Transcriptome Analysis Identified Candidate Genes Involved in Fruit Body Development under Blue Light in Lentinula edodes

Round 1

Reviewer 1 Report

The manuscript titled "Transcriptome Analysis Identified Candidate Genes Involved in Fruit Body Development under Blue Light in Lentinula edodes" uses different tools aiming to understand the mushroom's fruit body development for breeding application. The concept is interesting, considering the organoleptic and nutritional values of L. edodes and their specific conditions of growing.

General comments:

Despite the introduction section providing relevant content, it could be better to check it's grammar and spelling, aiming the improvement of its construction/presentation.

Line 44: italic form is missing in two cases. 

Also, I have some curiosities, and I hope the authors can help with their answers. 

1 - Table 1 and its discussion: which is the main difference/similarities regarding the results of blue light and darkness and those reported by the authors at Ref 11?   2 - Regarding the most important aspects of L. edodes for the consumers, the most promising fruiting bodies (blue light) fit those organoleptic and nutritional demands? Can the authors provide (add to the manuscript) further analysis considering trivial data in this regard, namely nutritional value, images, analysis of the fruit body colour/size and so on...?   3 - In the authors oppinion, which is the novelty of the presented work?

Author Response

Please see the attachment.

Author Response File: Author Response.docx

Reviewer 2 Report

The manuscript of Kim et al. reports the transcriptome analysis of fruit body development in Lentinula edodes strain Sanjo701ho under blue light condition. Even though the novelty of the study is limited to only Lentinula edodes mushroom, I think it’s a good addition to the literature. However, there are number of issues that must be addressed prior to publication. Some of the comments or suggestions are given below-

- The whole manuscript needs an improvement in English. Some of the statements are grammatically incorrect or too long or do not make sense. Some sentences need to be rephrased as well as some words needs to be replaced by the appropriate words to make it more understandable (please see the attached manuscript). The flow of reading is missing in some sections of the manuscripts. 

- As the mushroom needs special growth/culture conditions, please provide more details about cultural conditions in the “Materials and Methods” section.

- Authors may also think about putting figures of the mushroom under blue and no light (control) conditions in the main text (in addition to the supplementary figure 1).

- The authors did not use the proper language or right words when they describe the methodology of RNA-seq data analysis in M&M section and discuss the findings of RNA-seq analysis in “results and discussion” section. I believe this is maybe due to the language barrier rather than lack of understanding of the whole transcriptome analysis. Reading some recently published RNA-seq paper will help to properly describe the RNA-seq data analysis .

- Authors should put the supplementary table 2 in the main text as a main table. They can also think about putting some more information like quality data of the reads (%of duplicated sequence, %GC content), uniquely mapped reads, how many reads mapped to exons/CDS etc. in the table. Besides authors may also add the PCA analysis of the RNA-seq data.

- The 3.3 sub-section of “Result and discussion” has been written very poorly. Authors described the functions of the different members of the superfamily one by one instead of treating them as a family which ruined the flow of reading. Please rewrite the sub-section 3.3 focusing on their own findings like a research paper.

- In the sub-section 3.4 of the “Result and discussion” section, the authors should put more details of qRT-PCR study regarding the validation of the transcriptome data. It would be easy to follow the text if the authors put the gene name in the text like figures. I also would suggest to put the fig in the main text instead of putting as a supplementary figure (#2). Besides I am not sure why the authors decided to do the validation of the DEGs in time series samples instead of samples after 7 days of treatment like RNA-seq sample. If there is a reason for the time series, then the authors should discuss that in the result and discussion section.

-The caption/titles of the figures/tables should be self-explanatory. The caption of the figure/table should have enough information to make the figure/table understandable. I would suggest the authors to provide necessary details in the captions of the figures, especially fig 2 and fig 3.

- The authors also did not mention in the caption what the letters A, B and C mean in the fig 4. Besides, please make the fig 1 bigger and legible.

- Please also look carefully at the attached manuscript to see the reviewer’s specific comments and suggestions and other corrections/typos that were not mentioned here.

I would suggest accepting the paper with major revision. I strongly encourage the authors to improve the English of the whole manuscript especially the results and discussion section using the proper language, improve the flow of reading, put enough information to make the titles/captions of the figures self-explanatory, add the table and figures as requested and resubmit a REVISED manuscript.

Comments for author File: Comments.docx

Author Response

Please see the attachment.

Author Response File: Author Response.docx

Round 2

Reviewer 1 Report

The authors addressed the suggestions. Also, I am glad for clarifying the initial doubts, supporting the novelty of the present manuscript.

Therefore, I only have a suggestion. Regarding the Material and Methods section, it would be great if the authors add a sub-section regarding the statistical analysis of data. Just a simple statement, as it's obvious that analysis was performed for Table 1. Also, if providing statistical analysis of data from Figure 5, would be perfect.

Author Response

Please see the attachement.

Author Response File: Author Response.docx