HSP70 Gene Family in Brassica rapa: Genome-Wide Identification, Characterization, and Expression Patterns in Response to Heat and Cold Stress
Round 1
Reviewer 1 Report
The paper is nicely written and coherence is there throughout. Authors have properly made the framework and worked on it.
Still, few comments will improve the MS.
Thinking for the future: Phytoextraction of Cd using primed plants for sustainable soil clean-up
In this write cadmium rather than Cd
First use of cadmium must be accompanied by (Cd)
Edit “Limiting factor of phytoextraction is often limited”….repeated use of limited
‘Presented review focuses’ must be……………………….In this review,….
Citation missing in ‘In organic rich waters sorption of Cd by humic substances plays important role in speciation of Cd and its content in water is in the opposite direction of the organic matter content.’
And
‘Difference between these two pathways (apoplastic and symplastic) is mainly that apoplastic transport requires no energy and Cd ions passively move through different root parts to get to xylem with water containing Cd ions moving through free spaces along the cell walls and intercellular spaces, while symplastic movement is an active process and includes movement through cell cytoplasm and plasmodesmata.’
Apostrophe in “such protein carriers’………..” and “An increase of heavy metals’”
Species name must be in Italics. Plz check throughout
Write Nine in place of 9…..’ who in parallel studied 9 different phytohormones,’
Redundancy in some parts which matches with the conclusion. Plz check
In this introductory lines “The term priming in plant physiology is used for a process of short-lasting preconditioning/pre-treatment of plants using different biological or chemical agents………”. If the authors think the below citation is relevant, it may be cited as pretreatment and preconditioning is there……..
Pretreatment of seeds with thidiazuron delimits its negative effects on explants and promotes regeneration in chickpea (Cicer arietinum L.). Plant Cell Tiss Organ Cult 133, 103–114 (2018).
Nowdays nanoparticles are also used for soil clean up, which is discussed in
Silver Nanoparticle’s Toxicological Effects and Phytoremediation. Nanomaterials 2021, 11, 2164. https://doi.org/10.3390/nano11092164 and may be used
The paper is nicely written and coherence is there throughout. Authors have properly made the framework and still, few comments will improve the MS.
HSP70 Gene Family in Brassica rapa: Genome-wide Identifica- 2 tion, Characterization, and Expression Patterns in Response to 3 Heat and Cold Stress.
-its protparam…..not ProtParm tool
-Check throughout in MS… B. rapaHSP70. Somewhere its written different
-In table 1….again Brapa? Plz change
-in table Table 2. Ka/Ks values of B. rapaHSP70 duplicated genes…..Ka-Ks is in table…edit it
-In Predicted three-dimensional structure of HSP70 genes in B. rapa.What striking difference was seen?
Edit in Figure 7. ‘Smart graphical illustration of miRNAs targeting the HSP70 genes in B. rapa’, Brapa written in column on left side.
The bioinformatic analsysis and modelling, RT PCR etc. is in paper below, and it may be cited
Comparative structural modeling of a monothiol GRX from chickpea: Insight in iron–sulfur cluster assembly, 2012, International journal of biological macromolecules 51 (3), 266-273
Please elaborate and emphasise what differential results were observed in heat and cold stress?
In ‘In our study, we found that Bra-miR162, Bra- 386 miR165, Bra-miR172, Bra-miR316, Bra-miR375, Bra-miR396, Bra-miR397, Bra-miR408, 387 Bra-miR858, Bra-miR5714, and Bra-miR5717 families targeted the B. rapaHSP70 genes (Ta- 388 ble S3).’………will it be Brapa or Bra?
Please elaborate the conclusion and findings of your study
Overall a nicely written paper and English is good
Author Response
Please see the attachment
Author Response File: 
Author Response.pdf
Reviewer 2 Report
This article discusses the HSP70 gene family in Brassica rapa. With the help of genome-wide identification and characterization, they have discovered a total of 28 genes from the family. They have performed phylogenetic analysis, synteny analysis, chromosomal localization, gene duplication analysis, chromosomal localization, promoter analysis, 3D structure prediction, miRNA-associated HSP70 genes, expression profiling of HSP70 genes in various tissues and expression of HSP70 genes in response to heat and cold stress.
There are several mismatches between figures and results. Here are a few suggestions about the article below:
1. In line 94, the link for the BRAD database is not mentioned.
2. Throughout the article, different styles of writing, B. rapaHSP70 are followed (in italics, with space, without space, etc.).
3. As per Fig. 2, minimum genes are present on chromosomes A02, A04, and A05, not only (Line 138) A02 and A05.
4. For the location of protein (as per table 1), 3 proteins are localized in the nucleus and 5 in ER but the result states, 6 on the endoplasmic reticulum, and 2 on the nucleus (line 140).
5. The comparative phylogenetic tree (Fig. 3) does not match the mentioned results of different subgroups and the number of genes present in them.
6. For expression pattern of genes, the results mentioned does not match with the Figure (Fig. 9).
7. An elaborate explanation is required for predicted structures.
8. How many replicates were used for gene expression analysis? Statistical analysis of qRT data is required.
Author Response
Please see the attachment
Author Response File: Author Response.pdf
Reviewer 3 Report
1. Which program of BLAST (blastp or blastn) is used during the identification of genes?
2. What database of Brapa (either nucleotide or protein) was used to blast against the AtHSP genes?.
3. The exact E value must define for better search.
4. Here Pfam database is mentioned but, how and from which tools confirmation of genes was done? HMMER profiling of PF00012 should mention.
5. Any tools did not use to check the domain of the HSP70 gene like SMART or NCBI CD search, here MEME is mentioned but MEME uses for only MOTIF analysis.
6. Which sequence of HSP gene is used during GSDS analysis should mention (either coding sequence or DNA)
7. The figure1 is not clear (picture quality is not that good)
8. Tools for mapping genes on the chromosome are not mentioned.
9. The second point of the result (Evolutionary relationship of B. rapa HSP70 gene ), described groups in figure 3 is not correct. In figure 3, there are only 5 groups (A, B, C,D, and E) but in the writing section authors mentioned the F group which is not shown in Figure.
10. In the third point of result analysis of B. rapaHSP70 gene duplication and Ka/Ks analysis, the naming of the genes in figure 4A and the description of the figure are not matching and the same for the 4th point of result analysis i.e. Segmental duplication and synteny analysis of the BrapaHSP70 gene family among closely 189 related species.
11. The methods for prediction of the 3D structure of proteins should mention (homology modelling or ab initio modelling or threading or fold recognition method).
12. In line 215, the Figure number is not correct.
13. In the seventh point of result analysis (Genome-wide analysis of miRNA-associated B. rapaHSP70 genes), again the figure and what they have written in the result is not matching. For e.g. they found that six miRNAs 238 from different families targeted one gene, B. rapaHSP7022 but B. rapaHSP7022 is not shown in figure 7.
Author Response
Please see the attachment
Author Response File: Author Response.pdf
Round 2
Reviewer 2 Report
Authors have responded all points.
Reviewer 3 Report
The author has modified the manuscript according to the suggestions. can be accepted with modified version.
