peerj.com for pricing (be sure to provide your manuscript number and title) #]
1. Please check for grammatical mistakes in introduction portion as well as in discussion of results, as the prepositions are wrongly used in some sentences which have completely changed the meaning of some lines.
1. The paper still needs to be revised thoroughly. The author hasn’t mentioned the name of the institute from which seeds were procured for experimental work.
2. The analysis of main nutrient elements in the experimental soil viz. contents of total organic matter, nitrogen, phosphorus etc. hasn’t been mentioned, which is requisite for comparison and discussion of results.
3. The Humidity range and RH value of growth chamber is not mentioned.
4. How did the author select to work with the mentioned concentration of Jasmonic acid?
No comments
No Comments
In this article Yang et al., perform RNA-seq to better understand how Jasmonic acid(JA) mediates salinity tolerance in alfalfa. They report differences in transcriptomes between different conditions including salt treatment (S) and JA + salt (JS). They further note the pathways to which the differentially expressed genes belong and report the occurrence of alternative splicing (AS) by salt treatment and JS treatment. The RNA-seq data provided here will be useful for the research community to further dissect the pathways involved in alfalfa tolerance to salt treatment. However, the writing needs a good amount of work before it is published. Further, the organization and quality of the figures must be improved.
Comments:
1) The text is very difficult to read. This severely impairs a easy reading and comprehension of the manuscript. Some examples where the language could be improved include lines 39, 42, 47, 73, 75, 83, 96, 118, 206, 207,208, 214. I highly recommend having a colleague proficient in English and familiar with the subject matter review your manuscript, or contact a professional editing service.
2) In fig 1, having a venn diagram representing differentially expressed genes (not separating upregulated and downregulated) C vs S, S vs JS, and C vs J, and J vs JS will be informative. This would give a better representation of the genes that are common for different comparisons.
3) Volcano plots representing the different comparisons with p-values and log fold change and marking the important genes would be valuable representations of the data. This could substitute the bar graph in figure 1C.
4) The legend for the heat map in figure 1D needs more clarity and explanation. I am assuming the brackets on the top represent different comparisons but how they represent the data is not clear. In addition to this, what are groups 3 through -3. I am assuming those are expression levels.
5) Resolution of figures 3 and 4 must be improved.
No comments
1) The last sentence of abstract states “Subsequently, JA enhanced alfalfa salt tolerance by maintaining energy supplying and enhancing antioxidant.” One cannot come to this conclusion based on RNAseq and PCR data without additional experiments. I recommend that the authors either rephrase or remove this statement. Similar statement is made in line 337.
2) In line 215, set of DEGs uniquely induced by JS were mentioned. Can the authors also talk in detail about the genes that are differentially expressed both by and S and JS treatments but in opposite directions?
3) Lines 310 to 314 need clarification. Authors mention that the genes related to hydrogen peroxide are not enriched in JS versus S. However, the discussion around this statement is not clear.
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