ArticlePloS one2012
FREQ-Seq: a rapid, cost-effective, sequencing-based method to determine allele frequencies directly from mixed populations.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
24 citing papers in PubMed.
- Engineering Proteins Using Statistical Models of Coevolutionary Sequence Information.Cold Spring Harbor perspectives in biology · 2024Review
- FREQ-Seq2: a method for precise high-throughput combinatorial quantification of allele frequencies.G3 (Bethesda, Md.) · 2023Article
- High-throughput characterization of mutations in genes that drive clonal evolution using multiplex adaptome capture sequencing.Cell systems · 2021Article
- Mistranslation can promote the exploration of alternative evolutionary trajectories in enzyme evolution.Journal of evolutionary biology · 2021Article
- Genetic Context Significantly Influences the Maintenance and Evolution of Degenerate Pathways.Genome biology and evolution · 2021Article
- Potentiation of Aminoglycoside Lethality by CAntimicrobial agents and chemotherapy · 2019Article
- Bacterial predator-prey coevolution accelerates genome evolution and selects on virulence-associated prey defences.Nature communications · 2019Article
- Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution.Microbiology and molecular biology reviews : MMBR · 2018Review
- Genomic insights into the pathogenicity and environmental adaptability of Enterococcus hirae R17 isolated from pork offered for retail sale.MicrobiologyOpen · 2017Article
- Article
- Mistranslation can enhance fitness through purging of deleterious mutations.Nature communications · 2017Article
- High-throughput evaluation of synthetic metabolic pathways.Technology · 2016Article
- Cystic fibrosis-adaptedScience advances · 2015Article
- Parallel and Divergent Evolutionary Solutions for the Optimization of an Engineered Central Metabolism in Methylobacterium extorquens AM1.Microorganisms · 2015Article
- The genome-scale interplay amongst xenogene silencing, stress response and chromosome architecture in Escherichia coli.Nucleic acids research · 2015Article
- Article
- Population-genetic inference from pooled-sequencing data.Genome biology and evolution · 2014Article
- Mapping the fitness landscape of gene expression uncovers the cause of antagonism and sign epistasis between adaptive mutations.PLoS genetics · 2014Article
- Detecting rare structural variation in evolving microbial populations from new sequence junctions using breseq.Frontiers in genetics · 2014Article
- Adaptation of Enterococcus faecalis to daptomycin reveals an ordered progression to resistance.Antimicrobial agents and chemotherapy · 2013Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Understanding evolutionary dynamics within microbial populations requires the ability to accurately follow allele frequencies through time. Here we present a rapid, cost-effective method (FREQ-Seq) that leverages Illumina next-generation sequencing for localized, quantitative allele frequency detection. Analogous to RNA-Seq, FREQ-Seq relies upon counts from the >10(5) reads generated per locus per time-point to determine allele frequencies. Loci of interest are directly amplified from a mixed population via two rounds of PCR using inexpensive, user-designed oligonucleotides and a bar-coded bridging primer system that can be regenerated in-house. The resulting bar-coded PCR products contain the adapters needed for Illumina sequencing, eliminating further library preparation. We demonstrate the utility of FREQ-Seq by determining the order and dynamics of beneficial alleles that arose as a microbial population, founded with an engineered strain of Methylobacterium, evolved to grow on methanol. Quantifying allele frequencies with minimal bias down to 1% abundance allowed effective analysis of SNPs, small in-dels and insertions of transposable elements. Our data reveal large-scale clonal interference during the early stages of adaptation and illustrate the utility of FREQ-Seq as a cost-effective tool for tracking allele frequencies in populations.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.