Prokaryote genome fluidity is dependent on effective population size

Andreani, Nadia Andrea; Hesse, Elze; Vos, Michiel

doi:10.1038/ismej.2017.36

Cited by 97 publications

(94 citation statements)

References 16 publications

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“…For example, it has long been thought that a large pool of accessory genes would be beneficial in certain habitats (and habitat combinations), but the role of the pan-genome as an adaptive evolutionary entity has been recently disputed. In the respective debate [8,[61][62][63][64][65][66], analyses of pan-genome size estimates ( Fig. 2b) have led to the conclusion that pan-genomes are adaptive [8], while studies focusing on diversity measures such as genome fluidity led to the conclusion that pan-genome evolution is predominantly neutral [61].…”

Section: Discussionmentioning

confidence: 99%

“…In the respective debate [8,[61][62][63][64][65][66], analyses of pan-genome size estimates ( Fig. 2b) have led to the conclusion that pan-genomes are adaptive [8], while studies focusing on diversity measures such as genome fluidity led to the conclusion that pan-genome evolution is predominantly neutral [61]. Our analysis shows that environmental conditions and phylogenetic inertia affect size-related pan-genome features to a higher degree (than diversity features), suggesting that the adaptiveness of pan-genomes is at least partially explained by environmental preferences of species and their phylogenetic inertia (Fig.…”

Section: Discussionmentioning

confidence: 99%

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Disentangling the impact of environmental and phylogenetic constraints on prokaryotic strain diversity

Maistrenko¹,

Mende

Lϋetge

et al. 2019

Preprint

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Microbial organisms inhabit virtually all environments and encompass a vast biological diversity. The pan-genome concept aims to facilitate an understanding of diversity within defined phylogenetic groups. Hence, pan-genomes are increasingly used to characterize the strain diversity of prokaryotic species. To understand the interdependency of pan-genome features (such as numbers of core and accessory genes) and to study the impact of environmental and phylogenetic constraints on the evolution of conspecific strains, we computed pan-genomes for 155 phylogenetically diverse species using 7000 high-quality genomes. We show that many pan-genome features such as functional diversity and core genome nucleotide diversity are correlated to each other. Further, habitat flexibility as approximated by species ubiquity is associated with several pan-genome features, particularly core genome size. In general, environment had a stronger impact on pan-genome features than phylogenetic signal. Similar environmental preferences led to convergent evolution of pangenomic features in distant phylogenetic clades. For example, the soil environment promotes expansion of pan-genome size, while host-associated habitats lead to its reduction.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic strain diversity

Maistrenko¹,

Mende

Lϋetge

et al. 2019

Preprint

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“…However, since we observed similar high levels of recombination within the Mesotoga W and A lineages, additional forces must be responsible for the larger proportion of variable accessory genes. Perhaps more cryptic niches are available in low-versus hightemperature subsurface environments (McInerney et al, 2017), or Mesotoga may have larger effective population sizes than the hyperthermophiles (Andreani et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

Genomic analysis of the mesophilic Thermotogae genus Mesotoga reveals phylogeographic structure and genomic determinants of its distinct metabolism

Nesbø

Charchuk

Pollo

et al. 2018

Environmental Microbiology

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Summary The genus Mesotoga, the only described mesophilic Thermotogae lineage, is common in mesothermic anaerobic hydrocarbon‐rich environments. Besides mesophily, Mesotoga displays lineage‐specific phenotypes, such as no or little H2 production and dependence on sulfur‐compound reduction, which may influence its ecological role. We used comparative genomics of 18 Mesotoga strains (pairwise 16S rRNA identity >99%) and a transcriptome of M. prima to investigate how life at moderate temperatures affects phylogeography and to interrogate the genomic features of its lineage‐specific metabolism. We propose that Mesotoga accomplish H2 oxidation and thiosulfate reduction using a sulfide dehydrogenase and a hydrogenase‐complex and that a pyruvate:ferredoxin oxidoreductase acquired from Clostridia is responsible for oxidizing acetate. Phylogenetic analysis revealed three distinct Mesotoga lineages (89.6%–99.9% average nucleotide identity [ANI] within lineages, 79.3%–87.6% ANI between lineages) having different geographic distribution patterns and high levels of intra‐lineage recombination but little geneflow between lineages. Including data from metagenomes, phylogeographic patterns suggest that geographical separation historically has been more important for Mesotoga than hyperthermophilic Thermotoga and we hypothesize that distribution of Mesotoga is constrained by their anaerobic lifestyle. Our data also suggest that recent anthropogenic activities and environments (e.g., wastewater treatment, oil exploration) have expanded Mesotoga habitats and dispersal capabilities.

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“…The balance between selection and drift plays important roles in shaping bacterial genomes and are often studied by estimating the selection coefficient and the effective population size ( N e ) [18, 19]. Due to several technical and biological reasons (e.g.…”

Section: Introductionmentioning

confidence: 99%

Genomic analysis unveils important aspects of population structure, virulence, and antimicrobial resistance inKlebsiella aerogenes

Passarelli‐Araujo

Palmeiro

Moharana

et al. 2019

Preprint

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Klebsiella aerogenes is an important pathogen in healthcare‐associated infections. Nevertheless, in comparison to other clinically important pathogens, K. aerogenes population structure, genetic diversity, and pathogenicity remain poorly understood. Here, we elucidate K. aerogenes clonal complexes (CCs) and genomic features associated with resistance and virulence. We present a detailed description of the population structure of K. aerogenes based on 97 publicly available genomes by using both multilocus sequence typing and single‐nucleotide polymorphisms extracted from the core genome. We also assessed virulence and resistance profiles using Virulence Finder Database and Comprehensive Antibiotic Resistance Database, respectively. We show that K. aerogenes has an open pangenome and a large effective population size, which account for its high genomic diversity and support that negative selection prevents fixation of most deleterious alleles. The population is structured in at least 10 CCs, including two novel ones identified here, CC9 and CC10. The repertoires of resistance genes comprise a high number of antibiotic efflux proteins as well as narrow‐ and extended‐spectrum β‐lactamases. Regarding the population structure, we identified two clusters based on virulence profiles because of the presence of the toxin‐encoding clb operon and the siderophore production genes, irp and ybt. Notably, CC3 comprises the majority of K. aerogenes isolates associated with hospital outbreaks, emphasizing the importance of constant monitoring of this pathogen. Collectively, our results may provide a foundation for the development of new therapeutic and surveillance strategies worldwide.

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Prokaryote genome fluidity is dependent on effective population size

Cited by 97 publications

References 16 publications

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic strain diversity

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic strain diversity

Genomic analysis of the mesophilic Thermotogae genus Mesotoga reveals phylogeographic structure and genomic determinants of its distinct metabolism

Genomic analysis unveils important aspects of population structure, virulence, and antimicrobial resistance inKlebsiella aerogenes

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