Molecules for intragenus phylogenetic analysis

James McInerney jamm at nhm.ac.uk
Mon Dec 8 12:00:48 EST 1997


Hi,

Unfortunately this question is like "How long is a piece of string?"  In the
genus Aeromonas and Clostridium and many, many more, the 16S rRNA gene has
been of great service.  It can sometimes fail to give enough resolution, unfortunately.

For any given genus you should pick a gene, carry out a preliminary study
(say, sequence two species that you would consider to be closely related) and
if there are sufficient differences in the sequences, then you might have a
good candidate gene.  You could then proceed cautiously until you are
satisfied that you will carry out all of the study using this gene.

You should also consider other factors, such as whether or not there is a
database of the genes that you choose.  Having a large database of genes that
have been sequenced in other taxa, can give you something to align and analyse
in addition to your own dataset (for higher-order relationships perhaps).

Regards,

James



medp6059 at leonis.nus.sg wrote:
> 
> Could someone please advice me on a gene that I could use for resolving
> the fine phylogenetic structure
> within a genus of bacteria ?

-- 
=========
James O. McInerney               email: J.mcinerney at nhm.ac.uk
Molec. Biol. Comput. Officer,    phone: +44 171 938 9247
Department of Zoology,           Fax:   +44 171 938 9158
The Natural History Museum,
Cromwell Road,                    
London SW7 5BD.                  
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