Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq

Barrick, Jeffrey E.; Colburn, Geoffrey; Deatherage, Daniel E.; Traverse, Charles C.; Strand, Matthew D; Borges, Jordan J; Knoester, David B.; Reba, Aaron; Meyer, Austin G.

doi:10.1186/1471-2164-15-1039

Cited by 250 publications

(262 citation statements)

References 41 publications

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“…We used breseq (version 0.26.0) (56,57) to identify mutations in evolved genomes by comparing Illumina reads to a version of the complete genome sequence of REL606 (17) with updated feature annotations (included in Dataset S1). As necessary, we manually curated breseq results to eliminate spurious predictions and to resolve predictions of sequence junctions and changes in read-coverage depth into structural mutations (57). To check mutation predictions, we applied the reported sequence changes to the ancestral genome sequence and reran breseq to verify that there were no further discrepancies between the reads and the mutated reference genome.…”

Section: Methodsmentioning

confidence: 99%

Specificity of genome evolution in experimental populations of Escherichia coli evolved at different temperatures

Deatherage

Kepner

Bennett

et al. 2017

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

117

101

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Isolated populations derived from a common ancestor are expected to diverge genetically and phenotypically as they adapt to different local environments. To examine this process, 30 populations ofEscherichia coliwere evolved for 2,000 generations, with six in each of five different thermal regimes: constant 20 °C, 32 °C, 37 °C, 42 °C, and daily alternations between 32 °C and 42 °C. Here, we sequenced the genomes of one endpoint clone from each population to test whether the history of adaptation in different thermal regimes was evident at the genomic level. The evolved strains had accumulated ∼5.3 mutations, on average, and exhibited distinct signatures of adaptation to the different environments. On average, two strains that evolved under the same regime exhibited ∼17% overlap in which genes were mutated, whereas pairs that evolved under different conditions shared only ∼4%. For example, all six strains evolved at 32 °C had mutations innadR, whereas none of the other 24 strains did. However, a population evolved at 37 °C for an additional 18,000 generations eventually accumulated mutations in the signature genes strongly associated with adaptation to the other temperature regimes. Two mutations that arose in one temperature treatment tended to be beneficial when tested in the others, although less so than in the regime in which they evolved. These findings demonstrate that genomic signatures of adaptation can be highly specific, even with respect to subtle environmental differences, but that this imprint may become obscured over longer timescales as populations continue to change and adapt to the shared features of their environments.

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Section: Methodsmentioning

confidence: 99%

Specificity of genome evolution in experimental populations of Escherichia coli evolved at different temperatures

Deatherage

Kepner

Bennett

et al. 2017

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

117

101

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“…5; two indels identified in ref. 13 and one mistaken call have been added (see SI Material and Methods).…”

Section: Significancementioning

confidence: 99%

Determinants of spontaneous mutation in the bacteriumEscherichia colias revealed by whole-genome sequencing

Foster

Lee

Popodi

et al. 2015

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

150

205

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A complete understanding of evolutionary processes requires that factors determining spontaneous mutation rates and spectra be identified and characterized. Using mutation accumulation followed by whole-genome sequencing, we found that the mutation rates of three widely diverged commensal Escherichia coli strains differ only by about 50%, suggesting that a rate of 1-2 × 10 −3 mutations per generation per genome is common for this bacterium. Four major forces are postulated to contribute to spontaneous mutations: intrinsic DNA polymerase errors, endogenously induced DNA damage, DNA damage caused by exogenous agents, and the activities of error-prone polymerases. To determine the relative importance of these factors, we studied 11 strains, each defective for a major DNA repair pathway. The striking result was that only loss of the ability to prevent or repair oxidative DNA damage significantly impacted mutation rates or spectra. These results suggest that, with the exception of oxidative damage, endogenously induced DNA damage does not perturb the overall accuracy of DNA replication in normally growing cells and that repair pathways may exist primarily to defend against exogenously induced DNA damage. The thousands of mutations caused by oxidative damage recovered across the entire genome revealed strong local-sequence biases of these mutations. Specifically, we found that the identity of the 3′ base can affect the mutability of a purine by oxidative damage by as much as eightfold.A complete understanding of the evolution and stability of the genome requires that the determinants of spontaneous mutation be identified and characterized. Among the variety of mistakes that can occur during DNA transactions, four sources of sequence variation appear to dominate in prokaryotes: intrinsic DNA polymerase errors, endogenously induced DNA damage, DNA damage induced by exogenous agents, and the activities of error-prone polymerases. This conclusion is based on changes in the rates and spectra of mutations that occur when genes affecting these processes are deleted or amplified. In particular, loss of a DNA repair pathway often gives a mutator phenotype, indicating that the pathway of interest exerts an important limitation on spontaneous mutation (1). However, investigations of the mutagenic impact of various DNA repair pathways have relied almost exclusively on reporter genes, leaving open the possibility that the results are biased by the particular features of the selected loci. This concern can be avoided by allowing mutations to accumulate nonselectively in DNA repair-defective strains and identifying the resulting sequence changes by whole-genome sequencing (WGS). Although this approach may miss rare but interesting mutational processes, it can reveal the overall threats to genomic stability and identify features, such as local sequence context, that influence mutational frequencies. Surprisingly, this technique has been used with the eukaryote Caenorhabditis elegans (2) but has not been extensively applied to prokary...

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“…The breseq pipeline assembles a referencebased alignment to predict mutations compared to a previously sequenced genome (NCBI GenBank accession number NC_007779.1, E. coli K-12 W3110). Newer versions of breseq now predict structural variations, including large deletions, mobile element insertions, and gene duplications, all of which account for much of the genetic diversity in evolved clones (50)(51)(52)(53).…”

mentioning

confidence: 99%

“…We sequenced genomes of selected isolates and then identified genetic variants using the breseq pipeline (48)(49)(50). The breseq pipeline assembles a referencebased alignment to predict mutations compared to a previously sequenced genome (NCBI GenBank accession number NC_007779.1, E. coli K-12 W3110).…”

mentioning

confidence: 99%

Benzoate- and Salicylate-Tolerant Strains of Escherichia coli K-12 Lose Antibiotic Resistance during Laboratory Evolution

Creamer

Ditmars

Basting

et al. 2017

Appl Environ Microbiol

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Escherichia coli K-12 W3110 grows in the presence of membrane-permeant organic acids that can depress cytoplasmic pH and accumulate in the cytoplasm. We conducted experimental evolution by daily diluting cultures in increasing concentrations of benzoic acid (up to 20 mM) buffered at external pH 6.5, a pH at which permeant acids concentrate in the cytoplasm. By 2,000 generations, clones isolated from evolving populations showed increasing tolerance to benzoate but were sensitive to chloramphenicol and tetracycline. Sixteen clones grew to stationary phase in 20 mM benzoate, whereas the ancestral strain W3110 peaked and declined. Similar growth occurred in 10 mM salicylate. Benzoate-evolved strains grew like W3110 in the absence of benzoate, in media buffered at pH 4.8, pH 7.0, or pH 9.0, or in 20 mM acetate or sorbate at pH 6.5. Genomes of 16 strains revealed over 100 mutations, including single-nucleotide polymorphisms (SNPs), large deletions, and insertion knockouts. Most strains acquired deletions in the benzoate-induced multiple antibiotic resistance (Mar) regulon or in associated regulators such as rob and cpxA, as well as the multidrug resistance (MDR) efflux pumps emrA, emrY, and mdtA. Strains also lost or downregulated the Gad acid fitness regulon. In 5 mM benzoate or in 2 mM salicylate (2-hydroxybenzoate), most strains showed increased sensitivity to the antibiotics chloramphenicol and tetracycline; some strains were more sensitive than a marA knockout strain. Thus, our benzoate-evolved strains may reveal additional unknown drug resistance components. Benzoate or salicylate selection pressure may cause general loss of MDR genes and regulators. IMPORTANCE Benzoate is a common food preservative, and salicylate is the primary active metabolite of aspirin. In the gut microbiome, genetic adaptation to salicylate may involve loss or downregulation of inducible multidrug resistance systems. This discovery implies that aspirin therapy may modulate the human gut microbiome to favor salicylate tolerance at the expense of drug resistance. Similar aspirin-associated loss of drug resistance might occur in bacterial pathogens found in arterial plaques.

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Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq

Cited by 250 publications

References 41 publications

Specificity of genome evolution in experimental populations of Escherichia coli evolved at different temperatures

Specificity of genome evolution in experimental populations of Escherichia coli evolved at different temperatures

Determinants of spontaneous mutation in the bacteriumEscherichia colias revealed by whole-genome sequencing

Benzoate- and Salicylate-Tolerant Strains of Escherichia coli K-12 Lose Antibiotic Resistance during Laboratory Evolution

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