Genome sequence of the bialaphos producer Streptomyces sp. DSM 41527 and two putative phosphonate antibiotic producers Streptomyces sp. DSM 41014 and DSM 41981 from the DSMZ strain collection
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Streptomyces sp. DSM 41014, DSM 41527, and DSM 41981 are three strains from the DSMZ strain collection. Here, we present the draft genome sequences of DSM 41014, DSM 41527, and DSM 41981 with a size of 9.09 Mb, 8.45 Mb, and 9.23 Mb, respectively.
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The work presented is clear and the arguments well formed. This study would be a valuable contribution to the existing literature. This is a study that would be of interest to the field and community.
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The reviewers have highlighted minor concerns with the work presented. Please ensure that you address their comments. Please include the versions and parameter settings for all software used in your bioinformatics analysis. In parts the presentation of results is not entirely clear, please make sure you clarify the concerns raised by the reviewers.
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Comments to Author
The authors describe the genome sequencing of three Streptomyces strains that carry a phosphonate biosynthetic gene clusters. The rationale is clearly laid out. The cultivation, gDNA isolation and library preparation process is well described, however, the jump from past tense to present tense for the methodology description "reproduced directly from the sequencing company" and the direct copy off the company text feels awkward. My suggestion: please keep past tense and rewrite the section with own words. The genomes themselves are split in plenty of contigs (particularly the DSM41014 genome), means in other words that the genome sequences are still quite fragmented for today's standards (contig number should be 90x)
Please rate the manuscript for methodological rigour
Good
Comments to Author
The authors describe the genome sequencing of three Streptomyces strains that carry a phosphonate biosynthetic gene clusters. The rationale is clearly laid out. The cultivation, gDNA isolation and library preparation process is well described, however, the jump from past tense to present tense for the methodology description "reproduced directly from the sequencing company" and the direct copy off the company text feels awkward. My suggestion: please keep past tense and rewrite the section with own words. The genomes themselves are split in plenty of contigs (particularly the DSM41014 genome), means in other words that the genome sequences are still quite fragmented for today's standards (contig number should be 90x)
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?
Yes
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Comments to Author
In their manuscript, titled "Genome sequence of the bialaphos producer Streptomyces sp. DSM 41527 and two putative phosphonate antibiotic producers Streptomyces sp. DSM 41014 and DSM 41981 from the DSMZ strain collection", Zimmerman et al report, for the first time, the genomes of the three mentioned Streptomyces species obtained from the DSMZ culture collection. Discussed below are key points the authors should consider with regards to their report. 1. Methodological rigour, reproducibility and availability of underlying data The authors sufficiently report their strategy for cultivating the strains prior to shipping to MicrobesNG for sequencing. Likewise, their bioinformatics is sound. However, could they please report the settings used for their antiSMASH runs. 2. Presentation of results Table 1 …
Comments to Author
In their manuscript, titled "Genome sequence of the bialaphos producer Streptomyces sp. DSM 41527 and two putative phosphonate antibiotic producers Streptomyces sp. DSM 41014 and DSM 41981 from the DSMZ strain collection", Zimmerman et al report, for the first time, the genomes of the three mentioned Streptomyces species obtained from the DSMZ culture collection. Discussed below are key points the authors should consider with regards to their report. 1. Methodological rigour, reproducibility and availability of underlying data The authors sufficiently report their strategy for cultivating the strains prior to shipping to MicrobesNG for sequencing. Likewise, their bioinformatics is sound. However, could they please report the settings used for their antiSMASH runs. 2. Presentation of results Table 1 sufficiently describes the quality metrics of the authors' assemblies. However, the authors' findings from genome mining needs to be expanded upon: * Can the authors please provide a table of the antiSMASH results for each strain * For Figure 1, could the authors please indicate the length of the clusters being compared? Tools like clinker are readily accessible and available for BGC comparisons - As currently presented, the figure is insufficient to compare the three regions. In addition, there is no indication of what the colours on each ORF represent - this is inaccessible to someone unfamiliar with antiSMASH. * Can the authors please indicate if the three phosphonate BGCs are on contig edges In addition, it would be nice to see the phylogenetic trees associated with the authors' analyses. 3. How the style and organization of the paper communicates and represents key findings The paper concisely reports all information pertinent to a genome announcement. However, I am confused by what is written between lines 46 and 48; "Two additional Streptomyces strains, DSM 41014 and DSM 41981, were identified as potential phosphonate-producing strains based on the finding of phosphonate-specific biosynthesis genes in their genomes" - did the authors have genome sequence data available to them, identify phosphonate-specific genes, and then decide to resequence them? Please clarify. 4. Literature analysis or discussion The authors sufficiently review the history of phosphonate antibiotics. 5. Any other relevant comments I have no additional comments, the work here is sound - the authors need to clarify their presentation and writing where indicated. There are minor English errors - in particular, the methods section lifted from MicrobesNG is presented in present tense where it should probably be changed to past tense. On line 102, could the authors please reword "indicating they encode the same phosphonate natural compound" to "indicating they probably encode for the biosynthesis of similar phosphonate compounds". Although I don't disagree with the first statement, it's a hard conclusion to draw from genomic evidence alone and so is worth tempering.
Please rate the manuscript for methodological rigour
Satisfactory
Please rate the quality of the presentation and structure of the manuscript
Satisfactory
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
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