ArticleGenome biology and evolution2016
How Archiving by Freezing Affects the Genome-Scale Diversity of Escherichia coli Populations.
Article in Genome biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Carriage of antimicrobial-resistant E. coli in urban stray cats (Felis catus).Australian veterinary journal · 2026Article
- Clinical utility and limitations of whole-genome sequencing via nanopore technology and Bayesian modeling for outbreak transmission inference.Antimicrobial resistance and infection control · 2026Article
- Bacteriophage cocktail in drinking water suppresses systemic avian pathogenicCurrent research in microbial sciences · 2026Article
- Comparative genome analysis of enterohemorrhagic Escherichia coli ATCC 43894 and its pO157-cured strain 277.Journal of microbiology (Seoul, Korea) · 2025Article
- Attenuated Strains of Pseudomonas aeruginosa: A Promising Cell Factory for Rhamnolipid Production.Microbial biotechnology · 2025Review
- Genome-wide assessment of genetic diversity and transcript variations in 17 accessions of the model diatomISME communications · 2024Article
- Article
- Genomics of Diversification of Pseudomonas aeruginosa in Cystic Fibrosis Lung-like Conditions.Genome biology and evolution · 2022Article
- Comparison of E. coli based self-inducible expression systems containing different human heat shock proteins.Scientific reports · 2021Article
- Cryopreservation of clonal and polyclonal populations ofBiology methods & protocols · 2021Article
- Emerging Adaptive Strategies Under Temperature Fluctuations in a Laboratory Evolution Experiment ofFrontiers in microbiology · 2021Article
- Consequences of Cryopreservation in Diverse Natural Isolates of Saccharomyces cerevisiae.Genome biology and evolution · 2020Article
- Experimental evolution of phytoplankton fatty acid thermal reaction norms.Evolutionary applications · 2019Article
- High mutation rates limit evolutionary adaptation in Escherichia coli.PLoS genetics · 2018Article
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Authors and funding
3 authors.
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Abstract
In the experimental evolution of microbes such as Escherichia coli, many replicate populations are evolved from a common ancestor. Freezing a population sample supplemented with the cryoprotectant glycerol permits later analysis or restarting of an evolution experiment. Typically, each evolving population, and thus each sample archived in this way, consists of many unique genotypes and phenotypes. The effect of archiving on such a heterogeneous population is unknown. Here, we identified optimal archiving conditions for E. coli. We also used genome sequencing of archived samples to study the effects that archiving has on genomic population diversity. We observed no allele substitutions and mostly small changes in allele frequency. Nevertheless, principal component analysis of genome-scale allelic diversity shows that archiving affects diversity across many loci. We showed that this change in diversity is due to selection rather than drift. In addition, ∼1% of rare alleles that occurred at low frequencies were lost after treatment. Our observations imply that archived populations may be used to conduct fitness or other phenotypic assays of populations, in which the loss of a rare allele may have negligible effects. However, caution is appropriate when sequencing populations restarted from glycerol stocks, as well as when using glycerol stocks to restart or replay evolution. This is because the loss of rare alleles can alter the future evolutionary trajectory of a population if the lost alleles were strongly beneficial.
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