fast-evolving molecular marker in prokaryotes

[Diane R. Stothard]

Hi all!

I am working on an obligate-intracellular microorganism and would like
to examine population structure among strains.  I have tried using an
outer membrane protein, and it does evolve at a pretty fast rate, but
not fast enough.  Can anyone suggest another possibility?  RAPDs are out
of the question because of host-cell contamination. (I have thought of
the 16S-23S intergenic spacer region, but I'm not sure if it would be
more helpful or not.)  Please reply directly to me.

Thanks,
Diane