Transcriptome Analysis of Ganoderma lingzhi Liquid Fermentation Process Using Corn Straw as Matrix
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsDear authors
The reviewer has attached the comments in detail with the PDF file uploaded. The authors are suggested to revise the manuscript following the comments in the PDF file.
Many revision and improvements should be made in English writing before this manuscript can be accepted for publication. The reviewer has commented as much as possible. Still there are much more similar unsolved points. Thus the authors need to be very careful in the
The following are the detailed comments the authors may need.
1. There were several mixtures of "Ganoderma" and "Ganoderma lingzhi" in the manuscript. The concept “Ganoderma” generally indicates the genus Ganoderma, not the species “Ganoderma lingzhi”. So the authors must be very careful when “Ganoderma” appear in the bodytext.
2. This is not proper to use “possibility” for crop straw, because it has been widely used in cultivation of G. lingzhi for many years. The word "feasibility" is better.
3. Which contents of cellulose, hemicellulose, and lignin are needed and degraded by Ganoderma lingzhi most? The percentage of above contents in corn straw have not been introduced in the first part of this manuscript.
4. Genes encoding lignocellulose degrading enzymes in other macro-fungal species should be introduced as background knowledge in introduction part.
5. Are there any similarities or differences of transcriptome in different edible/medicinal species? It seemed that this point has not been discussed in the last part.
6. Is there any relationship for introduction of triterpenoids synthetization with the transcriptome of liquid fermentation process using corn straw as matrix? No concrete relationship is detailed in the introduction part.
7.Limited discussion about transcriptome lignocellulose degrading enzymes of other wood decaying fungi, e.g., Sanghuangporus, are compared at the last part of bodytext.
Comments for author File: 
Comments.pdf
Author Response
Comments 1: There were several mixtures of "Ganoderma" and "Ganoderma lingzhi" in the manuscript. The concept “Ganoderma” generally indicates the genus Ganoderma, not the species “Ganoderma lingzhi”. So the authors must be very careful when “Ganoderma” appear in the bodytext.
Response 1: Thank you for pointing this out. We agree with this comment. Therefore, We have clarified the use of “Ganoderma” and “Ganoderma lingzhi” and have made modifications in lines 39, 40, 41, and 43 of the text.
Comments 2:This is not proper to use “possibility” for crop straw, because it has been widely used in cultivation of G. lingzhi for many years. The word "feasibility" is better.
Response 2:Agree. We made changes to that paragraph in lines 56 and 57.
Comments 3:Which contents of cellulose, hemicellulose, and lignin are needed and degraded by Ganoderma lingzhi most? The percentage of above contents in corn straw have not been introduced in the first part of this manuscript.
Response 3: Agree.We have labelled the content cellulose (41.93%), hemicellulose (24.71%) and lignin (23.68%) in line 47.
Comments 4: should be introduced as background knowledge in introduction part.
Response 4: Agree.We have added a description of genes encoding lignocellulose degrading enzymes in other macro-fungal speciesgenes in lines 59 to 79.
Comments 5: Are there any similarities or differences of transcriptome in different edible/medicinal species? It seemed that this point has not been discussed in the last part.
Response 5: Agree. Lines 545 to 555 of the article describe the genes obtained from the transcriptome, which is broadly similar to that of Pleurotus ostreatus, and the cellulose-related genes are similar to those of 10 basidiomycete species.
Comments 6: Is there any relationship for introduction of triterpenoids synthetization with the transcriptome of liquid fermentation process using corn straw as matrix? No concrete relationship is detailed in the introduction part.
Response 6: Agree.We have added relationships between lignocellulose degradation, triterpenes, and polysaccharide metabolism in lines 95 to 107, all three of which are important pathways for carbon metabolism and interact with each other.
Comments 7: Limited discussion about transcriptome lignocellulose degrading enzymes of other wood decaying fungi, e.g., Sanghuangporus, are compared at the last part of bodytext.
Response 7: Agree. We add a discussion of Pleurotus ostreatus and 10 basidiomycete species to the final part of the paper
Comments 7: The authors are suggested to revise the manuscript following the comments in the PDF file.Many revision and improvements should be made in English writing before this manuscript can be accepted for publication.
Response 7: Agree. We have carefully read the reviewer's notes in the article and made corrections to try to polish the English writing.
Reviewer 2 Report
Comments and Suggestions for AuthorsThis manuscript is a study of G. lingzhi liquid fermentation on the utilization of corn straw at the molecular level. After 5 and12 days’ liquid fermentation culturing, the transcriptome analysis of Ganoderma lingzhi has been compared. The CAZy analysis of differential genes in the sequencing results was used to analyze the genes related to lignocellulose degradation. The important enzyme activity about degrading corn straw were showed clearly during the decaying process and the important genes have been found out. This is an interesting study to illustrate the decaying mechanism about corn straw with Ganoderma lingzhi, which is a famous medicinal fungi. However, there are two problems:
1. Authors did not provide the aim and significance. Besides the theoretical significance of this study, what practical helps could be provided about the results since the corn straw was the important a multifunctional and renewable biological resource?
2. Line90-91, the mycelium cultured in CSL for 0 days was set as the control group (CK), that for 5 days as the treatment group (LM), and that for 12 days as the treatment group (CH). I don’t think the CK is appropriate because there are two factors influencing the mycelium growth, fermentation and corn straw powder. It’s hard to judge that the differentially expressed genes were caused by fermentation or corn straw exactly. In fact, the mycelium cultured in liquid medium without corn straw powder, then incubated with same conditions. Please provide the reason about your CK selection.
3. Line 90-91, the reason of 5 days and 12 days selection were lack. Please add it.
Author Response
Comments 1: Authors did not provide the aim and significance. Besides the theoretical significance of this study, what practical helps could be provided about the results since the corn straw was the important a multifunctional and renewable biological resource?
Response 1: Thank you for pointing this out. We agree with this comment. Therefore, We added purpose and meaning in lines 108 to 123 of the article. The final aim is "To identify genes involved in lignocellulose degradation and the association between lignocellulose degradation, polysaccharide and triterpene synthesis and metabolism during liquid fermentation of Ganoderma lingzhi on corn stover substrate. It provides new ideas and methods for the subsequent utilisation of corn stover resources by Ganoderma lingzhi, as well as an important reference for the study of the mechanism of action of other medicinal fungi in the liquid fermentation process of corn stover. "
Comments 2: Line90-91, the mycelium cultured in CSL for 0 days was set as the control group (CK), that for 5 days as the treatment group (LM), and that for 12 days as the treatment group (CH). I don’t think the CK is appropriate because there are two factors influencing the mycelium growth, fermentation and corn straw powder. It’s hard to judge that the differentially expressed genes were caused by fermentation or corn straw exactly. In fact, the mycelium cultured in liquid medium without corn straw powder, then incubated with same conditions. Please provide the reason about your CK selection.
Response 2: Thank you for pointing this out. The main reasons for choosing CK were that the samples had the lowest lignocellulase activity through day 0, and that the sampling time was the 12th h of transfer into CSL, which was expressed for a certain period of time in CSL.
Comments 3: Line 90-91, the reason of 5 days and 12 days selection were lack. Please add it.
Response 3: We provide additional elaboration in lines 20 to 28.With the characterization of cellulase’s activity and xylanase’s activity on cellulose and hemicellulose, the level of gene expression of laccase, and manganese peroxidase’s live characterization of lignin, the level of gene expression of the combination of enzyme protein translation lags behind that of gene transcription.
Reviewer 3 Report
Comments and Suggestions for AuthorsThe manuscript entitled "Transcriptome analysis of Ganoderma lingzhi liquid fermentation process using corn straw as matrix" is an interesting piece of work and very well conceptualized and executed.
The manuscript needs english language correction. Some of the sentences are superfluous while some are repeated. Also some sentences are too long and difficult to understand.
I have made some correction on the body of the manuscript. Still the manuscript should be throughly checked and corrected for language corrections.
Comments for author File: Comments.pdf
Author Response
Comment: The manuscript needs english language correction. Some of the sentences are superfluous while some are repeated. Also some sentences are too long and difficult to understand. the manuscript should be throughly checked and corrected for language corrections.
Response: I understand your concerns. I will do a thorough review and make the necessary corrections to ensure the manuscript is clear, concise, and free of language errors. I'll pay close attention to eliminating superfluous and repeated sentences and breaking down long, complex ones for better comprehension.For example, line 39 is deleted: "Additionally, Ganoderma belongs to the white rot fungi”. Simplify the sentence in line 56 to read "In addition, the effectiveness of using Ganoderma to utilize corn straw is not ideal, with a certain level of uncertainty in its utilization.". Split paragraph 2.6 into two.
