![]() ![]() The genome sequences of non-K-12 strains, which are used for biotechnological applications ( Jeong et al., 2009 Archer et al., 2011), probiotics ( Toh et al., 2010 Reister et al., 2014), or phylogenomic studies of E. Even different stocks of the same sequenced strain can harbor genetic variations ( Freddolino et al., 2012), which cannot be ignored. ![]() Efforts to provide such information include the genome sequencing of E. The availability of accurate genome information for each strain is crucial to the success of a particular application. coli K-12 cells from diverse lineages have been developed for various purposes. There is a cautionary note concerning the representativeness of K-12 ( Hobman et al., 2007) due to its inherent intraspecies diversity and many genetic changes caused by extended storage in stab culture and/or frequent subculture during its early history. The continuously updated genome information is available through public online services such as EcoGene ( Zhou and Rudd, 2013 Zhou et al., 2013) and EcoCyc ( Karp et al., 2014). (1997), it has been regarded as a standard for the study of the K-12 strain, its derivatives, and even (micro)organisms beyond E. coli K-12 (MG1655) was first sequenced in Blattner et al. coli includes pathogenic strains that have brought about emerging public health concerns ( Kaper et al., 2004 Croxen and Finlay, 2010 Blount, 2015), and is one of the most sequenced species along with other important bacterial pathogens such as Streptococcus pneumoniae, Staphylococcus aureus, Salmonella enterica, and Mycobacterium tuberculosis. coli are used in everyday scientific applications as hosts for gene cloning, protein expression, and metabolite production. Many laboratory strains derived from the wild-type E. It is a versatile model microorganism on which most of the principles and tools of modern genetics and molecular biology are founded ( Blount, 2015). Our results extend current knowledge of the genotype of RR1 and its relatives, and provide insights into the pedigree, genomic background, and physiology of common laboratory strains.Įscherichia coli was discovered in 1885 and is the most widely studied organism in molecular biology. As well as identifying all known genotypes of RR1 on the basis of genomic context, we found novel mutations. However, because RR1 has experienced a series of genetic manipulations since branching from the common ancestor, it has a set of mutations different from those found in K-12 MG1655. We found that 96.9% of the RR1 genome is derived from K-12, and identified exact crossover junctions between K-12 and B genomic fragments. Finally, PCR and Sanger sequencing-based finishing were applied to resolve non-single nucleotide variant regions with aberrant read depths and breakpoints, most of them resulting from prophages and insertion sequence transpositions that are not present in the reference genome sequence. A hybrid genome sequence of K-12 MG1655 and B BL21(DE3) was constructed based on the initial mapping of Illumina HiSeq reads to each reference, and iterative rounds of read mapping, variant detection, and consensus extraction were carried out. coli strain RR1 (HB101 RecA +), which has long been used as a general cloning host. We determined the complete genome sequence of laboratory E. coli strains, however, genome sequence information is limited except for several well-known strains. There have been extensive genome sequencing studies for Escherichia coli strains, particularly for pathogenic isolates, because fast determination of pathogenic potential and/or drug resistance and their propagation routes is crucial. 4Department of Systems Biotechnology, Chung-Ang University, Anseong, South Korea.3Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.2Biosystems and Bioengineering Program, University of Science and Technology, Daejeon, South Korea.1Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.Haeyoung Jeong 1,2*, Young Mi Sim 3, Hyun Ju Kim 2 and Sang Jun Lee 4* ![]()
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