Using Next-Generation Sequencing Technology to Explore Genetic Pathways in Endophytic Fungi in the Syntheses of Plant Bioactive Metabolites
Round 1
Reviewer 1 Report
Endophytic fungal can synthesize bioactive compounds which are the same or structurally similar to those produced by their host plants, so, the research of endophytic fungi has attracted worldwide attention recent years. This manuscript entited”Using next-generation sequencing technology to explore genetic pathways in endophytic fungi able to synthesize plant bioactive metabolites” is interesting, the authors use of next-generation sequencing technologies for the comparative elucidation of the biosynthetic pathways of several important products of endophytic fungi, and it is believed to be helpful to relevant researchers.
Two points need to be corrected or clarified:
- L20, why the authors use “are revised”? I suggested change to “are viewed”.
- L135-L137, “In the current post-genomic era, all dilemmas concerning the genetic mechanisms underlying the production of plant secondary metabolites by endophytic fungi should soon be resolved”, does the author believe it will be solved soon?
Author Response
Endophytic fungal can synthesize bioactive compounds which are the same or structurally similar to those produced by their host plants, so, the research of endophytic fungi has attracted worldwide attention recent years. This manuscript entitled “Using next-generation sequencing technology to explore genetic pathways in endophytic fungi able to synthesize plant bioactive metabolites” is interesting, the authors use of next-generation sequencing technologies for the comparative elucidation of the biosynthetic pathways of several important products of endophytic fungi, and it is believed to be helpful to relevant researchers.
Thank you for your positive comments.
Two points need to be corrected or clarified:
- L20, why the authors use “are revised”? I suggested change to “are viewed”.
We leave this unchanged since the word ‘view’ is already used in the same sentence.
- L135-L137, “In the current post-genomic era, all dilemmas concerning the genetic mechanisms underlying the production of plant secondary metabolites by endophytic fungi should soon be resolved”, does the author believe it will be solved soon?
Thank you for this comment. We do agree that this sentence in its previous form might sound too strict and therefore we have changed it to: “In the current post-genomic era, dilemmas concerning the genetic mechanisms underlying the production of plant secondary metabolites by endophytic fungi might have a chance to be resolved”.
Reviewer 2 Report
The review "Using Next-Generation Sequencing Technology to Explore Genetic Pathways in Endophytic Fungi Able to Synthesize Plant Bioactive Metabolites" is quite interesting and has scientific merits but certain points required more attention by the authors to meet the journal standards.
Among these points:
1- The abstract part should be restructured to give more details about the the following (methods used, the number of references reviewed and the most relevant key findings about such review)
2- The criteria for including or excluding the references and therefore the compounds are totally missed (databases used, time range, language used,.......etc)
3- The table should be rearranged in an alphabetical order to help the readers following the compounds
4- A short paragraph at the end of each compound about the authors recommendations and suggestion will help in increasing the impact of the review
5- The similarity index is high and certain sentences are taken by copy and paste which need more work. Please find the attached PDF file
6- the review should be checked by an English native speaker to improve the quality of the work
Comments for author File: 
Comments.pdf
Author Response
The review "Using Next-Generation Sequencing Technology to Explore Genetic Pathways in Endophytic Fungi Able to Synthesize Plant Bioactive Metabolites" is quite interesting and has scientific merits but certain points required more attention by the authors to meet the journal standards.
Among these points:
1- The abstract part should be restructured to give more details about the following (methods used, the number of references reviewed and the most relevant key findings about such review)
The abstract has been integrated with some of the required information.
2- The criteria for including or excluding the references and therefore the compounds are totally missed (databases used, time range, language used, .......etc.)
Thank you for bringing this up. In fact, the information about the searching criteria is included in the chapter 4. We have specified the databases searched (SRA, PubMed and Google Scholar) and the type of experiments included (publicly accessible records of endophytic fungi genomes or transcriptomes) and expected outcome (fungal structural genes potentially involved in biosynthesis of plant bioactive metabolites). In our opinion, as NGS is a relatively new technology, there was no need to use any time restriction in our survey, therefore we have not specified any starting moment as a criterion. In our survey, we have screened all relevant experiments which appeared during the era of the NGS technology
existence (which is approximately dated as last 17 years, spanning from 2005 to 2021) and met other criteria set in the review. As a result, we have included in our paper 21 references dealing with at least 26 endophytic fungi strains which have been the subject of experimental activities involving massively parallel genome and transcriptome sequencing methods in the last eight years (2014 – 2021, see references [64 – 84]) - this information has been added in the Abstract. Simply, before the year 2014 we have not found any published work on NGS sequencing in endophytic fungi, which would be implemented to elucidate fungal biosynthetic pathways and/or structural genes potentially involved in biosynthesis of plant bioactive metabolites. The language of included references was English.
3- The table should be rearranged in an alphabetical order to help the readers following the compounds
We deliberately decided to use the same order of presentation adopted in chapter 4 rather than alphabetical order, considering that entries are not just compounds or compound families, but also functional categories.
4- A short paragraph at the end of each compound about the authors recommendations and suggestion will help in increasing the impact of the review
We do not think this is necessary, considering that the paper ends with a section dedicated to ‘future prospects’.
5- The similarity index is high and certain sentences are taken by copy and paste which need more work. Please find the attached PDF file
Thank you very much for pointing it out and attaching the file. We have made multiple amendments throughout the manuscript text to improve this aspect.
6- the review should be checked by an English native speaker to improve the quality of the work
The language style has been revised by an English native speaker.
Reviewer 3 Report
The manuscript reviewed “Using Next-Generation Sequencing Technology to Explore Genetic Pathways in Endophytic Fungi Able to Synthesize Plant Bioactive Metabolites”. The manuscript is interesting and beneficial to the readership of journal. However, the manuscript should be improved.
Title:
It could be revised to: “Using Next-Generation Sequencing Technology to Explore Genetic Pathways in Endophytic Fungi in the Syntheses of Plant Bioactive Metabolites”
Line 13: It is adequate to use only fungal species
Line 194: Authors are advised to include from which year to which year during the survey.
Line 270: Use words for numbers 1-10.
Figure 1: Please include chemical structures of Taxol, Huperzine A, Tephrosin, Skyrin
Line 412: Please check it is Rotenolone or Rotenone?
Line 429: Please include the reference.
There are too many abbreviations, authors are advised to incorporate a List of Abbreviations in the manuscript.
Author Response
The manuscript reviewed “Using Next-Generation Sequencing Technology to Explore Genetic Pathways in Endophytic Fungi Able to Synthesize Plant Bioactive Metabolites”. The manuscript is interesting and beneficial to the readership of journal. However, the manuscript should be improved.
Title: It could be revised to: “Using Next-Generation Sequencing Technology to Explore Genetic Pathways in Endophytic Fungi in the Syntheses of Plant Bioactive Metabolites”
Title has been changed.
Line 13: It is adequate to use only fungal species
We also added the word ‘strains’ considering that some studies refer to fungi which were not classified at the species level.
Line 194: Authors are advised to include from which year to which year during the survey.
In our opinion, as NGS is a relatively new technology, there was no need to use any time restriction in our survey, therefore we have not specified any starting moment as a criterion. In our survey, we have screened all relevant experiments which appeared during the era of the NGS technology existence (which is approximately dated as last 17 years, spanning from 2005 to 2021) and met other criteria set in the review. As a result, we have included in our paper 21 references dealing with at least 26 endophytic fungi strains which have been the subject of experimental activities involving massively parallel genome and transcriptome sequencing methods in the last eight years (2014 – 2021, see references [64 – 84]) - this information has been added in the Abstract. Simply, before the year 2014 we have not found any published work on NGS sequencing in endophytic fungi, which would be implemented to elucidate fungal biosynthetic pathways and/or structural genes potentially involved in biosynthesis of plant bioactive metabolites.
Line 270: Use words for numbers 1-10.
Thank you for spotting it. We have changed “4” into “four” and “10” into “ten”.
Figure 1: Please include chemical structures of Taxol, Huperzine A, Tephrosin, Skyrin
Figure 1 has been integrated with these chemical structures.
Line 412: Please check it is Rotenolone or Rotenone?
Thank you for your vigilance. In fact, both rotenolone (ID: HMDB0034145) and rotenone (ID: HMDB0034436) belong to plant-produced rotenoids. However, in the cited reference [79], the endophytic fungus P. stromaticum has been reported to produce two rotenoids previously known from plants: rotenolone and thephrosin.
Line 429: Please include the reference.
Thank you for raising this issue. We have double-checked information regarding viridiflorol production, and we have made necessary amendments in paragraph 4.6.3.
There are too many abbreviations, authors are advised to incorporate a List of Abbreviations in the manuscript.
Actually, most abbreviations refer to enzymes or their encoding genes and have been given in brackets after their first mention. This style is routinely used in papers dealing with these biochemical and biomolecular aspects; hence, we do not think that a List of Abbreviations is strictly necessary.
Round 2
Reviewer 2 Report
The review has much improved from the initial version. The authors amended most of the required points. It can be accepted in the present form
