Whole-genome sequencing-based characterization of Streptomyces sp. 6(4): focus on natural product
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We have sequenced the whole genome of Streptomyces sp. 6(4) isolated from tomato roots that presents antifungal activity against phytopathogenic fungi, mainly Bipolaris sorokiniana . The genome has almost 7 Mb and 3368 hypothetical proteins that were analysed and characterized in Uniprot with the emphasis on biological compounds. Multilocus sequence typing (MLST) analyses were performed in an effort to characterize and identify this isolate, resulting in a new sequence type (ST), classified as ST64. Phenetic and phylogenetic trees were constructed to investigate Streptomyces sp. 6(4) evolution and sequence similarity, and the isolate is a strain closer to Streptomyces prasinus and Streptomyces viridosporus . It is known that the genus Streptomyces possess huge metabolic capacity with the presence of cryptic genes. These genes are usually present in clusters, which are responsible for the production of diverse natural products, mainly antibiotics. In addition, 6(4) showed 11 biosynthetic gene clusters through antiSMASH, including 3 polyketide synthase (PKS) and non-ribosomal peptide synthase (NRPS) type clusters.
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The manuscript is well written and contributes to the literature. Thank you for addressing all reviewers comments satisfactorily and in a timely manner, this was very much appreciated.
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Comments to Author
1. Methodological rigour, reproducibility and availability of underlying data Good, much improved. 2. Presentation of results Good. 3. How the style and organization of the paper communicates and represents key findings Good. 4. Literature analysis or discussion Good- discussion and reference to literature has been improved.
Please rate the manuscript for methodological rigour
Good
Please rate the quality of the presentation and structure of the manuscript
Good
To what extent are the conclusions supported by the data?
Strongly support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between …
Comments to Author
1. Methodological rigour, reproducibility and availability of underlying data Good, much improved. 2. Presentation of results Good. 3. How the style and organization of the paper communicates and represents key findings Good. 4. Literature analysis or discussion Good- discussion and reference to literature has been improved.
Please rate the manuscript for methodological rigour
Good
Please rate the quality of the presentation and structure of the manuscript
Good
To what extent are the conclusions supported by the data?
Strongly support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
-
Comments to Author
The manuscript presented describes the genome sequence of Streptomyces sp. 6(4), a strain previously isolated from tomato root that shows antifungal activity against the plant-pathogen, Bipolaris sorokiniana. The MiSeq Illumina platform was used to sequence the genomic DNA and the genes present have been annotated using several methods. Phylogenetic analysis has been conducted to identify the species of the isolate and AntiSMASH analysis to predict biosynthetic genes and gene clusters present. The authors have made some preliminary suggestions as to which of these genes/BGCs may be responsible for the previously observed bioactivity. The manuscript is generally well presented. The workflow is easy to follow and the results are well interpreted. The methods section provides good detail and data are …
Comments to Author
The manuscript presented describes the genome sequence of Streptomyces sp. 6(4), a strain previously isolated from tomato root that shows antifungal activity against the plant-pathogen, Bipolaris sorokiniana. The MiSeq Illumina platform was used to sequence the genomic DNA and the genes present have been annotated using several methods. Phylogenetic analysis has been conducted to identify the species of the isolate and AntiSMASH analysis to predict biosynthetic genes and gene clusters present. The authors have made some preliminary suggestions as to which of these genes/BGCs may be responsible for the previously observed bioactivity. The manuscript is generally well presented. The workflow is easy to follow and the results are well interpreted. The methods section provides good detail and data are accessible in public databases.
Please rate the manuscript for methodological rigour
Good
Please rate the quality of the presentation and structure of the manuscript
Very good
To what extent are the conclusions supported by the data?
Strongly support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
No: Not applicable
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This study would be a valuable contribution to the existing literature. The reviewers have highlighted minor concerns with the work presented. Please ensure that you address their comments.
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Comments to Author
The authors have presented this manuscript which describes the whole genome sequencing of Streptomyces sp. 6(4), and the mining of this genome for specialised metabolite gene clusters. In this study they show that Streptomyces strain in question encodes 11 special metabolite gene clusters which include typical Streptomyces BGCs such as melanin, as well as T1PKSs and NRPS gene clusters. Streptomyces genome sequencing is often complex and you have been successful in obtaining a genome sequence which is sufficient to help you define the BGC responsible for antifungal production. 1. Methodological rigour Without access to the genome sequence itself, the overall quality of the genome assembly cannot be determined. I would therefore strongly recommend using software such as QUAST to show the number of …
Comments to Author
The authors have presented this manuscript which describes the whole genome sequencing of Streptomyces sp. 6(4), and the mining of this genome for specialised metabolite gene clusters. In this study they show that Streptomyces strain in question encodes 11 special metabolite gene clusters which include typical Streptomyces BGCs such as melanin, as well as T1PKSs and NRPS gene clusters. Streptomyces genome sequencing is often complex and you have been successful in obtaining a genome sequence which is sufficient to help you define the BGC responsible for antifungal production. 1. Methodological rigour Without access to the genome sequence itself, the overall quality of the genome assembly cannot be determined. I would therefore strongly recommend using software such as QUAST to show the number of contigs in your assembly, NC50 values etc. I feel this is particularly relevant given that Illumina sequencing alone is used here- without long read sequencing to bridge the gaps. You may wish to use software such as bandage- available on galaxy- to to display your contigs. This would also allow for the reader to guage how accurate the antismash predictions are likely to be. I feel this information is essential for the publishing of this paper 2. Presentation of results The phylogenetic trees which are presented show the species which are most closely related in a concise and effective way. However, although it appears 102 strains were used in the Neighbor-joining phenetic tree only a small number are shown. I would recommended using something like figtree to download the .newick file and present the whole tree to determine where the strain lies. You should also describe the software used for tree generation and display in your figure legend. 3. How the style and organization of the paper communicates and represents key findings The organisation of the paper communicates the findings well. 4. Literature analysis or discussion I feel there should be more discussion/comment regarding which gene cluster is likely to produce the anti-fungal compound of interest. A small figure showing the genes in some clusters may also be relevant. You may also wish to discuss the fact your strain doesn't appear to encode some very typical Streptomyces natural products such as hopene or geosmin. In Line 207: You write that you cannot define this as a species due to overlapping 16S sequencing. Could you please clarify that you mean the species cannot be described genomically- but chemotaxinomic assays can be used in future define the species boundaries. Perhaps a general comment about speciation in bacteria being complex may help, with reference to average nucleotide identity being used as a broad technique. 5. Any other relevant comments This paper needs to be thoroughly proof read for grammatical errors before re-submission. I have highlighted some below along with some other minor issues. Line 39: Change 'finding limitations' to 'limited' Line 26: Changed analysis to analyses. Define ST before using the abbreviation. Line 30: Change 'who' to 'which' Method: Could we have more information about the source if possible? Species of tomato, geographical location of the tomato plant etc. Line 61: estreptomycete?
Please rate the manuscript for methodological rigour
Satisfactory
Please rate the quality of the presentation and structure of the manuscript
Good
To what extent are the conclusions supported by the data?
Strongly support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
-
Comments to Author
The manuscript presented describes the full genome sequence of Streptomyces sp. 6(4), a strain previously isolated from tomato root that shows antifungal activity against the plant-pathogen, Bipolaris sorokiniana. The MiSeq Illumina platform was used to sequence the genomic DNA and the genes present have been annotated using several methods. Phylogenetic analysis has been conducted to identify the species of the isolate and AntiSMASH analysis to predict biosynthetic genes and gene clusters present. The manuscript is generally well presented. The workflow is easy to follow and the results are well interpreted. The methods section provides good detail and data are accessible in public databases. My specific recommendations are: 1. Where the authors discuss the functions of biosynthetic genes …
Comments to Author
The manuscript presented describes the full genome sequence of Streptomyces sp. 6(4), a strain previously isolated from tomato root that shows antifungal activity against the plant-pathogen, Bipolaris sorokiniana. The MiSeq Illumina platform was used to sequence the genomic DNA and the genes present have been annotated using several methods. Phylogenetic analysis has been conducted to identify the species of the isolate and AntiSMASH analysis to predict biosynthetic genes and gene clusters present. The manuscript is generally well presented. The workflow is easy to follow and the results are well interpreted. The methods section provides good detail and data are accessible in public databases. My specific recommendations are: 1. Where the authors discuss the functions of biosynthetic genes identified (lines 90-116), can any hypothesis be made regarding which genes or BGCs may be responsible for the antifungal activity of the strain observed in previous studies? While the characterisation of these genes/BGCs is clearly beyond the scope of this short communication, some discussion of this would add to the manuscript. 2. Table 1: The authors present analysis of the BGCs predicted to be present in the genome from AntiSMASH analysis and some key proteins present. Could any more detail regarding most similar BGCs in the database be added here to give more ideas about the biosynthetic potential of the strain? 3. Some revisions of the English could be applied through throughout the manuscript, with special attention to tenses and grammar. Some examples include: a. Line 25: 'with emphasize in…' should be 'with emphasis in' b. Line 85-86: 'it was detected' should be 'genes were detected' c. Line 91: 'One of this is' should be 'One of these is' 4. Line 61: Typo 'estreptomycete'
Please rate the manuscript for methodological rigour
Good
Please rate the quality of the presentation and structure of the manuscript
Very good
To what extent are the conclusions supported by the data?
Strongly support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
No: Not applicable
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