Gene Set Subtraction Reveals 633 Candidate Genes for Bamboo Culm Wall Thickening

Round 1

Reviewer 1 Report

The manuscript entitled “The subtraction of gene sets reveals unique genes for 2 bamboo culm wall thickening” presents a gene set of 633 genes after whole resequencing of 4 bamboos varieties.

I have some minor comments presented below:

 

Line 55:  replace as “and 1-2 times thicker than Schizostacyum…”

In Figure 1 Latin names of bamboo must be in italics also in line 74-75

Also Latin names in paragraph of results must be placed.

In Table 1 you have to write in the caption which bamboo refers to which letter A, B, C and D

I find the discussion section poor, I would like to see more in this section.

Author Response

Dear Reviewer,

Thank you for taking your valuable time to review our manuscript. We appreciate your review and comments! We have carefully considered your comments and made the following improvements.

1. We checked the writing of all Latin names in the manuscript and made corrections.
2. We have replaced the A, B, C and D in Table 1 with Latin scientific names.
3. We recognized the shortcomings of the discussion section and have reorganized it.We discussed the strengths and weaknesses of the experimental method and further interpreted the results.Please review the revised manuscript.

Thanks again for your review!

Best Wishes.

Reviewer 2 Report

Authors investigated the effects of the genome of Phyllostachys edulis‘Pachyloen’, Phyllostachys nidulariaf. farcta,Phyllostachys heterocladaf. solidawith thicker culm walls, and Schizostachyum dumetorumvar.xinwuensewith thin culm walls, aiming to pinpoint molecular mechanisms involved in the bamboo culm wall thickening. The topic of research is relevant to better understanding the plant traits regulation, which may ultimately contribute to ameliorate the results in plantations and bamboo industry. Authors developed a strategy of gene set subtractionto explore the candidate genes involved in the regulation of the bamboo culm wall thickening, and identified a set containing 633 genes.My major concern is related with the discussion of the results obtained, which I recommend authors to detail; also include vantages and disadvantages of the approach adopted.

Author Response

Dear Reviewer,

Thank you for taking your valuable time to review our manuscript. We appreciate your review and comments! We have carefully considered your comments and made the following improvements.

We recognized the shortcomings of the discussion section and have reorganized it. We discussed the strengths and weaknesses of the experimental method and further interpreted the results.

Please review our revised and resubmitted manuscript.

Thanks again for your review!

Best Wishes.

 

Round 2

Reviewer 2 Report

Authors followed all my recommendations; other minor inaccuracies along the text were also addressed.

Cordially,

This manuscript is a resubmission of an earlier submission. The following is a list of the peer review reports and author responses from that submission.

Round 1

Reviewer 1 Report

Authors claimed in Line 59. "Gene set subtraction is an innovative technique for biological genome research." Is there any references related to this claim? If yes, please list the reference, otherwise, more detailed explanation of how this method is applicable to this study should be provided. The experiment design is oversimplified the situation. 

 

Minor: All Latin names should be italic.

 

 

Reviewer 2 Report

The authors resequenced the genomes of 4 species of bamboo:  Phyllostachys edulis ‘Pachyloen’ (same species as reference genome), Phyllostachys nidularia f. farcta, and Phyllostachys heteroclada f. solida, with thicker culm walls, and Schizostachyum dumetorum var. xinwuense, with thin culm walls. Then they identified at genomic level genes in common in the species of thicker culm walls and not found in S. dumetorum, using a method they called subtraction of gene sets. The authors proposed the obtained gene set contains 633 genes related to bamboo culm wall thickness regulation.

 

The gene set subtraction method is introduced as “an innovative technique for biological genome research.”. This method seems to be presented in this paper for the first time, as no references were included, and it seems was invented by the authors. However, it is not clear how the gene set subtraction was actually done. It is not clear to me if this gene set selection is based on absence/presence genes, gene orthology or sequence differences based on SNPs.

Unfortunately, the authors do not prove the validity of the method and do not prove any of the genes are actually involved in the regulation of culm wall thickness, the results are only base on their assumptions.

They are comparing 3 species from the same genus with other species from a different genus. However, in table 1, it looks like species D (S. dumetorum), has in many cases a lower number of SNPs and InDels than the other species from the same genus as the reference. This is unexpected and it is not explained. It could happen for reads not mapping to the references for having too many differences. The sequencing depth of the different species could also affect. There are no statistics about sequencing depth or mapping efficiency. The promoter regions were not analyzed. Differences in these regions could affect the regulation and development of culm wall thickness.

Table 1 should show in a clear way which species are A, B, C and D. It is not clear what the total row stands for, and the format of the first column does not look good.

In the “Determination of differential gene set” section, the alignment to the reference genome produced 3,055, 4,309, 4,656, and 3,711 differential genes, for the respective species. It is not clear what they call differential genes or how these genes were obtained (using alignments of genome sequences). The same way, they wrote “P. edulis, P. nidularia and P. heteroclada, all of which have thick walled traits, had 1,524 identical differential genes.” It is not explained what are these identical differential genes or how they were identified.

The authors introduced a transcriptomic analysis from a previous paper they published (“Transcriptome Reveals the Specificity of Phyllostachys edulis ‘Pachyloen’ Shoots at Different Developmental Stages”), where they claimed their analysis revealed “many Phyllostachys edulis ‘Pachyloen’-specific genes that may play an important role in bamboo wall thickening.” It would be interesting to know which genes are in common between both analyses.

In several cases, figures and tables do not contain enough information to understand their content.

Species names are not always in italics. Additionally, in my opinion there is no need to use the long name with the variety name in every case. After the presentation of the species names, sometimes it would be easy to read if the short form is used in the text, i.e., P. edulis, P. nidularia, P. heteroclada and S. dumetorum.