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Genome Biol Evol
Genome Biol Evol
gbe
Genome Biology and Evolution
1759-6653
Oxford University Press UK

10.1093/gbe/evae178
evae178
Correction
AcademicSubjects/SCI01130
AcademicSubjects/SCI01140
Correction to: Genetic and Functional Diversity Help Explain Pathogenic, Weakly Pathogenic, and Commensal Lifestyles in the Genus Xanthomonas
9 2024
03 9 2024
03 9 2024
16 9 evae17803 9 2024
© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.
2024
https://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.
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pmcThis is a correction to: Michelle M Pena, Rishi Bhandari, Robert M Bowers, Kylie Weis, Eric Newberry, Naama Wagner, Tal Pupko, Jeffrey B Jones, Tanja Woyke, Boris A Vinatzer, Marie-Agnès Jacques, Neha Potnis, Genetic and Functional Diversity Help Explain Pathogenic, Weakly Pathogenic, and Commensal Lifestyles in the Genus Xanthomonas, Genome Biology and Evolution, Volume 16, Issue 4, April 2024, evae074, https://doi.org/10.1093/gbe/evae074

Following publication of the original article, errors in the annotation file used for labelling Figure 5, Figure S10 and Supplementary tables S11-S15 were identified. These errors also led to edits to annotations of specific genes listed in the Results section. Specific corrections are listed below point by point. However, these corrections do not change the inferences made in this study. Overall, the functional categories that were identified as associated with commensal or pathogenic lifestyles remain the same and conclusions from this study related to lifestyle of xanthomonads are not affected by these edits.

The following changes have been made to the article:

The annotations of orthogroups in Figure 5 have been corrected.

The annotations in Supplementary tables S11-S15 have been corrected.

While overall observations on enriched or unique genes associated with commensals and pathogens do not change at the functional category level, annotations of some specific genes that were listed in the Results section have been edited, as follows: The following sentence has been added to the section entitled “Association Analysis to Identify Genes and Features That Define the Lifestyle of Xanthomonas Species”: Genes encoding antitoxin, immunity proteins, genes involved in stress response, DNA repair were identified as those shared by commensals and weak pathogens.

The following text “SGNH hydrolase-like domain containing acetyltransferase protein, AlgX, is involved in alginate biosynthesis in Pseudomonas aeruginosa and virulence during cystic fibrosis. Although alginate is known to be involved in epiphytic fitness in Pseudomonas syringae (Yu et al. 1999), its contribution towards stress tolerance in xanthomonads remains to be investigated. Another gene belonging to PD-(D/E)XK nuclease superfamily, also characterized in contact-dependent DNA-degrading effectors (Sirias et al. 2020), was identified in both commensals and weak pathogens. Such nuclease effectors may impart a competitive advantage to the commensals and weak pathogens in a mixed species community as they establish their niche.” is now replaced by the following annotations for corresponding orthologs: “Another gene associated with commensal and weak pathogens belonged to the GNAT superfamily acetyltransferase family protein, conserved from bacteria to eukaryotes. These proteins function in processes ranging from antibiotic resistance to histone modification in bacteria (Favrot et al. 2016).”

Specific names of proteins involved in withstanding ROS have been added. “Enrichment of proteins such as SOS response associated peptidase family, thioredoxin reductase, in commensals and weak pathogens may explain why they can be simultaneously isolated along with pathogens from infected tissue and why they can withstand host defenses, including reactive oxygen species.”

Line 484 - Table S13 was changed to Table S14.

Line 487 – a citation of Table S13 was added.

The following text from manuscript that referred to incorrect annotation of specific ortholog was replaced: “Among the genes depleted in commensals and weak pathogens was an adenylosuccinate synthetase (S-AMPS) involved in de novo purine biosynthesis in the cytoplasm. This pathway is connected to the TCA cycle and, thus, to the central metabolism. This enzyme links GTP hydrolysis to inosine monophosphate (IMP) condensation with L-aspartate to produce adenylosuccinate (S-AMP). It can be hypothesized that pathogens may experience limitations of these compounds in their niche, for example, apoplast or xylem, and, thus, have evolved the ability to synthesize S-AMP. This enzyme was found in the periplasm-enriched fraction of Xanthomonas citri but not in X. fuscans subsp. aurantifolii type B (Zandonadi et al. 2020). Another gene involved in lipid metabolism, annotated as phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase or related enzyme was associated exclusively with pathogenic Xanthomonas. Xanthomonas campestris was characterized for its unique lipid metabolism pathways with a bifunctional enzyme for PE synthesis that functions in a serine-dependent or an ethanolamine-dependent pathway, depending upon the availability of substrates in-planta (Aktas & Narberhaus 2015).” This text has been replaced by the following text that refers to the correct annotation: “A cluster of genes involved in isoprenoid biosynthesis pathway were identified as those depleted in commensals and weak pathogens when compared to pathogens, more specifically associated with group 1 pathogenic xanthomonads (Table S15B). Isoprenoid biosynthesis is considered as important target for designing antimicrobial drugs in pathogenic bacteria (Heuston et al. 2012).”

The following references which are no longer relevant and their in-text citations have been deleted: Aktas et. al 2015, Sirias et. al 2020, Yu et. al 1999, and Zandonadi et. al. 2020

The following reference and its in-text citation has been added: Heuston et. al 2012 and Favrot et. al 2016.

The correct annotation file is uploaded on GitHub and thus, zenodo doi was updated to reflect the correct annotation file 10.5281/zenodo.11406858.

Despite editing lines on specific listed genes, the overall functional categories that differentiate between commensals and pathogens remain same as indicated previously throughout the abstract, results and discussion, i.e. cell wall degrading enzymes, regulators, chemotaxis related proteins or TonB-dependent receptors. The discussion section has no edits. Overall conclusion is not changed either.
