Document Type


Original Publication Date


Journal/Book/Conference Title

Genome Biology



DOI of Original Publication



Originally published at

Date of Submission

August 2014



Short-term laboratory evolution of bacteria followed by genomic sequencing provides insight into the mechanism of adaptive evolution, such as the number of mutations needed for adaptation, genotype-phenotype relationships, and the reproducibility of adaptive outcomes.


In the present study, we describe the genome sequencing of 11 endpoints of Escherichia coli that underwent 60-day laboratory adaptive evolution under growth rate selection pressure in lactate minimal media. Two to eight mutations were identified per endpoint. Generally, each endpoint acquired mutations to different genes. The most notable exception was an 82 base-pair deletion in the rph-pyrE operon that appeared in 7 of the 11 adapted strains. This mutation conferred an approximately 15% increase to the growth rate when experimentally introduced to the wild-type background and resulted in an approximately 30% increase to growth rate when introduced to a background already harboring two adaptive mutations. Additionally, most endpoints had a mutation in a regulatory gene (crp or relA, for example) or the RNA polymerase.


The 82 base-pair deletion found in the rph-pyrE operon of many endpoints may function to relieve a pyrimidine biosynthesis defect present in MG1655. In contrast, a variety of regulators acquire mutations in the different endpoints, suggesting flexibility in overcoming regulatory challenges in the adaptation.


© 2009 Conrad et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

Is Part Of

VCU Computer Science Publications

gb-2009-10-10-r118-s1.xls (100 kB)
Mutations reported for LactA, LactB, LactC, LactD, and LactE strains using Nimblegen CGS arrays.

gb-2009-10-10-r118-s2.xls (1778 kB)
Mutations reported for all strains using Solexa sequencing.

gb-2009-10-10-r118-s3.xls (1845 kB)
False negative rate of our mutation detection algorithm using a reference sequence genome with 'mutations' inserted at known locations.

gb-2009-10-10-r118-s4.xls (39 kB)
Regulons enriched for differential expression in LactA, LactB, LactC, LactD, and LactE strains.

gb-2009-10-10-r118-s5.xls (37 kB)
The presence and absence of mutations at time points or in colonies were used for determination of mutation trajectory and population mutation penetration.

gb-2009-10-10-r118-s6.xls (52 kB)
Primers used in this study.