A genotype is a list of mutant genes in an organism. In addition to mutations of the genome, other genetic elements such as prophage or plasmids can also be included. They are listed in brackets. The most popular prophages are DE3 (a λ derivative with the T7 RNA polymerase cloned in) and φ80dlacΔM15, which carries the half of the beta-galactosidase required for blue/white screening in plasmids like pUC19. The F plasmid also usually has a genotype because most F plasmids have E. coli chromosomal DNA in them. These are referred to as F’ (F prime).
It is assumed that any of the genes that are not mentioned in the genotype are wild type. A strain may have an unknown mutation. For example, JM109 is a lon mutant. The genotype of JM109 usually does not mention lon because it is not well known that it is there. It was discovered during the study of a different gene.1 Conversely, a mutation in a genotype does not always mean that the mutation is really there. At times, it has been deduced that the mutation is there based on the genotype from the properties of the parental strain. For example, almost every genotype claims that the HB101 is a proline auxotroph,2 but it has since been determined that it is not.3
A phenotype is a property that is genetically determined, but the mutated gene is unknown. For example, a strain that is resistant to phage T1 is referred to as T1R. The resistance could be due to an insertion sequence in the T1 receptor that is coded by the tonA gene (also known as the fhuA gene). If it is, the strain is referred to as tonA (or fhuA). If the tonA gene is found to be wild type, then another mutation must be causing the T1 resistance. Therefore, since it is still unknown, T1R is used to describe the strain. Another instance in which the phenotype is included is when the genotype does not clearly represent the trait. For example, the genotype rpsL indicates that the strain is resistant to streptomycin. StrR is used to indicate resistance to streptomycin instead as it clearly indicates the trait.
A marker is any mutation that distinguishes (“marks”) a strain. A marker can be a gene mutation or a phenotype. The presence of a prophage or of plasmids is not usually referred to as a “marker.”
Most likely, the strain that you are working with contains the mutations that you desire: recA, endA, lacΔM15, rpsL and tonA. However, it is important to remember that E. coli laboratory strains have been mutagenized, mixed up and transduced for years.4 As a result, the probability that the strain has all of the mutations in the genotype and only those mutations varies greatly. This is why trying different strain backgrounds is recommended when experiments are not working as expected.