Figure 3.
Spacer Acquisition Hotspots in Liquid and Solid Media. The reporter strain RC5311 carrying pRC1656 (ParaBAD) was used for both assays. Colonies were pooled after 5 days (solid phase) or after two passages (liquid). CRISPR arrays were PCR-amplified and sequenced using Oxford Nanopore. Unique spacers were mapped to the genome (10 kb bins) and plasmid (50 bp bins). “0 min” marks the origin of transfer in E. coli HfrH; “Rep. lacZ”marks the reporter. Details of mapping procedures are given in the “Materials and Methods” section.