YAC vectors show rearrangements because:
YACs propagate in highly recombinogenic yeast Saccharomyces cerevisiae, where homologous recombination machinery is exceptionally active. Large eukaryotic inserts often contain repetitive sequences, Alu repeats, microsatellites and segmental duplications that provide substrates for intra- and inter-molecular recombination. Recombination between repeats leads to deletions, chimerism and rearrangements of cloned DNA, causing insert instability and artifactual maps. Bacterial artificial chromosomes maintained in RecA-deficient Escherichia coli strains exhibit far lower rearrangement. Thus propens
Ref: NCERT Biology Class XII Principles on Klenow fill-in labeling, Lehninger Chapter 9 DNA cloning techniques, and Molecular Cloning by Sambrook Chapter 10 documenting end-labeling of cohesive termini.
