Genome sequence data for 61 isolates of Xanthomonas campestris pv. campestris from brassica crops in Serbia

  1. Tatjana Popović Milovanović
  2. Shannon Greer
  3. Renata Iličić
  4. Aleksandra Jelušić
  5. Daisy Brown
  6. Mikaeel Hussain
  7. Jamie Harrison
  8. Murray Grant
  9. Joana Vicente
  10. David John Studholme

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Abstract

This Data Note describes genome sequencing data for 61 isolates of the bacterial pathogen Xanthomonas campestris pv. campestris collected from Brassica and Raphanus crops between 2010 and 2021 in Serbia. We present the raw sequencing reads and annotated contig-level genome assemblies and we determined the races of ten isolates. The data can be used to test hypotheses, phylogeographic analyses and inform design of informative molecular markers for population genetics studies. When combined with phenotypic data, they could be used to dissect relationships between genotype and phenotypes such as host range and virulence. Finally, these genome sequences expand our inventory of plasmids known to reside in this pathogen.

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  2. Version published to 10.1099/acmi.0.000870.v2 on Access Microbiology
  3. Access Microbiology

    Please address the comments raised by the reviewers, in particular those that ask for more specifics in the Material and Methods section (eg specify symptoms of infection, what observation does the scoring correspond to) and briefly explain the main steps of the analysis in addition to the links provided. Please make sure that all versions and specify the parameters for bioinformatic analysis tools have been mentioned (eg: phylogenetic tree). I recommend strongly to clarify some results, for example the pathogenic versus weakly pathogenic (l 124), what exactly do you mean by this? Please also work on the plasmid section in terms of phrasing and appropiately explaining the rationale (eg. ll 174-176) Make sure all your citations are consistent in style and format throughout the manuscript.

  4. Access Microbiology

    Comments to Author

    The authors have presented genome sequence data for 61 serbian X. campestris pv. campestris isolates from brassica crops in Serbia, which is a valuable genomic resource for the scientific community. The data note is clear, designed properly, and data is accessible. However, I believe substantial changes are required to improve the value of this data note. I would like the authors to address the following points in the methodological, results and conclusion section to improve the value of the work carried out. Material and Methods Line No. 88-90: How did authors score the symptoms of infection? Was it based on the lesion length to distinguish between resistance and partial resistance? Line No. 92-95: The paragraph sentences should be rephrased to avoid repetition. If section 5.3 consists of just one line, it can be combined with section 5.4 under a single heading: "Genomic DNA extraction, sequencing and assembly". Line No. 97-107: Could authors please include the version for all the tools used wherever appropriate such as samtools, bowtie2, pilon? Line No. 106-107: Authors could explain tree construction method more clearly. Did authors use FastTree2 as implemented in PhaME for tree construction, or did they use it separately? PhaME implements various tools for complete analysis. Line No. 111-113: Mention the parameters used for executing plasmid search. For all the software's, the parameters used must be listed. Even if default parameters were used a general statement should be made. Results and Discussion Line No. 119-125: How different is isolate Xc452 from the others? Since the authors have genome sequences available, did they look into ANI values? Although this might be a lot to fit into data note, I noticed that the identification of isolates was done using previous methods based on PCR or MLSA. However, with the genome sequences available, the authors might gain useful information about the relatedness of isolates using ANI. What was the criteria for distinguishing pathogenic from weekly pathogenic. It would be appropriate if authors could show the pictures of the disease symptoms to clear between non-pathogenic or weakly pathogenic. Plasmid analysis: The authors have analyzed plasmid content in the isolates, as plasmids play an important role in the evolutionary diversification and adaptation of bacterial populations. However, the results related to plasmids seem to broadly explain what the authors observed without deriving any meaningful insights from the data. Though this is just a data note, it would have been more appropriate if the authors had commented on whether these are conjugative plasmids carrying core plasmid genes or if they possess any other beneficial traits related to virulence or antimicrobial resistance. Line No. 164: "6.4 Fourteen of the 61 strains contain a plasmid": The heading can be more general since the analysis is based on draft genomes and is not supported by any gel profile data, and the isolates possess more than one plasmid type. Line. No. 169: What's the percentage similarity of contigs detected in Xc7 and Xc261 with B-1459 plasmid. Line No. 172-174: Table 3 should be corrected as Table 4 and remove repeated accession numbers. Line No. 174-176: Why did authors choose to show a sequence comparison of Serbian Xcc genomes with the plasmid assembled from Xcc WHRI8978 in Figure 2. It would be appropriate to mention the plasmid as pWHRI8978 along with its GenBank accession number and size. Also, it is unclear whether authors identified this as a plasmid hit in the Serbian Xcc isolates through PLSDB or if they compared the entire genome sequence with pWHRI8978. Line No. 177-179: The authors mentioned that the Serbian isolates lack some genes VDR56_022750, VDR56_022755, VDR56_022760, and VDR56_022700. It would be helpful if authors could explain what does these genes code for and any significance of their absence in the Serbian isolates, at least in one or two sentences. Conclusion: The Conclusion is a repetition of the abstract Minor corrections: It would be appropriate to use either the word isolates or strains throughout the data note. Line No. 56-61: Include references Line No. 128: yielded is not the correct word. Figure 2: Is plasmid in Serbian strains is identical to pWHRI8978. Different colors represent strains. What about percentage identity or similarity? Table 2: In the reference column blank space could be filled as 'this study' Table with plasmid data should be labeled as Table 4 and correct Xc221-1 to 221-2 The authors have cited the literature well. However, the reference style is not appropriate and uniform.

    Please rate the manuscript for methodological rigour

    Satisfactory

    Please rate the quality of the presentation and structure of the manuscript

    Satisfactory

    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 to this study

  5. Access Microbiology

    Comments to Author

    This is an interesting and well-written data note presenting the genomes for 61 Xanthomonas campestris pv. campestris isolates. These isolates could help test various hypotheses, reconstruct the pathogen's evolutionary history, and identify genetic markers for population studies. Please see my comments below: Line 83 - "King's B medium": A reference needs to be added here for the medium. Line 85 - "OD600=~0.2": Why was an optical density of 0.2 selected? Was this chosen to match Vicente et al (2001) CFU/mL? If that's the case, what did OD600= 0.2 correspond to in CFU in your study? Line 93 - The protocol link does not work (error: DOI not found). Please correct this or include the necessary information here for reproducibility purposes. Line 123-125: Isolate Xc452 doesn't match any previously described race. What does this mean for the isolate? Could you please expand your discussion here? Have similar discrepancies been observed previously? Figure 1. Can you include more information regarding the creation of the phylogenetic tree? E.g. bootstraps, best-fit model used etc. What was the outgroup? Please include this information in the methods sections as well - I can see it in https://github.com/davidjstudholme/phylogenomics-Xanthomonas-1/blob/main/phame.ctl, but I think this information should be more prominent within the text. Table 1. Line 216-217: Regarding the asterisk indicating result variability - What does this mean? Variability between your replicates or between yours and previously published results? Please expand. References: Some of your references have extra numbering before the author names. I imagine this is a reference manager issue, but could you confirm all references are there correctly?

    Please rate the manuscript for methodological rigour

    Good

    Please rate the quality of the presentation and structure of the manuscript

    Very good

    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

  6. Version published to 10.1099/acmi.0.000870.v1 on Access Microbiology