Fig. 3

Generalized transduction by S. enterica phage P22 and E. coli phage P1. a Illustration of generalized transduction. Upon phage infection, the phage genome is replicated in the host cell by rolling circle replication resulting in genome concatemers and phage particles are produced. The phage genome is packaged into the phage head by a so-called head-full packaging mechanism, which relies on the recognition of a packaging (pac) site. The bacterial host chromosomes contain sites that resemble the pac site and thus lead to packaging of non-random pieces of the host chromosome into phage heads. The packaging happens in a processive fashion, i.e., after one phage head has been filled the packaging machinery continues to fill the next phage head with the remaining DNA molecule. The likelihood that the packaging machinery dissociates from the molecule increases the further away from the pac site it gets, thus leading to a decreased packaging efficiency over distance. b Salmonella enterica genome coverage pattern associated with generalized transduction by phage P22. Whole genome sequencing reads and purified phage particle reads were mapped to the S. enterica genome. In the lower part transduction, frequencies for 28 chromosomal markers along the chromosome are shown as determined by Schmieger [30]. Vertical lines indicate the positions of the chromosomal markers in green where the transduction frequency matches the read coverage, in grey where read coverage does not correspond to reported transduction frequency. c Escherichia coli genome coverage pattern associated with generalized transduction by E. coli phage P1