Figure - available from: mSystems®
This content is subject to copyright. Terms and conditions apply.
Genomic identification and characterization of the recent geranium Xh2022 bacterial blight outbreak. (A) Symptoms of blight in a geranium leaf and whole-genome average nucleotide identity analysis. Numbers in colored squares indicate geographic location. Lowercase letters show isolates from the same leaf. Colored rectangles indicate the collection year. Xhp, X. hortorum pv. pelargonii. Xhh, X. hortorum pv. hederae; Xhca, X. hortorum pv. carotae. (B) Clustering of the Xhp isolates based on principal component analysis of core chromosomal single nucleotide polymorphisms (SNPs). The number of SNPs differentiating the cluster of 2022 isolates from other clusters is shown in purple. (C) Time-scaled phylogeny of Xhp using an HKY nucleotide substitution model. Brackets indicate a 95% HPD credible interval for the date of each node. Colored dots indicate the collection year. (D) Mauve multiple Xhp chromosome alignment. Each chromosome is rotated to start with the DnaA sequence. Each color shows genetically similar blocks.
Source publication
The geranium industry, valued at $4 million annually, faces an ongoing Xanthomonas hortorum pv. pelargonii (Xhp) pathogen outbreak. To track and describe the outbreak, we compared the genome structure across historical and globally distributed isolates. Our research revealed Xhp population has not had chromosome rearrangements since 1974 and has th...
Citations
... Bacterial plant pathogens cause some of the most intractable diseases of crops worldwide [4][5][6][7]. Novel emergence and re-emergence of bacterial diseases continue to be reported across the globe and are associated with an upsurge in efforts devoted to understanding the nature of pathogen emergence, spread, and evolution [8][9][10][11][12][13][14][15][16][17]. A bacterial plant pathogen that emerged in the last few decades and is of global epidemiological consequences is Xanthomonas euvesicatoria pv. ...
... Whole genome analysis of X. hortorum pv. pelargonii strains from a 2022 epidemic of bacterial blight of geranium in the USA showed zero to seven chromosomal SNPs among isolates of the emergent strain that was distributed to multiple states in plant cuttings [9,91]. ...
Emerging and re-emerging plant diseases continue to present multifarious threats to global food security. Considerable recent efforts are therefore being channeled towards understanding the nature of pathogen emergence, their spread and evolution. Xanthomonas euvesicatoria pv. perforans (Xep), one of the causal agents of bacterial spot of tomato, rapidly emerged and displaced other bacterial spot xanthomonads in many tomato production regions around the world. In less than three decades, it has become a dominant xanthomonad pathogen in tomato production systems across the world and presents a compelling example for understanding diversification of recently emerged bacterial plant pathogens. Although Xep has been continuously monitored in Florida since its discovery, the global population structure and evolution at the genome-scale is yet to be fully explored. The objectives of this work were to determine genetic diversity globally to ascertain if different tomato production regions contain genetically distinct Xep populations, to examine genetic relatedness of strains collected in tomato seed production areas in East Asia and other production regions, and to evaluate variation in type III secretion effectors, which are critical pathogenicity and virulence factors, in relationship to population structure. We used genome data from 270 strains from 13 countries for phylogenetic analysis and characterization of type III effector gene diversity among strains. Our results showed notable genetic diversity in the pathogen. We found genetically similar strains in distant tomato production regions, including seed production regions, and diversification over the past 100 years, which is consistent with intercontinental dissemination of the pathogen in hybrid tomato production chains. Evolution of the Xep pangenome, including the acquisition and loss of type III secreted effectors, is apparent within and among phylogenetic lineages. The apparent long-distance movement of the pathogen, together with variants that may not yet be widely distributed, poses risks of emergence of new variants in tomato production.
... Plasmids are extra-chromosomal genetic elements that can harbour genes important for pathogenicity and virulence as well as survival in diverse environments [44]. They can play an essential role in adaptation and undergo rapid evolutionary processes [45]. ...
This Technical Resource describes genome sequencing data for 61 isolates of the bacterial pathogen Xanthomonas camp-estris pv. campestris collected from Brassica and Raphanus crops between 2010 and 2021 in Serbia. We present the raw sequencing reads and annotated contig-level genome assemblies and determine the races of ten isolates. The data can be used to test hypotheses and phylogeographic analyses and inform the design of informative molecular markers for population genetics studies. When combined with phenotypic data, they could be used to dissect relationships between genotypes and phenotypes such as host range and virulence. Finally, these genome sequences expand our inventory of plasmids known to reside in this pathogen.
... Another study of a single-season epidemic of X. hortorum pv. pelargonii in rooted cuttings distributed throughout the United States found very few mutations (Iruegas-Bocardo et al. 2023;Roman-Reyna et al. 2023). Together, these findings suggest that few mutations accumulate in a given Xanthomonas genome during a single-season epidemic. ...
Rapidly evolving bacterial pathogens pose a unique challenge for long-term plant disease management. In this study, we investigated the types and rate of mutations in bacterial populations during seasonal disease epidemics. Two phylogenetically distinct strains of the bacterial spot pathogen, Xanthomonas perforans, were marked, released in tomato fields, and recaptured at several time points during the growing season. Genomic variations in recaptured isolates were identified by comparative analysis of their whole-genome sequences. In total, 180 unique variations (116 substitutions, 57 insertions/deletions, and 7 structural variations) were identified from 300 genomes, resulting in the overall host-associated mutation rate of ∼0.3 to 0.9/genome/week. This result serves as a benchmark for bacterial mutation during epidemics in similar pathosystems.
[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
This Data Note describes genome sequencing data for 61 isolates of the bacterial pathogen Xanthomonas campestris pv. campestris collected from Brassica and Raphanus crops between 2010 and 2021 in Serbia. We present the raw sequencing reads and annotated contig-level genome assemblies and we determined the races of ten isolates. The data can be used to test hypotheses, phylogeographic analyses and inform design of informative molecular markers for population genetics studies. When combined with phenotypic data, they could be used to dissect relationships between genotype and phenotypes such as host range and virulence. Finally, these genome sequences expand our inventory of plasmids known to reside in this pathogen.
This Data Note describes genome sequencing data for 61 isolates of the bacterial pathogen Xanthomonas campestris pv. campestris collected from brassica crops between 2010 and 2021 in Serbia. We present the raw sequencing reads and annotated contig-level genome assemblies. These data can be used to test hypotheses, phylogeographic analyses and inform design of informative molecular markers for population genetics studies. When combined with phenotypic data, they could be used to dissect relationships between genotype and phenotypes such as host range and virulence. Finally, these genome sequences expand our inventory of plasmids known to reside in this pathogen.
