The Temporal Dynamics of Slightly Deleterious Mutations in Escherichia coli and Shigella spp.

Balbi, Kevin; Rocha, Eduardo P. C.; Feil, Edward J.

doi:10.1093/molbev/msn252

Cited by 70 publications

(67 citation statements)

References 66 publications

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“…This follows a pattern previously found in a large number of genomes (Balbi et al 2009;Hildebrand et al 2010). Since it is unlikely that all bacterial genomes are becoming AT-rich, it is commonly thought that this mutational bias is moderated by the action of natural selection or biased gene conversion (Rocha and Feil 2010).…”

Section: Mycobacterium Tuberculosis Complex Is Not Strictly Clonalsupporting

confidence: 87%

After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection

Namouchi¹,

Didelot²,

Schöck³

et al. 2012

Genome Res.

147

122

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Many of the most virulent bacterial pathogens show low genetic diversity and sexual isolation. Accordingly, Mycobacterium tuberculosis, the deadliest human pathogen, is thought to be clonal and evolve by genetic drift. Yet, its genome shows few of the concomitant signs of genome degradation. We analyzed 24 genomes and found an excess of genetic diversity in regions encoding key adaptive functions including the type VII secretion system and the ancient horizontally transferred virulence-related regions. Four different approaches showed evident signs of recombination in M. tuberculosis. Recombination tracts add a high density of polymorphisms, and many are thus predicted to arise from outside the clade. Some of these tracts match Mycobacterium canettii sequences. Recombination introduced an excess of non-synonymous diversity in general and even more in genes expected to be under positive or diversifying selection, e.g., cell wall component genes. Mutations leading to non-synonymous SNPs are effectively purged in MTBC, which shows dominance of purifying selection. MTBC mutation bias toward AT nucleotides is not compensated by biased gene conversion, suggesting the action of natural selection also on synonymous changes. Together, all of these observations point to a strong imprint of recombination and selection in the genome affecting both non-synonymous and synonymous positions. Hence, contrary to some other pathogens and previous proposals concerning M. tuberculosis, this lineage may have come out of its ancestral bottleneck as a very successful pathogen that is rapidly diversifying by the action of mutation, recombination, and natural selection.

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Section: Mycobacterium Tuberculosis Complex Is Not Strictly Clonalsupporting

confidence: 87%

After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection

Namouchi¹,

Didelot²,

Schöck³

et al. 2012

Genome Res.

147

122

View full text Add to dashboard Cite

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“…Based on recent studies showing that mutational bias from G/C to A/T is universal among bacterial genomes (129)(130)(131)(132), one explanation for the observed paucity in GϩC-rich codons in genomes of the SAG-O19 clade is that an inefficiency of purifying selection under such a mutational bias would accelerate the replacement of GϩC-rich codons. Thus, although counter to the more established theory that selection has been the exclusive force driving the evolution of surface ocean bacterial populations (8,133), there are also reasonable arguments in favor of the inefficiency of purifying selection playing a role, at least in the evolution of SAG-O19 genome composition.…”

Section: Evolution Of An Enigmatic Roseobacter Lineagementioning

confidence: 99%

Evolutionary Ecology of the Marine Roseobacter Clade

Luo

Moran

2014

Microbiol Mol Biol Rev

287

244

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SUMMARY Members of the Roseobacter clade are equipped with a tremendous diversity of metabolic capabilities, which in part explains their success in so many different marine habitats. Ideas on how this diversity evolved and is maintained are reviewed, focusing on recent evolutionary studies exploring the timing and mechanisms of Roseobacter ecological diversification.

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“…This background selection model is supported by the decrease of polymorphism and indications of purifying selection on nonsynonymous sites near the terminus (35). Moreover, there is additional evidence that selection serves to elevate genomic G+C contents in bacteria (61,62). Alternatively, a lower recombination rate near the replication terminus could lower the G+C content of the region by minimizing the G+C-biased repair of recombination-induced mismatches by biased gene conversion (63).…”

Section: How To Best Assess the Impact Of Recombination On E Coli Evmentioning

confidence: 99%

Impermanence of bacterial clones

Bobay

Traverse

Ochman

2015

Proc. Natl. Acad. Sci. U.S.A.

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Bacteria reproduce asexually and pass on a single genome copied from the parent, a reproductive mode that assures the clonal descent of progeny; however, a truly clonal bacterial species is extremely rare. The signal of clonality can be interrupted by gene uptake and exchange, initiating homologous recombination that results in the unique sequence of one clone being incorporated into another. Because recombination occurs sporadically and on local scales, these events are often difficult to recognize, even when considering large samples of completely sequenced genomes. Moreover, several processes can produce the appearance of clonality in populations that undergo frequent recombination. The rates and consequences of recombination have been studied in Escherichia coli for over 40 y, and, during this time, there have been several shifting views of its clonal status, population structure, and rates of gene exchange. We reexamine the studies and retrace the evolution of the methods that have assessed the extent of DNA flux, largely focusing on its impact on the E. coli genome.clonality | homologous exchange | recombination | genome evolution | E. coli R eproduction by binary fission virtually guarantees the clonality of a bacterial lineage. Apart from mutations and other rare events that might modify chromosome integrity during replication, the primary sequence of DNA in all daughter and descendent cells remains identical, generation after generation after generation. Unlike animals, in which parthenogenetic forms are ecologically constrained and relatively short-lived over evolutionary timescales (1-3), asexually reproducing bacteria have persisted since the origin of cellular life and represent the most diverse and widespread organisms on the planet. Naturally, the vast diversity present in bacteria could have arisen solely by asexual means-there has certainly been sufficient time and large enough population sizes to allow for enormous numbers of mutations (and combinations of mutations) to be experienced. Moreover, it seems as though some of the most extraordinary innovations in the history of life have occurred without intervention of the sexual process (4). Bacteria as Clonal OrganismsDespite their obligatory asexual mode of reproduction, the clonality of bacterial lineages can be disrupted by sex, or at least by what we refer to as sex. In bacteria, sex is the inheritance of genetic material from any source aside from their one parent cell and can occur by any of several processes. Foreign DNA can be introduced by cell-to-cell contact, transmitted to the cell by an infectious agent, or acquired directly from the environment; and, therefore, genes can be obtained from organisms representing any domain of life, and even from entities (i.e., viruses and phages) that are not classified to any domain of life. Moreover, events of sex in bacteria occur without known regularity and usually constitute a very small portion of the genome. In fact, sexually acquired DNA need not involve recombination at all but can persist...

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The Temporal Dynamics of Slightly Deleterious Mutations in Escherichia coli and Shigella spp.

Cited by 70 publications

References 66 publications

After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection

After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection

Evolutionary Ecology of the Marine Roseobacter Clade

Impermanence of bacterial clones

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