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Volume 10
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10.3390/pathogens10010046
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Article
Peer-Review Record

Orthology-Based Estimate of the Contribution of Horizontal Gene Transfer from Distantly Related Bacteria to the Intraspecific Diversity and Differentiation of Xylella fastidiosa

Pathogens 2021, 10(1), 46; https://doi.org/10.3390/pathogens10010046
by Giuseppe Firrao 1,2,*, Marco Scortichini 3 and Laura Pagliari 1
Reviewer 1: Anonymous
Reviewer 2: Anonymous
Pathogens 2021, 10(1), 46; https://doi.org/10.3390/pathogens10010046
Submission received: 24 November 2020 / Revised: 4 January 2021 / Accepted: 5 January 2021 / Published: 7 January 2021
(This article belongs to the Special Issue Progress on Understanding and Management of Xylella fastidiosa Infections)

Round 1

Reviewer 1 Report

This is an interesting study of the origins of the genes in the pan-genome of Xy. fastidiosa.  It seems to be carefully done.  However, there are many places in the manuscript where English grammar needs to be fixed. 

Author Response

English grammar has been fixed and language revised in the revised manuscript being submitted

Reviewer 2 Report

The authors describe genomics-based analysis evaluating the possibility for horizontally acquired genetic material in Xylella fastidiosa potentially originating from unrelated bacterial species. This pathogen is known to have high rates of recombination and the ability to acquire DNA by natural transformation so this is a very interesting and relevant topic. Many of the genes identified as originating from other species are toxin-antitoxin systems located in phage insertion regions which is a logical phenomenon. As the analysis is all computational it is limited to concluding that likely origins of certain genes in Xylella are from non-Xanthomonad species. It does not necessarily show actual mechanisms of horizontal gene transfer from other species or where this might occur in the X. fastidiosa lifecycle. However, it is still a valuable starting point for further experimental validation and better understanding of how new genetic material is acquired in Xylella. See the following points for additional clarification.

  1. Better explain how the subset of Xylella genomes was chosen for analysis. Was any independent analysis for sequence contamination conducted prior to the selection of this set of genomes? Particularly in the case of some older draft genomes there have been documented cases of sequence contamination that could impact this type of analysis (see L. Nunney, et al. Phytopathology 2012 102:5, 456-460). Several bioinformatics tools are available to do this.
  2. fastidiosa is a more conventional abbreviation for Xylella fastidiosa.
  3. Minor comments by line:

Line 35: “capable of colonizing”

Line 46: “cultural”

Line 260: “genes are enriched in X. fastidiosa pan-genomes”

Line 266: “there is compelling evidence”

Line 273: change “evidencing” to “showing”

Author Response

Please see attachment

Author Response File: Author Response.pdf

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