Draft genome sequences of 11 Xanthomonas strains associated with bacterial spot disease in Turkey
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Bacterial spot is an economically significant disease in tomato and pepper-producing countries globally. We report the whole-genome sequence of 11 Xanthomonas strains associated with bacterial spot disease on pepper, tomato and eggplant in the Southeastern Anatolia Region, Turkey. This genomic information can be used as a reference to study the genetic diversity of these species and contribute to illuminating pathogen evolution with respect to host specificity.
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Thank you addressing the comments raised by the reviewers and submitting this revised manuscript. I note you did not carry out one of the reviewer’s for a further phylogenetic analysis as it was beyond the scope of your intention for this work as a draft genome announcement.
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The reviewers have highlighted major concerns with the work presented. Please ensure that you address their comments. Please provide more detail in the Methods section and ensure that software is consistently cited and its version and parameters included. As already raised by the reviewers the manuscript requires a few more details in the methods section and some additional analyses are suggested by reviewer 1 to improve the value of the work overall
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Comments to Author
Review - Subedi et al. Access Microbiology "Draft Genome Sequences of 11 Xanthomonas Strains associated with bacterial spot disease in Turkey " The manuscript submitted by Subedi et al. describe the identification and whole genome sequencing (WGS) of 11 Xanthomonas isolates. Xanthommonas is a bacterial pathogen that is reported to cause spot disease, which results in a loss in yields of globally essential crops. With this study, the authors by performing WGS, could provide a resource for genomic information extracted from 11 Xanthomonas strain, that can be used to study genetic diversity and strain-specific markers that would contribute to the understanding of Xanthomonas pathogenicity and host specificity, which are valuable to develop strategies to eradicate this pathogen. The data presented …
Comments to Author
Review - Subedi et al. Access Microbiology "Draft Genome Sequences of 11 Xanthomonas Strains associated with bacterial spot disease in Turkey " The manuscript submitted by Subedi et al. describe the identification and whole genome sequencing (WGS) of 11 Xanthomonas isolates. Xanthommonas is a bacterial pathogen that is reported to cause spot disease, which results in a loss in yields of globally essential crops. With this study, the authors by performing WGS, could provide a resource for genomic information extracted from 11 Xanthomonas strain, that can be used to study genetic diversity and strain-specific markers that would contribute to the understanding of Xanthomonas pathogenicity and host specificity, which are valuable to develop strategies to eradicate this pathogen. The data presented in this paper is generally scientifically fine. The manuscript is relatively easy to follow. However, we list some points below that we feel should be addressed before publication. Relating to experimental procedure : * The authors performed Real-time PCR amplification to check the identity of the isolated strains. They claim that these PCR amplifications were performed using species-specific probes. However, the authors did not mention the gene markers they amplified. It will be helpful to add the information regarding the amplified genes and the primers used for the PCR analysis. * The authors performed whole genome sequencing (WGS) on the 11 isolated Xanthomonas strains. Here information about the sequencing procedure is missing such as the library preparation procedure and sequencing depth used per library. * Finally, can the authors discuss the mechanism behind Xanthomonas host range shift or speculate how this does work and if any genomic region transfer, or acquisition triggers adaptation to new hosts? Relating to Annoncement : - (Lines 39-41): this sentence needs rephrasing.
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
1. Methodological rigour, reproducibility and availability of underlying data The authors have provided sufficient information to access both raw sequencing reads and assemblies from NCBI. Likewise, the methods they have employed to assemble and analyse their genomes are sound. However, could the authors please address the following concerns: * Could the authors please report culture conditions (Media, temperature, shaking speeds) used to grow cultures up for both DNA extraction and for leaf infection assays? * Could the authors please provide the protocol used to isolate these strains as well as a description of the symptoms used to identify bacterial spot disease? * Could the authors please report the settings used when executing Trim Galore, SPAdes, pilon, and pyani? * As the authors have used an …
Comments to Author
1. Methodological rigour, reproducibility and availability of underlying data The authors have provided sufficient information to access both raw sequencing reads and assemblies from NCBI. Likewise, the methods they have employed to assemble and analyse their genomes are sound. However, could the authors please address the following concerns: * Could the authors please report culture conditions (Media, temperature, shaking speeds) used to grow cultures up for both DNA extraction and for leaf infection assays? * Could the authors please provide the protocol used to isolate these strains as well as a description of the symptoms used to identify bacterial spot disease? * Could the authors please report the settings used when executing Trim Galore, SPAdes, pilon, and pyani? * As the authors have used an in-house python script to calculate assembly statistics, could they please make this script available? * As NCBI have annotated the genomes, could the authors please comment on these annotations (e.g. number of genes, number of rRNAs, number of tRNAs)? * Do the authors have data for eggplant infections from their other other isolates to compare to isolate Tu-4? * Could the authors please conduct a phylogenetic analysis of their isolates. Although their ANI results confirm that they are all Xanthomonas (and, with an ANI>95%, suggest that X. perforans and X. euvesicatoria are a single species), it does not place them within their evolutionary context. * For the infection assays, could the authors please report the protocol used to infect leaves in sufficient detail for it to be replicated from infection to enumeration? Could the authors also report the number of infections carried out, and if these infections were carried out on separate leaves or one leaf? Did the authors carry out a control on a tomato or pepper plant to demonstrate the isolates were infectious? * For the RT-PCR, could the authors please briefly explain the assay and the cutoff values used to assign species identifications? 2. Presentation of results The results are presented satisfactorily, however there are minor changes needed: * Table 1: Could the authors please change Genome Length (Mb) to Genome Length (Mbp). Could the authors also include the same statistics for the reference genomes used in this work? * Table 2: Could the authors please provide an ANI-scaled coloured background to the cells to make the ANI values easier to parse? Alternatively, the results could be presented as a heatmap. * Figure 1: As there is not an even length of time between measurements, could the authors please present this data as a bar graph instead of a line graph, or space the x-axis evenly? In addition, the y axis is mislabelled as "Log10/cm2" where it presumably should be Log10CFU/cm2. * Figure 2: Do the researchers have a photo of the leaf used in panel C at day 0 of infection and if so could they please include this? 3. How the style and organization of the paper communicates and represents key findings The submission could benefit from a clearer subdivision into Introduction, Methodology, Results, and Discussion sections. The authors describe the work they have carried out in a logical order. 4. Literature analysis or discussion The authors sufficiently review the literature to familiarise the readership with Xanthomonas and its importance as an agricultural pathogen. Could the authors please expand on the significance of their finding of eggplant colonising Xanthomonas and on the phylogeny and taxonomy of Xanthomonas as a genus and how their isolates fit into it? As their ANI calculations suggest that all of their isolates are monospecific, could they also please discuss how their isolates compare to other published Xanthomonas populations? Finally, could the authors provide citations for Trim Galore and SPAdes. 5. Any other relevant comments I believe there are substantial changes required to the manuscript's content in order to ensure reproducibility of the analyses they have carried out. In addition, I believe that the authors need to substantially expand the methodology descriptions for how they cultured and isolated their strains and carried out infection assays. The additional analyses I have suggested do not preclude this work from publication, however are not onerous and would improve the value of the work carried out.
Please rate the manuscript for methodological rigour
Poor
Please rate the quality of the presentation and structure of the manuscript
Satisfactory
To what extent are the conclusions supported by the data?
Partially 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: No human or animal work carried out
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