Fig. 1. Selection strategy for identifying phage defence systems.

A fosmid library of random ~40 kb fragments of genomic DNA from 71 E. coli strains was transformed into an E. coli K12 host and then challenged with three different phages. Survivors were isolated and fragments mapped to their genome sequence. After eliminating duplicates, clones affecting adsorption, and clones harbouring restriction-modification or known defence systems, the unique fosmids corresponding to each phage selection were used to construct plasmid libraries, which were subjected to a second selection. Surviving clones were deep-sequenced and candidate defence loci pinpointed by mapping sub-library reads to genome sequences of the original fosmid inserts.