Xanthomonas citri pv. eucalyptorum strain 4866-2_S43 (formerly X. axonopodis pv. eucalyptorum): the causal agent of bacterial leaf blight on eucalypts recovered in Argentina
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We report the draft genome assembly of strain 4866-2_S43 isolated from a eucalyptus lesion in Argentina and what until recently was caused by Xanthomonas citri pv. eucalyptorum ( Xce ). The genome size is 5 188 607 bp, with a G+C content of 64.66%. Comparative analysis reveals that the closest relative of strain 4866-2_S43 is Xce LPF 602, isolated in Brazil. Comparison of the whole genome sequences revealed an average nucleotide identity (ANI) of 99.96% between the two strains. ANIs were determined between the whole genome sequence of strain 4866-2_S43 and the genomes of all currently validated Xanthomonas spp. These results revealed that strain 4866-2_S43 shared >95% similarity with X. citri pv. citri and X. citri pv. phaseoli , and <95% with X. euvesicatoria pv. alfalfae , X. euvesicatoria pv. perforans , and X. euvesicatoria pathovars euvesicatoria and eucalyptii .
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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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Please carefully consider the reviewers comments regarding Open Data and accessing NCBI records etc.
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Comments to Author
This manuscript describes the second genome sequence of a Eucalyptus pathogen of the species Xanthomonas citri, which was isolated in Argentina. It would be nice to learn how many strains were isolated and how they were identified as Xae strains (lines 41-42). The authors should also deposit their sequenced strain in an international strain collection in order to comply with FAIR principles (Findable, Accessible, Interoperable, Reusable). In addition to refer to Subedi et al. the authors should briefly mention which technology was used for sequencing, which assembly method was used, how high the coverage was, how many contigs were obtained, how good the quality of the assembly is (completeness, contamination). The manuscript should also indicate the NCBI BioProject and BioSample accession numbers. A …
Comments to Author
This manuscript describes the second genome sequence of a Eucalyptus pathogen of the species Xanthomonas citri, which was isolated in Argentina. It would be nice to learn how many strains were isolated and how they were identified as Xae strains (lines 41-42). The authors should also deposit their sequenced strain in an international strain collection in order to comply with FAIR principles (Findable, Accessible, Interoperable, Reusable). In addition to refer to Subedi et al. the authors should briefly mention which technology was used for sequencing, which assembly method was used, how high the coverage was, how many contigs were obtained, how good the quality of the assembly is (completeness, contamination). The manuscript should also indicate the NCBI BioProject and BioSample accession numbers. A comparison of the manuscript with the data deposited at NCBI reveals several inconsistencies: 4352 CDS (manuscript) versus 4416 CDS (NCBI); 54 tRNAs (manuscript) versus 48 tRNAs (NCBI). This needs to be clarified. Above all, however, the manuscript and the data at NCBI leave the reader with an unclear picture of the taxonomic position of the sequenced strain. At one point it is stated that the strain belongs to the species X. citri, but at the end of the text it is stated that the strain isolated in Argentina is placed as Xanthomonas axonopodis pv. eucalyptorum. In addition, the NCBI BioProject (PRJNA1070572) and BioSample (SAMN39652913) list the strain as Xanthomonas euvesicatoria. Three different species proposals for one strain - that's confusing. Authors must correct the NCBI submission if they do not want to risk NCBI staff categorising their sequence as problematic.
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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Comments to Author
Manuscript ACMI-D-24-00070 announces the availability of the genome sequence of strain 4866-2_S43 which, based on in silico similarity indices ANIb and dDDH, was classified as Xanthomonas citri pv. eucalyptorum. The methods are sound, and the conclusions agree with the results of the genome comparisons conducted. I only have some minor suggestions: _ Since it is already proven that the strain belongs to X. citri pv. eucalyptorum, the authors should use this scientific name and its abbreviation Xce in L22, L24 and elsewhere throughout the manuscript. The genome sequence comparisons conducted by the authors confirm that it is a X. citri: L58-61. This would be more consistent with the scientific name used in the title. _ It is now accepted that Xanthomonas perforans is a distinct pathovar of Xanthomonas …
Comments to Author
Manuscript ACMI-D-24-00070 announces the availability of the genome sequence of strain 4866-2_S43 which, based on in silico similarity indices ANIb and dDDH, was classified as Xanthomonas citri pv. eucalyptorum. The methods are sound, and the conclusions agree with the results of the genome comparisons conducted. I only have some minor suggestions: _ Since it is already proven that the strain belongs to X. citri pv. eucalyptorum, the authors should use this scientific name and its abbreviation Xce in L22, L24 and elsewhere throughout the manuscript. The genome sequence comparisons conducted by the authors confirm that it is a X. citri: L58-61. This would be more consistent with the scientific name used in the title. _ It is now accepted that Xanthomonas perforans is a distinct pathovar of Xanthomonas euvesicatoria, hence, the authors should use X. euvesicatoria pv. perforans in L28. The dendrogram presented by the authors support this. _ The abbreviation "pv." for pathovar should not be italicized in L37 and elsewhere. _ Italicize "Eucalyptus" in L40. _ Describe/explain what "D" means in L43. _ Correct the typo in L44: ºC. _ A search with accession no. JAZGJM000000000 in the DDBJ/EMBL/GenBank database did not show any results. On the other hand, when the same accession number is searched in the NCBI database, genome assembly ASM3635348v1 appears, which corresponds to the same strain code, recovered from eucalyptus in Corrientes, Argentina, submitted by the same Unidad de Genomica y Bioinformatica, but deposited as Xanthomonas euvesicatoria. I interpret that it is the same genome sequence as the one reported by the authors in the manuscript. I suggest the authors correcting the information at NCBI in order to avoid confusion in the scientific community.
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?
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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