ArticlePloS one2011
Using genomic sequencing for classical genetics in E. coli K12.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
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- Adaptive genetics reveals constraints on protein structure/function by evolving E. coli under constant nutrient limitation.BMC biology · 2025Article
- Cell Geometry and Membrane Protein Crowding Constrain Growth Rate, Overflow Metabolism, Respiration, and Maintenance Energy.bioRxiv : the preprint server for biology · 2025Article
- Spatiotemporal development of expanding bacterial colonies driven by emergent mechanical constraints and nutrient gradients.Nature communications · 2025Article
- Lineage-dependent variations in single-cell antibiotic susceptibility reveal the selective inheritance of phenotypic resistance in bacteria.Nature communications · 2025Article
- Overall biomass yield on multiple nutrient sources.NPJ systems biology and applications · 2025Article
- Direct measurement of dynamic attractant gradients reveals breakdown of the Patlak-Keller-Segel chemotaxis model.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- High quality genomes produced from single MinION flow cells clarify polyploid and demographic histories of critically endangered Fraxinus (ash) species.Communications biology · 2024Article
- Functional decomposition of metabolism allows a system-level quantification of fluxes and protein allocation towards specific metabolic functions.Nature communications · 2023Article
- Direct measurement of dynamic attractant gradients reveals breakdown of the Patlak-Keller-Segel chemotaxis model.bioRxiv : the preprint server for biology · 2023Article
- Revisiting Fur Regulon Leads to a Comprehensive Understanding of Iron and Fur Regulation.International journal of molecular sciences · 2023Article
- Dissociation kinetics of small-molecule inhibitors in Escherichia coli is coupled to physiological state of cells.Communications biology · 2023Article
- Tracking of Diversity and Evolution in the Brown Rot FungiFrontiers in microbiology · 2022Article
- Small RNA GcvB Regulates Oxidative Stress Response ofAntioxidants (Basel, Switzerland) · 2021Article
- Article
- From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions.Molecular systems biology · 2021Article
- Global coordination of metabolic pathways in Escherichia coli by active and passive regulation.Molecular systems biology · 2021Article
- Gain of SpontaneousFrontiers in bioengineering and biotechnology · 2021Article
- Metabolic engineering ofJournal of biological research (Thessalonike, Greece) · 2020Article
- Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
We here develop computational methods to facilitate use of 454 whole genome shotgun sequencing to identify mutations in Escherichia coli K12. We had Roche sequence eight related strains derived as spontaneous mutants in a background without a whole genome sequence. They provided difference tables based on assembling each genome to reference strain E. coli MG1655 (NC_000913). Due to the evolutionary distance to MG1655, these contained a large number of both false negatives and positives. By manual analysis of the dataset, we detected all the known mutations (24 at nine locations) and identified and genetically confirmed new mutations necessary and sufficient for the phenotypes we had selected in four strains. We then had Roche assemble contigs de novo, which we further assembled to full-length pseudomolecules based on synteny with MG1655. This hybrid method facilitated detection of insertion mutations and allowed annotation from MG1655. After removing one genome with less than the optimal 20- to 30-fold sequence coverage, we identified 544 putative polymorphisms that included all of the known and selected mutations apart from insertions. Finally, we detected seven new mutations in a total of only 41 candidates by comparing single genomes to composite data for the remaining six and using a ranking system to penalize homopolymer sequencing and misassembly errors. An additional benefit of the analysis is a table of differences between MG1655 and a physiologically robust E. coli wild-type strain NCM3722. Both projects were greatly facilitated by use of comparative genomics tools in the CoGe software package (http://genomevolution.org/).
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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.