Genome-Wide Identification and Analysis of Cell Cycle Genes in Birch
Round 1
Reviewer 1 Report
This manuscript reports on 59 cell cycle genes including 17 core genes and their chromosomal positions in birch. This information is very important for science and useful to scientists. Therefore, it should be published. However, revision is needed to improve its English writing and correct typos. Followings are just some examples noted:
- A Space is missing between two words in many places.
- Citations should be given for Howard and Pelc (1953), Hunt (1980s), etc.
- Better words could be used. The “procedure” of cell cycle is the result of ……could be changed to “process” or “progression.”
- Incomplete phrases or sentences need to be filled with something. ….its use in industrial production and ornamental “?” “And use TBtools for visualization.”
- According to the starting position of B. pendula cell cycle gene on the birch chromosome, “we” use the TBtools software to determine the chromosome location image of the birch cell cycle gene. The sentence is not clear in conveying its meaning.
- Species name Betula platyphylla should be in italic.
Suggestion to authors:
You are doing important research for science because cell cycle genes belong to “essential genes” in all organisms. For your future research, I suggest that you expand the scope to include other essential genes (such as genes for photosynthesis, respiratory, and circadian rhythms, etc.) as well as genes for adaptation (responses to biotic and abiotic stresses). Once you map all these genes on chromosomes, the manuscript would be suitable for publication in the special issue “Mapping Essential Genes and Adaptation Genes Based on Genome Assembly and Annotation of Plants and Animals” in International Journal of Molecular Sciences (IJMS), another journal of MDPI (https://0-www-mdpi-com.brum.beds.ac.uk/journal/ijms/special_issues/Genome_Assembly)
Author Response
Thank you for your detailed comments on my article. I have made the corresponding amendments and hope to get your corrections.
Please see the attachment.
Author Response File: 
Author Response.docx
Reviewer 2 Report
I had difficulty reading this paper due to the English writing. Please have this paper re-edited before submitting.
Some examples:
1) Incomplete sentences:
And use TBtools for visualization.
2) Duplicated words and spaces:
... was downloaded from[13] from the public databaseof NCBI SRA.
3) Methods has very little information on processing:
The clean reads of each sample were obtained by filtering out reads of low quality.
The methods used for cleaning reads must be shown.
4) Single word sentence?
Results.
5) Capitalization is used mid-sentence. Is this 2 sentences? When you say "Could compute", does this mean it was used to compute or not?
RSEM could compute transcript abundance, estimating the number of RNA-seq fragments corresponding to each gene, Draw a heat map of the differential expression of cell cycle genes with the value of Log2 (TPM+1).3.
6) Section 3.2 is incomplete, it looks like it ends without a period and mid-sentence:
3.2. Chromosome distribution of cell cycle genes in B. pendula
Based on the genomic information of B. pendula, the chromosomal distribution of 59 B. pendula cell cycle genes was simply analyzed. According to chromosome location analysis, 59 B. pendula cell cycle genes are unevenly distributed on 14 chromosomes of birch
7) Headings needs to be spelled out. You can't use undefined acronyms in section headings. For example, I don't know what CDK and CYC mean.
8) I have no idea what is going on in these sentences. There is mid-sentence capitalization and the new sentence is not capitalized.
We identified 15 BpCDKs in the B. pendula genome, Constructed a phylogenetic tree for the BpCDKs(Figure 2a). reveal the evolutionary relationships within these groups.
Author Response
Thank you for your detailed comments on my article. I have made the corresponding amendments and hope to get your corrections.
Please see the attachment.
Author Response File: Author Response.docx
Reviewer 3 Report
Dear Authors,
Reviewer comments forests-1493634
The manuscript entitled „Genome-wide identification and analysis of cell cycle genes in Betula pendula“ represents a valuable comprehensive study on cell cycle genes in Betula bendula including their structural (basic protein characteristics such as number of amino acids, molecular weight, isoelectric point (PI), instability index, grand average of hydropathicity, domain analysis, phylogenetic tree construction) and expression characteristics including expression patterns in major organs including flower, leaf, root and xylem as shown in Figure 7 based on the publicly available data from an RNAseq experiment.
The manuscript thus represents a purely bioinformatics study which provides useful and comprehensive information on cell cycle related genes in Betula pendula based on exploitation of publicly available data on birch genome and RNAseq studied transcriptome in the previous studies.
I can recommend the manuscript publication due to the fact that the manuscript provides complex data on birch cell cycle related genes in a comprehensive way.
I have only a few minor formal comments on the present mansucript version which are provided below:
Materials and methods:
Appropriate web page address and date of access have to be added to the Betula pendula genomic data source mentioned in Materials and methods.
Abstract, line 2: Add the word „analysis“ following „this“ in the statement „This analysis provides a basis for understanding…“
Abstract, line 9: Add a space between the words „59“ and „cell cycle genes“, i.e., „59 cell cycle genes“.
Introduction, page 1, line 10: Use the present form of the verb „depend“ instead of „depended“ in the statement „Growth and development of plant depend on accretion, division and differentiation of cells,…“
Introduction, page 1, line 11: Use a plural form in the words „these processes“.
Introduction, page 1, line 13: Modify the word form „firstly“ to „first“ in „Cyclin D (CYCD) was expressed first,…“
Introduction, page 1, line 14: Add a space between the words „and“ and „cyclin-dependent kinase inhibitor (CKI)…“
Introduction, page 2, line 2: Correct the typing error in the term „anaphase“ in „anaphase promoting complex (APC) protein pathway….“
Materials and methods, page 2, line 2 in the section: Add a space between the word „publication“ and the following reference.
Materials and methods, page 2, line 10: Correct the typing error in the symbol „pI“ (not „PI“) used for the protein isoelectric point.
Materials and methods, page 2, line 15 in the section: Add a space between the words „B. pendula“ and „cell cycle genes“.
Materials and methods, page 2, line 18 in the section: Add a space between „a“ and „phylogenetic“.
Materials and methods, page 3, line 1: Add a space between the word „the genome“ and the following web address.
Page 3, line 13: Shift the heading „3. Results“ on a new line!!
Results, page 5, line 10: Modify the verb „lengthen“ to „prolong“ in the sentence „CDKB1.1 can prolong hypocotyl cells, promote cotyledon cell development,…“
Results, page 5, line 21: Please add adequate number to the last motif in the statement „…contain motif 1, motif 2, motif 3, and motif ??“
Results, Figure 2, Figure 3, Figure 4, Figure 5 and Figure 6 legends: Some statements in the figure legends corresponding to the phylogenetic trees should be rephrased, e.g., „TBtools software was used to compare gene structure. „TBtools software was used to visualize…“ Moreover, add a comma between the words „grey lines“ and „respectively.“
Results, page 8, line 22: Add a space between the gene name „BpRb1“ and „is“.
Results, page 8, line 24: Replace the word „in“ by „at“ in the statement „at temporal and spatial level.“
Results, page 8, line 30: Write the plant scientific name „A. thaliana“ in italics.
Results, page 8, line 31 (the last line on the page): Add a space between the two sentences, the first one ending with „..flower and leaves.“ and the second one starting with „BpWEE1 is abundant in leaves.“
Discussion, page 9, line 10: Add a space between „mitosis“ and the following reference.
Discussion, page 10, line 3: Add a space between „stamen“ and the following reference.
Discussion, page 10, line 5: Add a space between the words „on“ and „separate“.
Comments for author File: 
Comments.pdf
Author Response
Thank you for your detailed comments on my article. I have made the corresponding amendments and hope to get your corrections.
Please see the attachment.
Author Response File: Author Response.docx
