Genome-Wide Identification and Characterization of Hsf and Hsp Gene Families and Gene Expression Analysis under Heat Stress in Eggplant (Solanum melongema L.)

Round 1

Reviewer 1 Report

The manuscript “Genome-wide identification and characterization of Hsf and 2 Hsp gene families and gene expression analysis under heat 3 stress in eggplant (Solanum melongema L.)” is based on innovative research and provides novel knowledge about the genome-wide 87 identification of the Hsf and Hsp genes in eggplant to infer their 88 expansion and evolutionary history. The paper is well written with a clear approach towards the identification of eggplant genome in relation to the role of Hsf and Hsp genes under heat stress.

 

Title: The title is fine and supports the arguments which have been addressed in this research.

Abstract:

Line 17: Replace “thermotolerant” with “thermotolerance”.

 

Keywords: Keywords are well explanatory.

Introduction

The overview of the introduction is fine, but the authors have mentioned some additional and irrelevant details which are not related to the topic, specifically the classification of Hsps. This section needs to be very precise with more relevant literature. Following are some of the major points that need to be addressed:

Line 55: Italicize the names of the genes

Materials and Methods

The methodology designed for the proposed experiment is a bit complicated, which statistical software was used to analyze the data? Please mention.

Results and Discussion

Line 170: What was the reason for comparing Hsf and Hsp gene families in eggplant with rice as it's an agronomic crop? Justify with scientific reasoning.

Line 372-373: There is no need to add it here.

Conclusion

The author should include and suggest the future prospects of the proposed study and pertaining results.

References

Few of the references are not properly formatted. Please refer to the author's guidelines provided by the journal.

Good Luck

Author Response

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Reviewer 2 Report

The manuscript is well written and clearly describes the different Hsp and Hsf genes expressed under heat stress in Eggplant. 

I think the author understates the significance of this research, in terms of the broader implications of heat stress proteins found in egg plant with other solanaceous crops. If the authors can expand more on this area rather than focus on the numbers of Hsp, Hsf etc.. it would be more useful to the readers

Author Response

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Author Response File: Author Response.docx

Reviewer 3 Report

Gong et al. have set out to characterize the size and expression profiles of the genes for the major heat-shock protein (HSPs), and the transcription factor believed to control them, in eggplants.  To do this, they searched the published eggplant genome for BLAST-annotated sequences matching the known HSPs of Arabidopsis.  After discussing the relationships of each member of each family to the others, they extracted RNA from two lines of eggplant, one showing tolerance, and one showing sensitivity, to 42 C treatments.  The researchers were extremely careful to use matched leaves for each RNA extraction.  These samples were then analyzed using qPCR to assess the timing of gene induction of 11 [or 12?] different genes.

 

The paper is well organized, and for the most part free of typographical or grammatical errors.  The few that I recognized, as well as comments on the design, are listed below:

 

Line 17: change thermotolerant to thermotolerance;

Lines 34-35: I would rearrange the sentence to read: “Plants live in complex environments where multiple abiotic stresses such as salt, drought, and extreme temperature may seriously restrict their growth and development. ”;

Line 319: they say they tested 11 genes, but it looks like they report on 12 in Fig. 5.  Could they clarify?

Line 326: could they say in the legend what the triangles represent?

Line 346: delete the extra parentheses ();

Line 349: I am not sure what the phrase “the same events” means.  Please change.;

Line 408: perhaps say, “not just involving Hsfs”;

Line 415: I didn’t understand the term, “instantaneous structural conservation”;

All supplemental figures: I believe the spelling should be “neighbor”.  You should check with the journal.

 

Additional concerns:

 

1. Based purely on personal experience, I have found that it is not always wise to assume that genomes based on 454 and Illumina data are wholly reliable. The authors found a fair amount of HSPs smaller (as small as 85AA for Hsc70; 137AA for Hsp90) or larger (as large as 1476AA for Hsp70; 1971AA for Hsp100) than the canonical sizes. Perhaps these are correct, but perhaps they are chimeric genes created in silico by misassembly.  The increased size of some gene families could be due to these kinds of errors.

 

If they are correct, I would expect 1) they could be verified by PCR and sequencing, and 2) could be present in some other Solanum spp.  Since the large HSPs are among the most conserved classes of genes, perhaps the authors could search for their homologs in eggplants relatives like S. torvum, S. lycopersicum, S. tuberosum, etc.  If they are real, and unique to eggplant, there is an interesting story there to pursue. (the fact that 2 other groups (line 383) studying poorly related plants also showed truncated proteins didn’t seem convincing precedence to me.)

 

2. The authors studied 2 eggplant lines differing in heat tolerance. I think it is important to know 1) how much do they differ in their tolerance (some kind of lab demonstration would be very helpful), and 2) how related are they?  Were very different genes introduced during their creation, was one the product of outcrossing, or the result of long-term serial selection; did they have a common ancestor recently?

 

3. I didn’t follow the reasoning in line 211 relating family size and protein localization. Could the authors explain this further?

 

4. Line 275: I am unsure what is being said here. Could the authors just say “cooperate to carry out a common physiological process.”;

 

5. Figure 3 is quite attractive, but I feel it is too complex to be of any use. I would delete it.

 

6. Figure 4: I think the authors should adjust their color scale to show the range of colors in the heat maps. The scale in the lower rt is neither as green nor as red as some squares in the heat map.

 

 

 

 

 

Author Response

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