Transcriptome Sequencing Analysis of Birch (Betula platyphylla Sukaczev) under Low-Temperature Stress
Round 1
Reviewer 1 Report
The manuscript forests-892502 entitled "Transcriptome sequencing analysis of birch (Betula platyphylla) under low temperature stress" by Siyu Yan et al., deals about the transcriptomic analyses on birch leaves exposed to low temperature stress in order to detect differentially expressed genes in a time course experiment.
The experimental design looks well engineered, but the manuscript has serious flaws that makes me recommend the rejection of the paper in this form.
The main weakness is the English language: I am not feeling comfortable to provide a valuable review for a manuscript which is hard to follow, full of grammar mistakes and phrases without a sense. My task is to provide a review and not to edit proofs. Please edit extensively the English language and resubmit.
Other notes
1. abstract, line 12. please rephrase. Moreover, this statement is in contrast with what declared at line 81-82. How many replicates has the time point 1.5 h ? I would remove this statement in the abstract
2. introduction, line 35. please rephrase and fix the grammar.
3. line 72. change 'period' in 'time frame'.
4. Paragraph 2.1.
line 76. what do you mean with "birch tissue culture seedlings"?
line 78. suffered?
line 80-81. the composition of the samples and replicates must be better specified; it's not clear in this form. Again, check how many replicates have been used for the 1.5 h time point.
line 83. were samples surface disinfected? which was average leaves size? did you check dry weight? CTAB method needs a reference. Illumina HiSeq type must be provided: single/paired end? amplicon size? read length....
5. Paragraph 2.2.
specify the birch genome version used in this study
specify the STAR version (and the version of all the software and databases used in this study)
please include in the DEG discovery pipeline HTSFilter ( Rau A, Gallopin M, Celeux G, Jaffrezic F (2013). “Data-based filtering for replicated high-throughput transcriptome sequencing experiments.” Bioinformatics, 29(17), 2146-2152.), a package that implements a filtering procedure for replicated transcriptome sequencing data based on a global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions.
line 105. expand TF
line 111. specify the PCR machine
line 112. please rephrase! it's not a cooking recipe...
line 113. please rephrase!
6. Supplementary Tables and Figure are missing; I can't evaluate what is stated in Results (line 124). The legends for those items provided in 'Appendix' are too scarce.
7. line 127 here Authors say they used "HISAT2 to align the clean reads to the silver birch reference genome", while in M&M they said they used STAR...please clarify.
I didn't go further: There are too weak points to be fixed before to assume valid the results and discussion.
Author Response
Please see the attachment.
Author Response File: 
Author Response.docx
Reviewer 2 Report
Authors Yan et al. presented here manuscript entitled
„Transcriptome sequencing analysis of birch (Betula platyphylla) under low temperature stress“
Authors described a study of a transcriptome in seedlings of Betula platyphylla, exposed to lower temperatures.
The work showed roles of different genes in reaction of Betula seedlings on the cold stress. Authors also discussed differencies of observed up- and down- regulated genes in comparison with another plant species.
The work is interesting. Escecially the Discussion part is very properly written and explained.
However, I recommend to further enhance readability of the manuscript. Especially in Results, the text is clogged with names and abbreviations of genes. Such form of tabulation of results should increase clarity of the text.
Further comments:
Page 2, lines 72-73. Sentence „Our results will be further used for molecular breeding of birch species.“ has no further relation in the manuscript.
Page 2, line 89. In the sentence „All the Clean reads...“ should be „clean“ (non-capital).
Page 3, lines 102-105. Verb in the sentence beginning with „According to the highest ranking in the BLAST results...“ should be in the past tense.
Page 3, lines 107-108. Verb in the sentence beginning with „Screen out genes related...“ should be in the past tense.
Page 3, sentences in lines 112-114 should have verbs in the past tense.
Page 5, line 168: word „calmodulin“ in the middle of sentence should not be capitalised.
Page 5, lines 171-172: word „calcium“ in the middle of sentence should not be capitalised.
Page 6, Table 2, first two lines: missing „t“ in the word „dependent“
Page 6, Table 2: unite writing of capital letters
Page 7, Table 3, missing „t“ in the word „deficient“
Pages 8 - 9, Table 3: unite writing of capital letters
Pages 9 - 10, Table 4: unite writing of capital letters
Pages 11 - 12, Table 5: unite writing of capital letters
Pages 12 - 13, Table 6: unite writing of capital letters
Page 13, line 253: „after plants“ is not correct formulation
Page 15, lines 296-297: word „calmodulin“ in the middle of sentence should not be capitalised
Page 17, lines 395-396: The last sentence of the paragraph is not correctly formulated.
Page 17, line 401: phrase „inseparable from“ should be replaced with some better expression, like „connected with“.
Author Response
Please see the attachment.
Author Response File: Author Response.docx
