Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 121(1)

Published: Dec. 26, 2023

Pangenomes exhibit remarkable variability in many prokaryotic species, much of which is maintained through the processes horizontal gene transfer and loss. Repeated acquisitions near-identical homologs can easily be observed across pangenomes, leading to question whether these parallel events potentiate similar evolutionary trajectories, or remarkably different genetic backgrounds recipients mean that postacquisition trajectories end up being quite different. In this study, we present a machine learning method predicts presence absence genes Escherichia coli pangenome based on complex patterns other accessory within genome. Our analysis leverages repeated E. observe evolution following events. We find substantial set highly predictable from alone, indicating selection potentiates maintains gene–gene co-occurrence avoidance relationships deterministically over long-term bacterial robust differences host history. propose at least part understood as with govern their likely cohabitants, analogous an ecosystem’s interacting organisms. findings indicate intragenomic fitness effects may key drivers evolution, influencing emergence pangenome.

Language: Английский

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Modern Plant Breeding Techniques in Crop Improvement and Genetic Diversity: From Molecular Markers and Gene Editing to Artificial Intelligence—A Critical Review

Plants, Journal Year: 2024, Volume and Issue: 13(19), P. 2676 - 2676

Published: Sept. 24, 2024

With the development of new technologies in recent years, researchers have made significant progress crop breeding. Modern breeding differs from traditional because great changes technical means and concepts. Whereas initially focused on high yields, modern focuses orientations based different crops’ audiences or by-products. The process starts creation material populations, which can be constructed by natural mutagenesis, chemical physical mutagenesis transfer DNA (T-DNA), Tos17 (endogenous retrotransposon), etc. Then, gene function mined through QTL mapping, Bulked-segregant analysis (BSA), Genome-wide association studies (GWASs), RNA interference (RNAi), editing. at transcriptional, post-transcriptional, translational levels, functions genes are described terms post-translational aspects. This article mainly discusses application above scientific technological methods advantages limitations diversity. In particular, editing technology has contributed to research.

Language: Английский

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Multi-layered genome defences in bacteria

Current Opinion in Microbiology, Journal Year: 2024, Volume and Issue: 78, P. 102436 - 102436

Published: Feb. 17, 2024

Bacteria have evolved a variety of defence mechanisms to protect against mobile genetic elements, including restriction-modification systems and CRISPR–Cas. In recent years, dozens previously unknown (DSs) been discovered. Notably, diverse DSs often coexist within the same genome, some co-occur at frequencies significantly higher than would be expected by chance, implying potential synergistic interactions. Recent studies provided evidence that enhance or complement one another. Here, we review interactions between mechanistic, regulatory, ecological evolutionary levels.

Language: Английский

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Bacterial lifestyle shapes pangenomes

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(21)

Published: May 14, 2024

Pangenomes vary across bacteria. Some species have fluid pangenomes, with a high proportion of genes varying between individual genomes. Other less different genomes tending to contain the same genes. Two main hypotheses been suggested explain this variation: differences in species' bacterial lifestyle and effective population size. However, previous studies not able test these because features size are highly correlated each other, phylogenetically conserved, making it hard disentangle their relative importance. We used phylogeny-based analyses, 126 species, tease apart causal role factors. found that pangenome fluidity was lower i) host-associated compared free-living ii) obligately dependent on host, live inside cells, more pathogenic motile. In contrast, we no support for competing hypothesis larger sizes lead pangenomes. Effective appears correlate variation is also driven by lifestyle, rather than relationship.

Language: Английский

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Environment-independent distribution of mutational effects emerges from microscopic epistasis

Science, Journal Year: 2024, Volume and Issue: 386(6717), P. 87 - 92

Published: Oct. 3, 2024

Predicting how new mutations alter phenotypes is difficult because mutational effects vary across genotypes and environments. Recently discovered global epistasis, in which the fitness of scale with background genotype, can improve predictions, but environment modulates this scaling unknown. We measured ~100 insertion 42 strains Saccharomyces cerevisiae six laboratory environments found that epistasis nearly invariant Instead, tunes one parameter, at most switch sign. As a consequence, distribution predictable Our results suggest effective dimensionality genotype-to-phenotype maps surprisingly low.

Language: Английский

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Proteome expansion in thePotyviridaeevolutionary radiation

FEMS Microbiology Reviews, Journal Year: 2022, Volume and Issue: 46(4)

Published: Feb. 8, 2022

Potyviridae, the largest family of known RNA viruses (realm Riboviria), belongs to picorna-like supergroup and has important agricultural ecological impacts. Potyvirid genomes are translated into polyproteins, which in turn hydrolyzed release mature products. Recent sequencing efforts revealed an unprecedented number potyvirids with a rich variability gene content genomic layouts. Here, we review heterogeneity non-core modules that expand structural functional diversity potyvirid proteomes. We provide family-wide classification P1 proteinases Types A B, discuss pretty interesting sweet potato potyviral ORF (PISPO), putative zinc fingers, alkylation B (AlkB)-non-core found within cistrons. The atypical inosine triphosphate pyrophosphatase (ITPase/HAM1), as well pseudo tobacco mosaic virus-like coat protein (TMV-like CP) discussed alongside homologs unrelated virus taxa. Family-wide abundance multitasking helper component proteinase (HC-pro) is revised. Functional connections between highlighted support host niche adaptation immune evasion main drivers Potyviridae evolutionary radiation. Potential biotechnological synthetic biology applications leader finally explored.

Language: Английский

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Modern microbiology: Embracing complexity through integration across scales

Cell, Journal Year: 2024, Volume and Issue: 187(19), P. 5151 - 5170

Published: Sept. 1, 2024

Language: Английский

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Prokaryote pangenomes are dynamic entities

Current Opinion in Microbiology, Journal Year: 2022, Volume and Issue: 66, P. 73 - 78

Published: Jan. 31, 2022

Prokaryote pangenomes are influenced heavily by environmental factors and the opportunity for gene gain loss events. As field of pangenome analysis has expanded, so need to fully understand complexity how eco-evolutionary dynamics shape pangenomes. Here, we describe current models evolution discuss their suitability accuracy. We suggest that dynamic entities under constant flux, highlighting influence two-way interactions between environment. New classifications core accessory genes also considered, underscoring continuous evaluation nomenclature in a fast-moving field. conclude future should incorporate encompass dynamic, changeable nature.

Language: Английский

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Antibiotic resistance: Time of synthesis in a post-genomic age

Computational and Structural Biotechnology Journal, Journal Year: 2021, Volume and Issue: 19, P. 3110 - 3124

Published: Jan. 1, 2021

Antibiotic resistance has been highlighted by international organizations, including World Health Organization, Bank and United Nations, as one of the most relevant global health problems. Classical approaches to study this problem have focused in infected humans, mainly at hospitals. Nevertheless, antibiotic can expand through different ecosystems geographical allocations, hence constituting a One-Health, Global-Health problem, requiring specific integrative analytic tools. evolution transmission are multilayer, hierarchically organized processes with several elements (from genes whole microbiome) involved. However, their traditionally gene-centric, each element independently studied. The development robust-economically affordable genome sequencing approaches, well other -omic techniques transcriptomics proteomics, is changing panorama. These technologies allow description system, either cell or microbiome whole, overcoming problems associated gene-centric approaches. We currently time combining information derived from studies more holistic view spread resistance. This synthesis process requires accurate integration into computational models that serve analyse causes consequences acquiring AR, fed curated databases capable identifying involved acquisition In review, we capacities drawbacks tools use for analysis aiming identify useful targets effective corrective interventions.

Language: Английский

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Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types

Microbial Genomics, Journal Year: 2022, Volume and Issue: 8(11)

Published: Nov. 23, 2022

The Escherichia coli species contains a diverse set of sequence types and there remain important questions regarding differences in genetic content within this population that need to be addressed. Pangenomes are useful vehicles for studying gene types. Here, we analyse 21 E. type pangenomes using comparative pangenomics identify variance both pangenome structure content. We present functional breakdowns core genomes enriched metabolism, transcription cell membrane biogenesis genes. also uncover metabolism genes have variable classification, depending on which allele is present. Our approach allows detailed exploration the context species. show ongoing gain loss type-specific, may consequence distinct type-specific evolutionary drivers.

Language: Английский

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