Comment by greazy

Backbone refers to the cloning plasmid.

Plasmids are grown inside of bacteria which have their own genome with all sorts of oddities like transposons.

Transposons are 'jumping' bits of dna that can insert themselves (given the right criteria is met).

So a transposon(s) from the E. coli genome inserted itself into the plasmid.

This causes all sorts of problems for people who use them to clone (insert) dna into them.