FIG. 3.

Bcep781 genome is highly circularly permuted. (A) PFGE of Bcep781 genomic DNA incubated with (A) NdeI, (B) NheI, (C) T4 DNA ligase, or (D) no pretreatment and visualized by ethidium bromide staining. Shown also are the relative positions of the NdeI and NheI restriction sites on the linearized Bcep781 map. (B) Bcep781 genomic DNA end cloning. A diagram of the end cloning strategy is shown. XbaI linkers (boxes) were ligated to Bcep781 genomic DNA. This was then digested to completion with XbaI and XhoI, which has 27 sites in the Bcep781 genomic DNA. The resulting end fragments were ligated into the XbaI/XhoI-digested vector and transformed into XL1-Blue cells. Below this are the relative positions of 47 independent end fragments, determined by sequencing randomly picked transformants and then aligning these fragments with the Bcep781 genomic sequence (bottom). Each horizontal dash represents an independent clone. Positions of the 27 XhoI sites in the Bcep781 genome are indicated with vertical lines. Alignment was made in Sequencher and converted to a line drawing.