Evolution, genomics and epidemiology of <i>Pseudomonas syringae</i>

Baltrus, David A.; McCann, Honour C.; Guttman, David S.

doi:10.1111/mpp.12506

Cited by 126 publications

(106 citation statements)

References 149 publications

(185 reference statements)

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“…These orthologs were concatenated and ClonalFrameML (Didelot and Wilson, 2015) was 609 used to identify recombination tracts that could inflate the branch length of members of the OTU as described 610 above. TMRCA of the OTU was estimated by calculating the mid-point-root to tip sequence divergence for a 611 representative of all 107 strains within OTU5, then dividing the median value of this distance by the neutral 612 substitution rate (Kimura, 1968) (we used here the point estimate of 8.7x10 -8 with our estimate of sd=6.0x10 -8 613 (McCann et al, 2017)). While we consider all sites (degenerate and non-degenerate) in the putatively non-614 recombined core, in addition to the fact that substitution rate is likely inaccurate for the longer timescale 615 analysed in the present study, both of these inaccuracies would likely lead to the underestimation of the age.…”

Section: Pan-genome Analysis and Phylogenetics 587mentioning

confidence: 99%

“…These studies, which have observed a range of different patterns, are unfortunately 47 often limited to the historic strains that are available, and the conclusions vary for different collections, even of 48 the same pathogen species (Pirnay et al, 2009). 49Questions of pathogen epidemiology are of particular relevance when considering the genus 50Pseudomonas, which includes pathogens and commensals of both animals and plants (Baltrus et al, 2017) and is 51 (which was not peer-reviewed) is the author/funder. All rights reserved.…”

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confidence: 99%

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confidence: 99%

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Stability of association betweenArabidopsis thalianaandPseudomonaspathogens over evolutionary time scales

Karasov

Almario

Friedemann

et al. 2018

Preprint

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SummaryCrop disease outbreaks are often associated with clonal expansions of single pathogenic lineages. To determine 20 whether similar boom-and-bust scenarios hold for wild plant pathogens, we carried out a multi-year multi-site 21 survey of Pseudomonas in the natural host Arabidopsis thaliana. The most common Pseudomonas lineage 22 corresponded to a pathogenic clade present in all sites. Sequencing of 1,524 Pseudomonas genomes revealed 23 this lineage to have diversified approximately 300,000 years ago, containing dozens of genetically distinct 24 pathogenic sublineages. These sublineages have expanded in parallel within the same populations and are 25 differentiated both at the level of gene content and disease phenotype. Such coexistence of diverse sublineages 26indicates that in contrast to crop systems, no single strain has been able to overtake these A. thaliana 27 populations in the recent past. Our results suggest that the selective pressures acting on a plant pathogen in 28 wild hosts may be more complex than those in agricultural systems. 29 Introduction 30In agricultural and clinical settings, pathogenic colonizations are frequently associated with expansions of single 31 or a few genetically identical microbial lineages (Butler et al., 2013; Cai et al., 2011;Kolmer, 2005; Park et al., 32 2015;Stukenbrock and McDonald, 2008; Yoshida et al., 2013). The conditions that lead to such epidemics-such 33 as reduced host genetic diversity (Zhu et al., 2000), absence of competing microbial communities (Brown et al., 34 2013) or high transmission rates (Park et al., 2015)-are, however, by no means a universal feature of 35 pathogenic infections. Instead, many, if not most, pathogens can colonize host populations that are both 36 genetically diverse and that can accommodate a diversity of other microbes (Barrett et al., 2009; Falkinham et 37 al., 2015;Woolhouse et al., 2001). 38Factors that drive pathogen success in such more complex situations are less well understood than for 39 clonal epidemics. For example, if a pathogen species persists at high numbers in non-host environments, does 40 each host become infected by a different pathogen strain? Or does a multitude of genetically distinct pathogens 41 infect each host? And do different colonizing strains use disparate mechanisms to become established even 42 within genetically similar host individuals? The answers to these questions inform on how (and if) a host 43 population can evolve partial or even complete pathogen resistance (Anderson and May, 1982; Barrett et al., 44 2009; Karasov et al., 2014a;Laine et al., 2011). Several studies over the past 20 years have attempted to infer 45 the distributions of non-epidemic pathogens in both host and non-host environments (Falkinham et al., 2015; 46 Wiehlmann et al., 2007). These studies, which have observed a range of different patterns, are unfortunately 47 often limited to the historic strains that are available, and the conclusions vary for different collections, even of 48 the same pathogen ...

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Section: Pan-genome Analysis and Phylogenetics 587mentioning

confidence: 99%

mentioning

confidence: 99%

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Stability of association betweenArabidopsis thalianaandPseudomonaspathogens over evolutionary time scales

Karasov

Almario

Friedemann

et al. 2018

Preprint

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“…tomato DC3000 is required for virulence in planta in every pathogenic strain investigated so far, and its presence is strongly correlated with pathogenic potential on agriculturally relevant plants. On the other hand, the rhizobial system does not appear to be required for virulence in planta but was acquired via multiple horizontal gene transfers by strains within the P. syringae complex (Baltrus et al 2017).…”

Section: Introductionmentioning

confidence: 99%

“…However, its role in virulence remains elusive (Romanchuk et al 2014). Recently, Baltrus et al (2017) described four different Type Three Secretion Systems (T3SS) in P. syringae pathovars: canonical, rhizobial, single and atypical. The canonical system present in P. syringae pv.…”

Section: Introductionmentioning

confidence: 99%

Genome analysis of Pseudomonas syringae pv. lachrymans strain 814/98 indicates diversity within the pathovar

et al. 2017

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Although many Pseudomonas syringae strains have already been determined, only a few genomes of strains belonging to pathovar lachrymans have been sequenced so far. In this study we report the genome sequence of P. syringae pv. lachrymans strain 814/98, which is highly virulent to cucumber. The genome size was estimated to be 6.58 Mb, with 57.97% GC content. In total, 6024 genes encoding proteins and 92 genes encoding RNAs were identified in this genome. Comparisons with the available sequenced genomes of pathovar lachrymans as well as with other P. syringae pathovars were conducted, revealing the presence of three unique plasmids and 24 type III effector proteins (TTEs) in strain 814/98. The phylogenetic analyses of MLST loci and TTEs clearly showed the existence of two distinct clusters of strains within pathovar lachrymans, which were grouped into either phylogroup 1 or 3, supporting non-monophyly within this pathovar.

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The metabolic burden associated with plasmid acquisition: An assessment of the unrecognized benefits to host cells

Curtsinger,

Martínez‐Absalón,

Liu

et al. 2024

BioEssays

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Bacterial conjugation, wherein DNA is transferred between cells through direct contact, is highly prevalent in complex microbial communities and is responsible for spreading myriad genes related to human and environmental health. Despite their importance, much remains unknown regarding the mechanisms driving the spread and persistence of these plasmids in situ. Studies have demonstrated that transferring, acquiring, and maintaining a plasmid imposes a significant metabolic burden on the host. Simultaneously, emerging evidence suggests that the presence of a conjugative plasmid can also provide both obvious and unexpected benefits to their host and local community. Combined, this highlights a continuous cost‐benefit tradeoff at the population level, likely contributing to overall plasmid abundance and long‐term persistence. Yet, while the metabolic burdens of plasmid conjugation, and their causes, are widely studied, their attendant potential advantages are less clear. Here, we summarize current perspectives on conjugative plasmids’ metabolic burden and then highlight the lesser‐appreciated yet critical benefits that plasmid‐mediated metabolic burdens may provide. We argue that this largely unexplored tradeoff is critical to both a fundamental theory of microbial populations and engineering applications and therefore warrants further detailed study.

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Evolution, genomics and epidemiology of Pseudomonas syringae

Cited by 126 publications

References 149 publications

Stability of association betweenArabidopsis thalianaandPseudomonaspathogens over evolutionary time scales

Stability of association betweenArabidopsis thalianaandPseudomonaspathogens over evolutionary time scales

Genome analysis of Pseudomonas syringae pv. lachrymans strain 814/98 indicates diversity within the pathovar

The metabolic burden associated with plasmid acquisition: An assessment of the unrecognized benefits to host cells

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