Phylogenetic insights derived from six Xanthomonas draft genome sequences associated with bacterial spot disease of tomato and pepper in Turkey

  1. Amandeep Kaur
  2. Jeffrey B. Jones
  3. Erica M. Goss
  4. Yesim Aysan
  5. Marcus M. Dillon

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Abstract

Xanthomonas spp. are increasingly recognized as a global threat to agriculture, impacting a broad range of economically important crops. We report the whole-genome sequences of six Xanthomonas strains isolated from tomato and pepper plants in Turkey that were experiencing symptoms of bacterial spot disease. Phylogenomic analysis with representative Xanthomonas genomes from each species revealed that three of these strains belonged to Xanthomonas perforans , two to Xanthomonas euvesicatoria and one to Xanthomonas campestris . We then analysed the phylogenomic relatedness of these strains with other strains from these respective species and characterized their type III secreted effector content. These genomic data represent a valuable resource for understanding the genetic diversity and local epidemiology of bacterial spot disease in Turkey.

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  1. Version published to 10.1099/acmi.0.001144.v3 on Access Microbiology
  2. Access Microbiology

    hank you very much for submitting your revised manuscript addressing the reviewers' comments. I am pleased to let you know that your manuscript is now accepted for publication. Congratulations!

  3. Access Microbiology

    Comments to Author

    The authors have addressed all my concerns satisfactorily. The recommendation is to accept the revised version.

    Please rate the manuscript for methodological rigour

    Very 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

  4. Access Microbiology

    Comments to Author

    I thank the authors for carefully reviewing the manuscript and addressing all of my questions and concerns. I believe the current manuscript version is substantially improved and I do not have further comments.

    Please rate the manuscript for methodological rigour

    Very 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

  5. Version published to 10.1099/acmi.0.001144.v2 on Access Microbiology
  6. Access Microbiology

    Thank you very much for submitting your manuscript to Access Microbiology. It has now been reviewed by two experts in the field, whose comments are attached below. They have provided a number of helpful suggestions to strengthen the manuscript and to improvie the coherence and clarity. Please pay special attention to comments refering to data availability. Please provide a revised manuscript (including a tracked-changes document) along with a point-by-point response to the reviewer comments witin 3 months.

  7. Access Microbiology

    Comments to Author

    The authors report the isolation, genome sequencing and identification of sixe Xanthomonas strains from tomato and pepper plants in Turkey. The work and the write-up are well done. However, given that the reviewer did not have access to the draft genomes, the taxonomy could not be verified. The authors are requested to provide the wgs accession numbers of the genome sequences and request NCBI to make data publicly available immediately after processing. BioProject and BioSample numbers donot provide access to the deposited genomes. Other comments: Title: Please add the plants (tomato and pepper) in the title. Lines 35-37: As indicated above provide the wgs accession number here. Line 82: please, delete ", 2021" Line 94: Please, add "Illumina" Line 117: How genes are in this core genome alignment? Line 139: "Accession numbers for each assembly are listed in Table 1." The authors should be more specific that "The biosample accession number ….". What the reviewer will require is the wgs accession number for each strain to validate the taxonomy. Lines 160-170: It would be interesting to investigate the pathogenicity of Xc YA1028. The authors should also reduce the speculation that strain has undergone a host shift to infect pepper because no pathogenicity was generated. Lines 219-261: The gene present/absent analysis using incomplete genomes is always problematic since the lack of a gene may be because it was not assembled correctly. The authors should provide a limitation statement analyzing draft incomplete genomes for absence of gene. The same is valid in some cases of multiple copies of a gene which might be due to misassembly of raw reads.

    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

  8. Access Microbiology

    Comments to Author

    The manuscript "Phylogenetic insights derived from six Xanthomonas draft genomes sequences associated with bacterial spot disease in Turkey" by Kaur et al. describes the isolation, sequencing, and genomic characterization of few isolates from tomato and pepper plants displaying bacterial spot symptoms in Turkey. Isolates were identified as belonging to X. perforans, X. euvesicatoria and X. campestris, and their phylogenomic relationships within each species, as well as their effector repertoires, were characterized. The manuscript addresses an important pathogen that is harmful to important crops worldwide. However, despite the scientific interest, I have comments and suggestions (some are major) that require attention from the authors. "Introduction" section 1. In ln. 51, I suggest authors to be more specific and add "X. hortorum pv. gardneri" instead of only "X. hortorum". This is because this species has a broad host range but only pv. gardneri is the tomato/pepper pathogen. "Materials and methods" section 2. "Sample collection" subsection. 2.1 Authors mention in their introduction that the importance of this study relates to providing "additional genomic data on bacterial spot pathogens collected over time from a more diverse array of locations in Turkey". Related to that, I ask the authors to complement this subsection by providing the information of how the sampled locations, Adana, Mersin, and Kayseri, relate to tomato and pepper producing regions in Turkey. Are these locations related to the highest producing regions in Turkey? Why were they chosen for sampling? 2.2 How were the isolated strains confirmed as Xanthomonas before genome sequencing? Was any test performed such as serological or PCR? 2.3 How were the plant tissues chosen for collection? Isolation of only six strains seems like a low number. Were the samples highly symptomatic? Is bacterial spot widespread and severe in Turkey? Adding all this information mentioned here, either in introduction or in this subsection, will help to better guide the reader on the disease status in Turkey and the importance of this study. 3. "Whole genome sequencing and assembly" subsection. 3.1 This is a minor comment, but I suggest adding the manufacturer for the library kit and sequencer used here. 4. "Phylogenetics analysis" subsection. 4.1 How were the additional strains detailed in Supplementary Table 1 chosen for the analysis described here? I am particularly curious about the X. campestris strains since this is a diverse species with many different pathovars and thus host ranges and possibly different effector repertoires. 4.2 I strongly recommend adding the metadata information for the type strains shown in figure 1 in Supplementary Table 1 as well. "Results and Discussion" section 5. "Species-level identification of isolated strains" subsection. 5.1 I suggest authors to also provide average nucleotide identity (ANI) values for these strains and the reference genome for the species to which they were assigned. This would be a nice complementary result showing a percentage number with a well-established cutoff for taxonomically assigning isolates to the species level. 5.2 I would have expected to see authors test the ability of X. campestris YA1028 to cause bacterial spot symptoms in pepper or not. This seems like a straightforward analysis that would help to elucidate their isolation of this species from symptomatic pepper. Was a known bacterial spot pathogen also isolated from the same sample? Although it is highly unlikely that X. campestris is causing the observed disease, no isolation of the pathogen but isolation of a "commensal" Xanthomonas spp. in that host is also unlikely. General comments 6. My main concern is that it is not clear what previous information about bacterial spot-causing Xanthomonas was available from Turkey and what novelty this study brings. For instance, additional genomes of these pathogens from Turkey are shown in figure 2. It was not clear until that figure that these resources already existed, and sequencing of only 5 additional strains (considering that one, X. campestris, is likely not a bacterial spot pathogen) seems like a small number to fulfill the gap that authors mention in the introduction. Also, it is not mentioned the importance of sampling the areas described here (see comment #2.1 above). Lns. 207-208 suggest that there are other important areas that could have been sampled and that are important to address the knowledge gap stated here. Thus, as is, this is an interesting study but feels preliminary. I suggest authors to make it clearer what new information they bring and the importance of sequencing and analyzing these few additional isolates. 7. Authors mention in the "Conclusion" section that these isolates are collected from recent outbreaks in Turkey. This information has not been provided or discussed before in the manuscript, which could help fulfill the gap noted above on comment #6. 8. I believe that some additional genomic analyses could have been performed to assess the diversity of these strains, such as antimicrobial resistance (i.e. copper, etc) and other important mechanisms for niche colonization (type 4 and 6 secretion systems, for example). Comments and suggestions by line number Ln. 224. I counted 22 core T3SE families instead of 21. Please verify.

    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?

    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?

    Yes

  9. Version published to 10.1099/acmi.0.001144.v1 on Access Microbiology