Evaluation of the taxonomic accuracy and pathogenicity prediction power of 16 primer sets amplifying single copy marker genes in the<i>Pseudomonas syringae</i>species complex

Fautt, Chad; Hockett, Kevin L.; Couradeau, Estelle

doi:10.1101/2022.11.01.514712

Cited by 1 publication

(1 citation statement)

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“…Phylogroups were assigned to all genomes as outlined in 27 , with any genomes unassignable to a phylogroup due to sharing less than 95% ANI with any reference strain assumed to be outside PSSC. Although not considered as PSSC members here, these genomes were kept in our dataset, with the logic that they represent the outer boundaries of what might reasonably be considered to be the species group 28,29 .…”

Section: Methodsmentioning

confidence: 99%

Genomic evidence for widespread reciprocal recognition and killing amongPseudomonas syringaestrains

Fautt,

Hockett,

Delattre

et al. 2024

Preprint

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Community assembly dynamics are in part driven by competition between community members. Diverse bacteria antagonize competitors through the production of toxic compounds, such as bacteriophage-derived tailocins. These toxins are highly specific in their targeting, which is determined by interactions between the tailocin’s tail fiber and competitors’ lipopolysaccharide O-antigen moieties. Tailocins play a pivotal role in mediating microbial interactions among the economically significant plant pathogens within thePseudomonas syringaespecies complex, with the potential to alter community structure and disease progression in host plants. Previous work looking at 45P. syringaestrains has demonstrated that at least two phylogenetic clades of tail fibers are encoded in the conserved tailocin region across the species complex, which roughly corresponds to two clusters of targeting activity. To better understand the full diversity of tail fibers associated with tailocins in the species complex, we screened 2,161 publicly available genomes for their tailocin tail fiber content, predicted protein structures that represent the diversity of fibers, and investigated forces possibly driving the distribution of fibers throughout the species complex. Here we present evidence that while the two previously described tail fiber clades are indeed widespread among virulentP. syringaestrains, their distribution is largely uncorrelated with phylogeny. Instead, we found that the presence of one tail fiber or the other is strongly correlated with the allelic diversity of another gene, associated with lipopolysaccharide O-antigen structure, dTDP-4-dehydrorhamnose reductase. Our findings suggest the presence of two reciprocally targeting groups of strains distributed throughout theP. syringaespecies complex that transcend phylogenetic relationships.

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Section: Methodsmentioning

confidence: 99%