Draft genome sequences for ten strains of Xanthomonas species that have phylogenomic importance
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Here we report draft-quality genome sequences for pathotype strains of eight plant-pathogenic bacterial pathovars: Xanthomonas campestris pv. asclepiadis , X. campestris pv. cannae , X. campestris pv. esculenti , X. campestris pv. nigromaculans , X. campestris pv. parthenii , X. campestris pv. phormiicola , X. campestris pv. zinniae and X. dyei pv. eucalypti (= X. campestris pv. eucalypti ). We also sequenced the type strain of species X. melonis and the unclassified Xanthomonas strain NCPPB 1067. These data will be useful for phylogenomic and taxonomic studies, filling some important gaps in sequence coverage of Xanthomonas phylogenetic diversity. We include representatives of previously under-sequenced pathovars and species-level clades. Furthermore, these genome sequences may be useful in elucidating the molecular basis for important phenotypes, such as biosynthesis of coronatine-related toxins and degradation of fungal toxin cercosporin.
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I am pleased to tell you that your article has now been accepted for publication in Access Microbiology.
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Overall, the study was well received. From my understanding of the reviewer's comments, most highlighted a need to calculating dDDH and visualise ANI results in a heatmap. The others should be relatively minor to address (ie. spelling/phrasing/formatting). This is a study that would be of interest to the field and community. The reviewers have highlighted minor concerns with the work presented. Please ensure that you address their comments.
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Comments to Author
1. Methodological rigour, reproducibility and availability of underlying data - 2. Presentation of results 3. How the style and organization of the paper communicates and represents key findings 4. Literature analysis or discussion 5. Any other relevant comments The study/resource is important and timely for the community working in the area of plant pathogens in general and Xanthomonas in particular. Below are the major comments that authors need to address to strengthen the manuscript DNA gyrase gene sequence is available for all the strains sequenced in the study. The authors need to make sure that gyrase gene sequence is identical to the corresponding sequence in the genome of that particular strai Line 49- 34 valid species available. Figure 1: Species names in the phylogenetic tree are …
Comments to Author
1. Methodological rigour, reproducibility and availability of underlying data - 2. Presentation of results 3. How the style and organization of the paper communicates and represents key findings 4. Literature analysis or discussion 5. Any other relevant comments The study/resource is important and timely for the community working in the area of plant pathogens in general and Xanthomonas in particular. Below are the major comments that authors need to address to strengthen the manuscript DNA gyrase gene sequence is available for all the strains sequenced in the study. The authors need to make sure that gyrase gene sequence is identical to the corresponding sequence in the genome of that particular strai Line 49- 34 valid species available. Figure 1: Species names in the phylogenetic tree are not in italics Table 1: Adding genome assembly statistics such as genome coverage and contamination, N50 value will make the genome assembly more reliable. Line 108, Line 124, Line 151: Provide ANI data and dDDH values to strengthen the statement. Provide ANI values in a table or heatmap format to make the paper more comprehensible to the reader. Further, calculation of digital DNA-DNA hybridization values might help in the taxonomic refinement of these strains along with phylogeny and ANI. Line 162: There are more genomes available for X. euroxanthea in the NCBI GenBank database. Adding these genomes to the phylogeny might clear whether NCPPB 4013 falls amongst the X. euroxanthea clade or in close association with them. Line 177: The authors need to provide ANI and dDDH values of X. campestris pv. cannae with X. sontii and X.sacchari to support their statement that "There is also a case to incorporate "X. sontii" into this species, given its close phylogenetic affinity"
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?
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
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Comments to Author
The manuscript provides very useful information on genome sequences for unique strains that represent strains that are not widely distributed and represent underrepresented strains within several species. I do not see that it is necessary to include species level clades as headings as they are only informative relating to the article by Parkinson et al, 2009 and in my opinion are somewhat confusing. I believe the manuscript would benefit from including average nucleotide identities throughout the manuscript and in table format. The authors point to >96% ANI but >95% is ofter referred to as the cut-off for species. X cannabis is not a species and apparently the article by Jacobs et al. is not sufficient for species status. I have made many comments directly on the pdf. 1. Methodological rigour, …
Comments to Author
The manuscript provides very useful information on genome sequences for unique strains that represent strains that are not widely distributed and represent underrepresented strains within several species. I do not see that it is necessary to include species level clades as headings as they are only informative relating to the article by Parkinson et al, 2009 and in my opinion are somewhat confusing. I believe the manuscript would benefit from including average nucleotide identities throughout the manuscript and in table format. The authors point to >96% ANI but >95% is ofter referred to as the cut-off for species. X cannabis is not a species and apparently the article by Jacobs et al. is not sufficient for species status. I have made many comments directly on the pdf. 1. Methodological rigour, reproducibility and availability of underlying data - Fine 2. Presentation of results - discussed above 3. How the style and organization of the paper communicates and represents key findings - Could be improved 4. Literature analysis or discussion - Brief but fine 5. Any other relevant comments. No
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?
No: not applicable
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Comments to Author
Jamie Harrison and co-workers present ten novel genome sequences of underexplored taxa in the genus Xanthomonas, which will be useful for follow-up studies using phylogenomic approaches. The short descriptions of the sequenced representatives of them are interesting to read. Methods are well described at protocols.io. There are a few points that the authors should consider when revising their manuscript: (i) L25 and elsewhere: There seems to be some confusion in the literature over the proper spelling of the pathovar name "phormicola". In the original description by Takimoto (1933), the name "Bacterium phormicola" was used, and the spelling "phormicola" was later also used for Xanthomonas. However, in its first Comprehensive List of Names of Plant Pathogenic Bacteria, the Committee corrected several …
Comments to Author
Jamie Harrison and co-workers present ten novel genome sequences of underexplored taxa in the genus Xanthomonas, which will be useful for follow-up studies using phylogenomic approaches. The short descriptions of the sequenced representatives of them are interesting to read. Methods are well described at protocols.io. There are a few points that the authors should consider when revising their manuscript: (i) L25 and elsewhere: There seems to be some confusion in the literature over the proper spelling of the pathovar name "phormicola". In the original description by Takimoto (1933), the name "Bacterium phormicola" was used, and the spelling "phormicola" was later also used for Xanthomonas. However, in its first Comprehensive List of Names of Plant Pathogenic Bacteria, the Committee corrected several pathovar names according to Latinization rules, and added a connecting vowel "i" in compound names. Since then, the spelling used in publications has been "phormiicola". We therefore suggest to use the correct name following Latin rules, i.e. "phormiicola". (ii) Line (L) 25/26: Is X. dyei pv. eucalypti a type or a pathotype strain? (iii) L61/62: When looking at GenBank, it is not really true that there are no genome sequences available for Slc 2, 3, 4, 5 and 6. It's probably more precise to say that they have not been formally described yet. (iv) L93: It was not Jacobs and colleagues who for the first time proposed "Xanthomonas cannabis" as a new species name. In fact, Netsu et al. (J. Gen. Plant Pathol. 80: 164-168) speculated in 2014 that their Japanese strain of Xanthomonas campestris pv. cannabis caused the same disease as observed earlier by Watanabe ("Sen-i sakumotsu byo gaku". Asakura Publishing, Tokyo, pp 112-113). In 1947, Watanabe had named the causal bacterium as "Pseudomonas cannabis", and subsequently, Okabe and Goto proposed in 1955 to reclassify it into the genus Xanthomonas as "X. cannabis" ("Bacterial plant diseases in Japan: I. A list of bacterial diseases and their pathogens". Rep. Fac. Agric. Shizuoka Univ. 5: 63-71). Based on this historical account, Jacobs and collaborators used the name suggested by Okabe and Goto, "X. cannabis". (v) L98: esculenti in italics (vi) L101: NCPPB 2877 (with space in between) (vii) L164: When ANI values are not conclusive, i.e. between 94% and 96%, it is advised to complement the analysis by calculating digital DNA-DNA hybridization (dDDH) values (e.g. https://www.dsmz.de/services/online-tools/genome-to-genome-distance-calculator-ggdc). Please add and discuss this information here. (viii) L177/178: Please provide ANI and dDDH values when suggesting to incorporate "X. sontii" in the species X. sacchari. (ix) L200: What is meant with "species X. hortorum lineage"? (x) References 1, 5, 7, 11, 20, 23, 33, 34, 53, 55, 61, 62, 64 and 65 are not correct. (xi) For ref. 45, one may better cite: Daub ME, Ehrenshaft M (2000). The Photoactivated Cercospora Toxin Cercosporin: Contributions to Plant Disease and Fundamental Biology. Annu. Rev. Phytopathol. 38: 461-490. doi: 10.1146/annurev.phyto.38.1.461.
Please rate the manuscript for methodological rigour
Very 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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