Whole Transcriptome-Based Study to Speculate upon the Silkworm Yellow Blood Inhibitor (I) Gene and Analyze the miRNA-Mediated Gene Regulatory Network
, Shangshang Ma 2,3, Rehab Hosny Taha 4, Qin Yao 2, Yi Yuan 2,3,* and Keping Chen 2,*
Round 1
Reviewer 1 Report
In general, several redrafting and reviewing is required for the whole typescript.
A. High similarity index
According to “iThenticate”, the similarity index is high in all sections, mainly in the materials and methods.
B. English Language
English in the whole manuscript needs to be thoroughly edited.
C. Scientific Names
The scientific name (Bombyx mori) should be written (italicized) in full when first cited in the introduction, then is abbreviated according to standard format. Need correction in the whole manuscript including Figures/Tables.
D. Full term of abbreviations
The first time you use an abbreviation, it's important to spell out the full term.
COG, KEGG, GO, FPKM.
E. Introduction
- See comments B and C.
- Lines 48-50 are a repeat of most of Lines 45-47.
- Lines 75-82 without references.
F. Results
- See comments B, C, and D.
- Most of the Figures with low quality. Fix that when making images larger don’t lose quality, mainly within labelling.
- Figure 1 is not clear and needs to enhance the quality.
- Figure 2, in the legend use the abbreviation DEGs instead of the full term. The bar chart needs explanation in the legend. Is it DETs or DEGs in the Y axis?
- Figure S1, why not Figure 3? also needs to enhance the quality. In the legend use the abbreviation DE- instead of the full term. Is it DETs or DEGs in the Y axis?
- Figure 3 needs to enhance the quality. The legend is not related to the shown figure.
- Line 163 correct to “not expressed in both groups”.
- Reference 6 is not Kozo et al.
- Line 171, XP_004923505.1 ??
- Figure 4, in the legend use the abbreviation DEGs instead of the full term. Why A306?
- Line 188, correct to KWMTBOMO10339 and KWMTBOMO16553
- Figure 5, enhance the quality, correct to KWMTBOMO10339 and KWMTBOMO16553 in the legend.
- Line 208 abbreviate to DE-mRNA
- Lines 210-219, use DE- with a hyphen.
G. Materials and Methods
- See comments B and D.
- Delete the space between the number and “C”, representing Celsius
- Line 392, delete the repeated word
- Line 410, don’t repeat the full terms of the previously abbreviated term
- Line 411, is it method or methods?
- Line 414, don’t repeat the full terms of the previously abbreviated term
- Line 416, correct to DE-circRNA
- Line 441, LncRNA
- Line 459, correct to Cytoscape 3.2.1
- Line 474-475, the total volume is not 20.
- Statistical analysis: indicate which method you employed to determine the difference.
H. References
- The scientific names should be italicized.
- Unify the page numbering style.
- Unify the journal name style.
Author Response
Please see the attachment.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
The authors present an extensive and interesting study. In order for the paper to be accepted, the authors should consider my comments, some of which are more important, and others are technical.
The title of the article needs to be corrected. Maybe it should be changed to: “Whole transcriptome-based study to speculate upon the silkworm yellow blood inhibitor (I) gene and analyze the miRNA-mediated gene regulatory network”
Figure 4 indicates that there are 92 DEGs, but they are not listed and only two genes are considered in the following discussion: KWMTBOMO10339 and KWMTBOMO16553. What are the rest?
It can be seen even by eye that the degree of similarity of the sequences in Figure 5 does not correspond to the values indicated in the text in lines 184-187.
The meaning of coloring positions in Figure 5 is not explained. Figures A and B are not marked.
There are many more sequences in the phylogenetic trees than in the alignments of Figure 5.
Figures 1 and 6, as well as 5B are too small, the font is not vector and the letters on them are not readable.
References to additional tables in the text begin with Table S2 and end with S1. Renumber tables.
Supplementary Figure S1 is placed in the main text.
What is T_mRNA in Figure 3 and Table S5 and beyond?
Line 184 - sequence homology > sequence similarity
Line 195 - amino acid sequence similarity > - amino acid sequences
Lines 26, 29, 214, 468 - 2 > two
Lines 215,227,468 - 5 > five
Phylogenetic trees cannot show similarity in gene functions as stated in Lines 268, 272.
Line 282 – “KWMTBOMO16553 identified in the silkworm this time also has the PDZ protein domain”. It is necessary to mark this domain on the alignment in Figure 5
Please add references for DESeq2, DESeqR, edgeR, GO seq v1.10.0, DNAMAN, CIRI2, find_circ, and Cytoscape3.2.1 packages in 4. Section.
Lines 462-464 - it is a duplication of lines 380-383 and must be deleted.
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
Round 2
Reviewer 2 Report
Authors corrected the text according comments. Below are some additional remarks.
1) Line 39 Bombyx mori (B. mori) > Bombyx mori L.
2) In Figure 5, the color highlights are hard to see.
3) In the trees in Figure 6, it is not necessary to indicate the origin of the proteins from B. mori each time. This can be indicated in the figure legend.
Specify bootstrap values on tree nodes.
The sentence “The Neighbor-Joining tree was generated by MEGA7. One thou-sand bootstraps were performed for checking the reproducibility of the result” in the Fig. 6 legend should be placed in Materials and Methods.
4) I note again that phylogenetic trees cannot show similarity in gene functions as stated in Lines 261-266
5) Decipher the abbreviation DE at the first mention in the text
6) In my Report 1 I asked why, out of the 92 DEGs found, only two genes are considered in the following discussion: KWMTBOMO10339 and KWMTBOMO16553. Such a question may naturally arise from readers. The authors gave an exhaustive answer to it. It seems to me that it should be included in the text of the article, may be in the Discussion.
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
