Draft Genomes Announcement of Vietnamese Xanthomonas euvesicatoria strains causing Bacterial spot on Pepper
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Xanthomonas euvesicatoria, the primary causal agent of bacterial spot of pepper (BSP), poses a significant global challenge, resulting in severe defoliation and yield losses substantial economic losses for pepper growers. We present the whole genome sequences of eight X. euvesicatoria strains associated with BSP in Vietnam. These genomes contribute to representation of pepper production regions in the global sample of X. euvesicatoria genomes, enabling the development of precise global disease management strategies.
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Thank your for the vised version of your manuscript and for addressing the comments raised by the reviewers. I would like to ask you to make sure that Table 1 is readible as the cells are in an awkward size and the words are spread over several lines currently, it is hard to read and please change the page format to portrait and only keep landscape for the Table/Figure.
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The reviewers have highlighted minor 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. In line with the reviewers comments please include some further details in your methods section on sample preparation and in particular on the software tools used for the analysis in terms of version numbers and settings used for the analysis as well as clarifying some details around the introduction and result sections as specified by the reviewers.
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Comments to Author
The paper is clear, concise and well-structured. With the exception of the comment beneath about adding an additional sentence or two on the context of the current availability of sequencing data for X.euvesicatoria, the paper has clear reasoning for how these strains will be of use to the wider community for a pathogen that has not been well characterized in isolates from Vietnam previously. The methodology used, both the key analytical stages, and the particular software used for the analyses are both sound. I have one question about the filtering of the assembly as mentioned in the comments below. The results are presented in a clear and easy-to-digest way and all of the deposited data is clearly labeled and easily accessible. I think a couple of details could be changed slightly to improve the …
Comments to Author
The paper is clear, concise and well-structured. With the exception of the comment beneath about adding an additional sentence or two on the context of the current availability of sequencing data for X.euvesicatoria, the paper has clear reasoning for how these strains will be of use to the wider community for a pathogen that has not been well characterized in isolates from Vietnam previously. The methodology used, both the key analytical stages, and the particular software used for the analyses are both sound. I have one question about the filtering of the assembly as mentioned in the comments below. The results are presented in a clear and easy-to-digest way and all of the deposited data is clearly labeled and easily accessible. I think a couple of details could be changed slightly to improve the paper as suggested in the comments below. In particular, I think it would be good to give the context of these genomes with what is already available to the community. Looking at the accession for the type strains it looks like LMG27970 is still a relatively fragmented genome, with nearly 1,500 contigs in the assembly. However, there are several complete X.euvesicatoria genomes available on NCBI. What was the reason for this type strain in particular? The other type strain used only has three contigs. It would be worth including the completeness information with your assemblies for comparison and pointing that your assemblies are comparable/better than type strains in terms of size/N50 etc. However overall, i'm happy with the paper with a few minor adjustments. Comments: The document orientation is in landscape for most pages rather than portrait, it would be good to edit this and leave only the tables in a landscape format. Line 14: Substantial economic losses - if figures are known, it would be good to add a number/statistic here Line 15: I would say they're not contributing to the representation of all pepper production regions - they are adding the representation of one region. Instead, something along the lines of these genomes gives better representation of the diversity of X.euvesicatoria genomes in Vietnam, a region that is currently underrepresented in the genomes available for X.euvesicatoria despite being one of the larger pepper producers in the Asia-Pacific region Line 23: Are there any suitable newer references? Line 29: Lack of genomic data for Vietnam. There are 161 X.euvesicatoria genomes currently submitted in NCBI, including yours. What is the geographic split, are yours the only Vietnamese ones currently? I would add a sentence saying the broad geographical regions covered by the sequencing data currently out there. Line 37: Where are the 3 that aren't from 5 cities in Vietnam from? Line 51: You say you discard the contigs bigger than 500bp and k-mers higher than 2 for the assembly, should this be ? It makes sense to exclude the shorter reads and lower coverage regions. Line 53: Which version of pilon? Line 55: Why these type strains? Line 64: What is the amylolytic activity of the type strains? Line 80: I would change the ANI percentage to two significant figures, this makes the difference a bit more clear (like it is in table 2). VTM17 looks a lot more similar to the type strains than the other strains you isolated. Line 82: genetic diversity linked to other factors could be checked by Amrfinder or something similar. I am aware this is a genome announcement so discussing this would be out of the scope, but if you ran it and found nothing, it might be worth mentioning. Table 1: The species column is redundant because all of the strains have the same value. I would remove this column. It would be useful to put the type strain information in this table for comparison. Table 2: I would call this a figure rather than a table. I would add in the legend that the type strains are shown in red.
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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Comments to Author
- l.37: Please describe whether a single leaf was used for each isolation, or whether multiple leaves were pooled (if known, please state how many), as this is not clear from the text. - l.38: Please state length of incubation for obtaining individual colonies (presumably in aerobic conditions?) - l.47: Please state conditions for growth of isolates for gDNA extraction. - l.48: I recognize that a 3rd party sequenced your strain but you must provide details about Illumina library preparation and sequencing, such as kit name and vendor, with any modifications to manufacturer's protocol. - l.49: Please state the number of raw reads obtained. - l.50: "Trim Galore" -> "TrimGalore"; also please provide a version number for this software, and state parameters used. - l.51: Please rephrase (unless it was your …
Comments to Author
- l.37: Please describe whether a single leaf was used for each isolation, or whether multiple leaves were pooled (if known, please state how many), as this is not clear from the text. - l.38: Please state length of incubation for obtaining individual colonies (presumably in aerobic conditions?) - l.47: Please state conditions for growth of isolates for gDNA extraction. - l.48: I recognize that a 3rd party sequenced your strain but you must provide details about Illumina library preparation and sequencing, such as kit name and vendor, with any modifications to manufacturer's protocol. - l.49: Please state the number of raw reads obtained. - l.50: "Trim Galore" -> "TrimGalore"; also please provide a version number for this software, and state parameters used. - l.51: Please rephrase (unless it was your intent) as this implies that k-mer coverage of >2.0 was discarded. - l.52: Please make it clear which reads are being referred to as "validated reads" - I could not tell. - l.52: Please provide a version number for SAMtools - l.53: Please state a version number for Pilon, and how many rounds of polishing were applied. - l.71, Table 1: Please state exact assembled genome length and GC% content for each sequenced isolate. This could be included in table 1. - Table 1, l.90: Please upload raw reads to SRA and provide the corresponding SRA accessions for each sequencing run/isolate. A BioProject accession is not sufficient for reproducibility as further read data can be added to a BioProject. - ll.80-81: A problem with the phrasing here is that ANI is relative to the reference/comparator genome, and the statement does not include that, as it stands. Table 2 shows the authors' intent (ANI% vs all other sequenced strains), but this does not come across as written. - For all software, the parameters used (even if they are default) must be listed. If default parameters are routinely used, a blanket statement could be made, e.g. "Unless otherwise noted, default parameters were used for all software." - Please provide the necessary metadata as indicated above - Please provide future revisions of this manuscript formatted in landscape.
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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