A plant pan-genome immunity landscape Plant pathogens elicit an immune response through effector proteins. In turn, genomes encode genes that determine species-specific recognition of these effectors by a process known collectively as effector-triggered (ETI). By examining range strains the pathogen Pseudomonas syringae infect model Arabidopsis thaliana , Laflamme et al. generated P. Type III Effector Compendium (PsyTEC) and in turn identified responsible for ETI Arabidopsis. This analysis...

Diverse Gram-negative pathogens like Pseudomonas syringae employ type III secreted effector (T3SE) proteins as primary virulence factors that combat host immunity and promote disease. T3SEs can also be recognized by plant hosts activate an triggered immune (ETI) response shifts the interaction back toward immunity. Consequently, are pivotal in determining potential of individual P. strains, ultimately help to restrict a subset unable recognize their repertoires T3SEs. While number families...

Pseudomonas syringae is a highly diverse bacterial species complex capable of causing wide range serious diseases on numerous agronomically important crops. We examine the evolutionary relationships 391 agricultural and environmental strains using whole-genome sequencing genomic analyses.We describe phylogenetic distribution all 77,728 orthologous gene families in pan-genome, reconstruct core genome phylogeny 2410 genes, hierarchically cluster accessory genome, identify diversity type III...

Abstract Mutations are the ultimate source of variation used for evolutionary adaptation, while also being predominantly deleterious and a genetic disorders. Understanding rate insertion-deletion mutations (indels) is essential to understanding processes, especially in coding regions, where such can disrupt production proteins. Using direct estimates indel rates from 14 phylogenetically diverse eukaryotic bacterial species, along with measures standing we obtain results that imply an inverse...

The vast diversity in nucleotide composition and architecture among bacterial genomes may be partly explained by inherent biases the rates spectra of spontaneous mutations. Bacterial with multiple chromosomes are relatively unusual but some relevant to human health, none more so than causative agent cholera, Vibrio cholerae Here, we present genome-wide mutation wild-type mismatch repair (MMR) defective backgrounds two species, low-%GC squid symbiont V. fischeri pathogen cholerae, collected...

Staphylococcus aureus exhibits many defenses against host innate immunity, including the ability to replicate in presence of nitric oxide (NO·). S. NO· resistance is a complex trait and hinges on this pathogen metabolically adapt NO·. Here, we employed deep sequencing transposon junctions (Tn-Seq) library generated USA300 LAC define complete set genes required for resistance. We compared list NO·-resistance persist within murine skin infections (SSTIs). In total, identified 168 that were...

Abstract Spontaneous mutations are ultimately essential for evolutionary change and also the root cause of many diseases. However, until recently, both biological technical barriers have prevented detailed analyses mutation profiles, constraining our understanding process to a few model organisms leaving major gaps in role genome content structure on mutation. Here, we present genome-wide view molecular spectrum Burkholderia cenocepacia, clinically relevant pathogen with high %GC multiple...

Significance The fitness effect of many mutations depends on the genotype individual in which they occur. Are these dependencies predictable? Do build existing variation between individuals to promote divergence, or do act favor genetic cohesion? We examine questions by measuring that conferred a benefit laboratory-evolved population when transferred into genetically and phenotypically diverse natural isolates same species. found effects were predicted strain added but not ecological...

The Arabidopsis nucleotide-binding leucine-rich repeat protein ZAR1 can recognize at least six distinct families of pathogenic effector proteins to mount an effector-triggered immune response. This remarkable immunodiversity appears be conveyed by receptor-like cytoplasmic kinase (RLCK) complexes, which associate with sense several effector-induced perturbations. Here we show that the recently identified ZAR1-mediated responses against HopX1, HopO1, and HopBA1 Pseudomonas syringae rely on...

Limosilactobacillus reuteri strain DSM 20016 is specialised to colonize the human gut for much longer than other L. strains and most Lactobacillaceae family members. These adaptations, along with its safe-to-consume food status public acceptance as a probiotic, make it an attractive chassis synthetic biology endeavours aimed at introducing novel functions into microbiome, including feedback systems sensing disease state therapeutic applications remedying chronic disorders. Here, we perform...

The causes and consequences of spatiotemporal variation in mutation rates remain to be explored nearly all organisms. Here we examine relationships between local replication timing three bacterial species whose genomes have multiple chromosomes: Vibrio fischeri, cholerae, Burkholderia cenocepacia Following five accumulation experiments with these bacteria conducted the near absence natural selection, clones from each lineage were sequenced analyzed identify spectra. In lineages lacking...

Beneficial mutations fuel adaptation by altering phenotypes that enhance the fit of organisms to their environment. However, phenotypic effects often depend on ecological context, making distribution across multiple environments essential understanding true nature beneficial mutations. Studies address both genetic basis and consequences adaptive remain rare. Here, we characterize direct pleiotropic fitness a collection 21 first-step mutants derived from naïve adapted genotypes used in...

The trade-off between growth rate and yield can limit population productivity. Here we tested for this life-history in replicate haploid diploid populations of Saccharomyces cerevisiae propagated glucose-limited medium batch cultures 5000 generations. single clones isolated from the lineages, measured as both optical density at end a cycle, declined during selection was negatively correlated with rate. Initially, did not pay cost adaptation but haploidized after about 1000–3000 generations...

Abstract Mutation accumulation (MA) experiments employ the strategy of minimizing population size evolving lineages to greatly reduce effects selection on newly arising mutations. Thus, most mutations fix within MA lines independently their fitness effects. This approach, more recently combined with genome sequencing, has detailed rates, spectra, and biases different mutational processes. However, a quantitative understanding virtually unseen by remained an untapped opportunity. Here, we...

The bacterial genus Xanthomonas is responsible for disease outbreaks in several hundred plant species, many of them economically important crops. In the era next-generation sequencing, thousands strains from this have now been sequenced as part isolated studies that focus on outbreak characterization, host range, diversity, and virulence factor identification. However, these data not synthesized we lack a comprehensive phylogeny genus, with some species designations public databases still...

ABSTRACT Pseudomonas syringae is a highly diverse bacterial species complex capable of causing wide range serious diseases on numerous agronomically important crop species. Here, we examine the evolutionary relationships 391 agricultural and environmental strains from P. using whole-genome sequencing genomic analyses. Our collection includes 11 13 previously described phylogroups isolated off over 90 hosts. We describe phylogenetic distribution all orthologous gene families in pan-genome,...

is a highly diverse genus that includes species cause disease in both plants and animals. Recently, pathogenic pseudomonads from the

ABSTRACT Mutation accumulation (MA) experiments employ the strategy of minimizing population size evolving lineages to greatly reduce effects selection on newly arising mutations. Thus, most mutations fix within MA lines independently their fitness effects. This approach, more recently combined with genome sequencing, has detailed rates, spectra, and biases different mutational processes. However, a quantitative understanding virtually unseen by remained an untapped opportunity. Here, we...

Abstract Understanding how mutations affect survivability is a key component to knowing organisms and complex traits evolve. However, most have minor effect on fitness these effects are difficult resolve using traditional molecular techniques. Therefore, there dire need for more accurate precise measurements methods. Here, we measured the in Burkholderia cenocepacia HI2424 mutation accumulation (MA) lines droplet-digital polymerase chain reaction (ddPCR). Overall, from ddPCR-MA correlated...

ABSTRACT Spontaneous mutations are ultimately essential for evolutionary change and also the root cause of many diseases. However, until recently, both biological technical barriers have prevented detailed analyses mutation profiles, constraining our understanding process to a few model organisms leaving major gaps in role genome content structure on mutation. Here, we present genome-wide view molecular spectrum Burkholderia cenocepacia , clinically relevant pathogen with high %GC-content...

ABSTRACT The vast diversity in nucleotide composition and architecture among bacterial genomes may be partly explained by inherent biases the rates spectra of spontaneous mutations. Bacterial with multiple chromosomes are relatively unusual but some relevant to human health, none more so than causative agent cholera, Vibrio cholerae . Here, we present genome-wide mutation wild-type mismatch repair (MMR) defective backgrounds two species, low-GC% squid symbiont V. fischeri pathogen ,...

Abstract Beneficial mutations fuel adaptation by altering phenotypes that enhance the fit of organisms to their environment. However, phenotypic effects often depend on ecological context, making distribution across multiple environments essential understanding true nature beneficial mutations. Studies address both genetic basis and consequences adaptive remain rare. Here, we characterize direct pleiotropic fitness a collection 21 first-step mutants derived from naïve adapted genotypes used...