The Rhs family of composite genetic elements was assessed for variatio
n among independent Escherichia coli strains of the ECOR reference col
lection. The location and content of the RhsA-B-C-F subfamily correlat
es highly with the clonal structure of the ECOR collection. This corre
lation exists at several levels: the presence of Rhs core homology in
the strain, the location of the Rhs elements present, and the identity
of the Rhs core-extensions associated with each element. A provocativ
e finding was that an identical 1518-bp segment, covering core-extensi
on-b1 and its associated downstream open reading frame, is present in
two distinct clonal groups, but in association with different Rhs elem
ents. The sequence identity of this segment when contrasted with the d
ivergence of other chromosomal segments suggests that shuffling of Rhs
core extensions has been a relatively recent variation. Nevertheless
the copies of core-extension-b1 were placed within the respective Rhs
elements before the emergence of the clonal groups. In the course of t
his analysis, two new Rhs elements absent from E. coli K-12 were disco
vered: RhsF, a fourth member of the RhsA-B-C-F subfamily, and RhsG, th
e prototype of a third Rhs subfamily.