Review Reports

Round 1

Reviewer 1 Report

The present work “Comparative transcriptome analysis provides insights into the seed germination in cotton in response to chilling stress”  by Shen et al. describes transcriptomic comparison between two cotton varieties (cold-tolerant variety KN27-3 and susceptible variety XLZ38).   During germination 7535 DEGs were identified and  among them were  enriched  those   involved in energy metabolism. Fuethermore hormone content measurements and the related gene expression analysis indicated that IAA,  CTK and GA3 may promote germination of the cold-tolerant variety.

The work is well written and sound well and it is worthy of publication after minor revision

Minor issues:

1) in the abstract  to show  data regarding hormone content measurements

2) Fig 1 b, to change  bar chart color (to use the same colors  as in c and d)

 

Author Response

Thank you for your suggestions. All your suggestions are very important for my
manuscript writing and research work. According to the deficiencies and shortcomings proposed by the experts, we have made detailed modifications to the corresponding positions of the manuscript. In the response manuscript, revisions were clearly highlighted using "Track Changes". Thanks again for your suggestions, and hope to learn more from you.

Point 1: In the abstract to show data regarding hormone content measurements

Response 1: Thank you for your valuable suggestions, which have been modified in the abstract section on line 33-39. Added description of hormone content measurements. The content of auxin (IAA), cis-zeatin riboside (cZR), and trans-zeatin riboside (tZR) in KN27-3 are higher than that in XLZ38 at five stages (from 12 h to 54 h). GA3 was expressed at a higher level in KN27-3 from 18 h to 54 h post imbibition compared to that in XLZ38. And abscisic acid (ABA) content of KN27-3 is lower than that in XLZ38 at five stages. Results from hormone content measurements and the related gene expression analysis indicated that IAA, CTK and GA3 may promote germination of the cold-tolerant variety, while ABA inhibits it.

Point 2: Fig 1 b, to change bar chart color (to use the same colors as in c and d)

Response 2: Thank you for your suggestion, bar chart color has been modified.

Reviewer 2 Report

I have  one concern. I found somehow misleading the description of  how biological replicate were carried out and clarification is needed. Namely, Authors in M&M section and figure legend  refer to three replicates, but at page 3  lines 112-113 they stated that :<>.  I am wondering whether replicates were processed together for transcriptome analysis.   If so, qRT-PCR  analysis  to validate RNA-seq data would have been necessary.

Author Response

Thank you for your suggestions. All your suggestions are very important for my
manuscript writing and research work. According to the deficiencies and shortcomings proposed by the experts, we have made detailed modifications to the corresponding positions of the manuscript. In the response manuscript, revisions were clearly highlighted using "Track Changes". Thanks again for your suggestions, and hope to learn more from you.

Point 1: I have one concern. I found somehow misleading the description of how
biological replicate were carried out and clarification is needed. Namely, Authors in M&M section and figure legend refer to three replicates, but at page 3 lines 112-113 they stated that :<>. I am wondering whether replicates were processed together for transcriptome analysis. If so, qRT-PCR analysis to validate RNA-seq data would have been necessary.

Response 1: Thank you for your valuable suggestions. There is indeed a misleading information in the interpretation of biological replicates. Replicates are “three independent biological replicates”, not processed together for RNA extraction and RNA-Seq analysis. Description at page 3 lines 112-113 has been modified as follows. 

In order to understand the reasons for the different chilling resistance in the two
cotton varieties, samples at five imbibition time points were harvested for RNA
extraction and RNA-Seq analysis. At each time point, three biological replicates were designed in both two varieties, and embryo at five imbibition time points of were collected. A total of thirty samples were obtained.