Incongruence between multi‐locus sequence analysis (<scp>MLSA</scp>) and whole‐genome‐based phylogenies: <i><scp>P</scp>seudomonas syringae</i> pathovar <i>pisi</i> as a cautionary tale

Baltrus, David A.; Dougherty, Kevin; Beckstrom-Sternberg, Stephen M.; Beckstrom-Sternberg, James S.; Foster, Jeffrey T.

doi:10.1111/mpp.12103

Cited by 29 publications

(28 citation statements)

References 22 publications

(33 reference statements)

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“…The resulting diagram is presented in Figure 1 . Even though whole-genome-based phylogenies were recently demonstrated to be more accurate than MLST [ 50 ], we still decided to use the MLST approach, due to the poor assembly quality of some of the analyzed genomes, which resulted in a large number of partial and split genes. The presence of such sequences would introduce a bias to the analysis using the whole genome/proteome sequences.…”

Section: Resultsmentioning

confidence: 99%

Genomics-Based Exploration of Virulence Determinants and Host-Specific Adaptations of Pseudomonas syringae Strains Isolated from Grasses

Dudnik

Dudler

2014

Pathogens

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The Pseudomonas syringae species complex has recently been named the number one plant pathogen, due to its economic and environmental impacts, as well as for its role in scientific research. The bacterium has been repeatedly reported to cause outbreaks on bean, cucumber, stone fruit, kiwi and olive tree, as well as on other crop and non-crop plants. It also serves as a model organism for research on the Type III secretion system (T3SS) and plant-pathogen interactions. While most of the current work on this pathogen is either carried out on one of three model strains found on dicot plants with completely sequenced genomes or on isolates obtained from recent outbreaks, not much is known about strains isolated from grasses (Poaceae). Here, we use comparative genomics in order to identify putative virulence-associated genes and other Poaceae-specific adaptations in several newly available genome sequences of strains isolated from grass species. All strains possess only a small number of known Type III effectors, therefore pointing to the importance of non-Type III secreted virulence factors. The implications of this finding are discussed.

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Section: Resultsmentioning

confidence: 99%

Genomics-Based Exploration of Virulence Determinants and Host-Specific Adaptations of Pseudomonas syringae Strains Isolated from Grasses

Dudnik

Dudler

2014

Pathogens

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“…Convergent evolution of closely related EHB Whole-genome sequences can provide a broader picture of evolutionary relationships among bacterial strains than phylogenies built from single loci [39]. We inferred phylogenies for our focal strains and related bacteria based on a subset of conserved loci, as well as whole-genome data.…”

Section: Resultsmentioning

confidence: 99%

Absence of Genome Reduction In Diverse, Facultative Endohyphal Bacteria

Baltrus

Dougherty

Arendt

et al. 2016

Preprint

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Fungi interact closely with bacteria, both on the surfaces of the hyphae and within their living tissues (i.e. endohyphal bacteria, EHB). These EHB can be obligate or facultative symbionts and can mediate diverse phenotypic traits in their hosts. Although EHB have been observed in many lineages of fungi, it remains unclear how widespread and general these associations are, and whether there are unifying ecological and genomic features can be found across EHB strains as a whole. We cultured 11 bacterial strains after they emerged from the hyphae of diverse Ascomycota that were isolated as foliar endophytes of cupressaceous trees, and generated nearly complete genome sequences for all. Unlike the genomes of largely obligate EHB, the genomes of these facultative EHB resembled those of closely related strains isolated from environmental sources. Although all analysed genomes encoded structures that could be used to interact with eukaryotic hosts, pathways previously implicated in maintenance and establishment of EHB symbiosis were not universally present across all strains. Independent isolation of two nearly identical pairs of strains from different classes of fungi, coupled with recent experimental evidence, suggests horizontal transfer of EHB across endophytic hosts. Given the potential for EHB to influence fungal phenotypes, these genomes could shed light on the mechanisms of plant growth promotion or stress mitigation by fungal endophytes during the symbiotic phase, as well as degradation of plant material during the saprotrophic phase. As such, these findings contribute to the illumination of a new dimension of functional biodiversity in fungi.

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“…Perhaps the greatest challenge with taxonomic classification of P, syringae is the broad phenotypic versatility and variability that strains display. This bacterium is an environmentally ubiquitous hemibiotroph that can be isolated from environmental sources including rivers, lakes, leaf litter, and clouds [33-35]. For any given strain, host range can be difficult to catagorize because the occurrence and severity of symptoms is dependent on the precise environmental conditions and sensitivity to these conditions is itself influenced by phylogenetic placement [36].…”

Section: The P Syringae Sensu Lato Species Complex As An Examplementioning

confidence: 99%

Divorcing Strain Classification From Species Names

Baltrus

2016

Preprint

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Confusion about strain classification and nomenclature permeates modern microbiology. Although taxonomists have traditionally acted as gatekeepers of order, the numbers of and speed at which new strains are identified has outpaced the opportunity for professional classification for many lineages. Furthermore, the growth of bioinformatics and database fueled investigations have placed metadata curation in the hands of researchers with little taxonomic experience. Here I describe practical challenges facing modern microbial taxonomy, provide an overview of complexities of classification for environmentally ubiquitous taxa like Pseudomonas syringae, and emphasize that classification and nomenclature need not be the one in the same. A move toward implementation of relational classification schemes based on inherent properties of whole genomes could provide sorely needed continuity in how strains are referenced across manuscripts and data sets.

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Incongruence between multi‐locus sequence analysis (MLSA) and whole‐genome‐based phylogenies: Pseudomonas syringae pathovar pisi as a cautionary tale

Cited by 29 publications

References 22 publications

Genomics-Based Exploration of Virulence Determinants and Host-Specific Adaptations of Pseudomonas syringae Strains Isolated from Grasses

Genomics-Based Exploration of Virulence Determinants and Host-Specific Adaptations of Pseudomonas syringae Strains Isolated from Grasses

Absence of Genome Reduction In Diverse, Facultative Endohyphal Bacteria

Divorcing Strain Classification From Species Names

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