Comparisons of dN/dS are time dependent for closely related bacterial genomes

Rocha, Eduardo P. C.; Smith, John Maynard; Hurst, Laurence D.; Holden, Matthew T. G.; Cooper, Jessica E.; Smith, Noel H.; Feil, Edward J.

doi:10.1016/j.jtbi.2005.08.037

Cited by 389 publications

(430 citation statements)

References 44 publications

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“…The identity of the SNPs suggests that they reflect recent diversification without evidence for either purifying or positive selection (14). Specifically, the SNPs are not biased toward protein-altering substitutions.…”

Section: Resultsmentioning

confidence: 97%

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011

Grad

Lipsitch

Feldgarden

et al. 2012

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

255

232

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International audienceThe degree to which molecular epidemiology reveals informationabout the sources and transmission patterns of an outbreakdepends on the resolution of the technology used and the samplesstudied. Isolates of Escherichia coli O104:H4 from the outbreak centeredin Germany in May–July 2011, and the much smaller outbreakin southwest France in June 2011, were indistinguishable by standardtests. We report a molecular epidemiological analysis usingmultiplatform whole-genome sequencing and analysis of multipleisolates from the German and French outbreaks. Isolates from theGerman outbreak showed remarkably little diversity, with onlytwo single nucleotide polymorphisms (SNPs) found in isolates fromfour individuals. Surprisingly, we found much greater diversity (19SNPs) in isolates from seven individuals infected in the French outbreak.The German isolates form a clade within the more diverseFrench outbreak strains. Moreover, five isolates derived from a singleinfected individual from the French outbreak had extremelylimited diversity. The striking difference in diversity between theGerman and French outbreak samples is consistent with severalhypotheses, including a bottleneck that purged diversity in theGerman isolates, variation in mutation rates in the two E. coli outbreakpopulations, or uneven distribution of diversity in the seedpopulations that led to each outbreak

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Section: Resultsmentioning

confidence: 97%

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011

Grad

Lipsitch

Feldgarden

et al. 2012

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

255

232

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“…A possible explanation for these high ratios is that the genes were acquired recently and are still in the process of adaptation to their new context. Unusually high dN/dS ratios have also been observed in other closely related strains (Rocha et al, 2006) as a result of paralog formation, that is, recent gene duplications in which one gene undergoes a process of neo-or sub-functionalization.…”

Section: Resultsmentioning

confidence: 91%

Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains

et al. 2010

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Genomic and metagenomic data indicate a high degree of genomic variation within microbial populations, although the ecological and evolutive meaning of this microdiversity remains unknown. Microevolution analyses, including genomic and experimental approaches, are so far very scarce for non-pathogenic bacteria. In this study, we compare the genomes, metabolomes and selected ecological traits of the strains M8 and M31 of the hyperhalophilic bacterium Salinibacter ruber that contain ribosomal RNA (rRNA) gene and intergenic regions that are identical in sequence and were simultaneously isolated from a Mediterranean solar saltern. Comparative analyses indicate that S. ruber genomes present a mosaic structure with conserved and hypervariable regions (HVRs). The HVRs or genomic islands, are enriched in transposases, genes related to surface properties, strain-specific genes and highly divergent orthologous. However, the many indels outside the HVRs indicate that genome plasticity extends beyond them. Overall, 10% of the genes encoded in the M8 genome are absent from M31 and could stem from recent acquisitions. S. ruber genomes also harbor 34 genes located outside HVRs that are transcribed during standard growth and probably derive from lateral gene transfers with Archaea preceding the M8/M31 divergence. Metabolomic analyses, phage susceptibility and competition experiments indicate that these genomic differences cannot be considered neutral from an ecological perspective. The results point to the avoidance of competition by micro-niche adaptation and response to viral predation as putative major forces that drive microevolution within these Salinibacter strains. In addition, this work highlights the extent of bacterial functional diversity and environmental adaptation, beyond the resolution of the 16S rRNA and internal transcribed spacers regions.

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“…dN/dS was calculated for concatenated alignments of CDSs from the nonrepetitive, core genome for each pairwise combination of 9 isolates (630, BI-9, CF5, M68, M120, CD196, BI-1, 2007855, and R20291). It was previously suggested when effective population size is infinite or sufficiently large; the trajectory of 1/(dN/dS) exhibits a linear trend with time, but when population size decreases, the increase of 1/(dN/dS) with time reaches a plateau (29). S (number of synonymous substitutions) or dI (number of intergenic SNPs) have been used as a measure of time since divergence, although synonymous changes and intergenic regions could also be subject to selection forces that deviate from neutral.…”

Section: Resultsmentioning

confidence: 94%

“…A ratio significantly smaller than 1 suggests strong purifying selection, whereas a ratio close to 1 is usually taken as indicating a neutral selection pressure. However, it has been shown that for very closely related genomes, dN/dS can be close to 1 (29), either because time has been too short for selection to act (29) or because nucleotide substitutions within a species may represent segregating polymorphisms rather than fixed differences (30). dN/dS was calculated for concatenated alignments of CDSs from the nonrepetitive, core genome for each pairwise combination of 9 isolates (630, BI-9, CF5, M68, M120, CD196, BI-1, 2007855, and R20291).…”

Section: Resultsmentioning

confidence: 99%

Evolutionary dynamics of Clostridium difficile over short and long time scales

Sebaihia

Lawley

et al. 2010

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

352

389

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Clostridium difficile has rapidly emerged as the leading cause of antibiotic-associated diarrheal disease, with the transcontinental spread of various PCR ribotypes, including 001, 017, 027 and 078. However, the genetic basis for the emergence of C. difficile as a human pathogen is unclear. Whole genome sequencing was used to analyze genetic variation and virulence of a diverse collection of thirty C. difficile isolates, to determine both macro and microevolution of the species. Horizontal gene transfer and large-scale recombination of core genes has shaped the C. difficile genome over both short and long time scales. Phylogenetic analysis demonstrates C. difficile is a genetically diverse species, which has evolved within the last 1.1–85 million years. By contrast, the disease-causing isolates have arisen from multiple lineages, suggesting that virulence evolved independently in the highly epidemic lineages.

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Comparisons of dN/dS are time dependent for closely related bacterial genomes

Cited by 389 publications

References 44 publications

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011

Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains

Evolutionary dynamics of Clostridium difficile over short and long time scales

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