Eugene Berezikov wrote:
>=20
> Dear Netters,
>=20
> I have a question concerning use of rDNAs and others multiple genes in =
phylogenetic
> studies.
> rRNA genes are known to be organized in tandem repeats so that many cop=
ies of the gene
> are present in genome (by the way, does anybody know how many?). These =
copies may have
> differences. Than, which one to chose for phylogenetic analysis?
> How this problem has been circumvated?
>=20
> Thanks,
> Eugene Berezikov.
Yes there is frequently more than one ribosomal RNA operon in a genome.=20
Often there are hundreds (sometimes only one..i.e. Mycoplasma). They
evolve together and generally they have the same sequence. However it
has been found across the phylogenetic spectrum that organisms exist
with ribosomal RNAs that have different sequences. In some prokaryotes
(I can't remember which, but the work was done in Karl-Heinz Schleiffers
lab in Munich, Germany), a noticeable number of differences were found
between 16S rRNA genes within one bacterium. It was probably still
small enough to represent an allelic variant. Tim Littlewood here at
the museum tells me that he has found two kinds of ribosomal RNA genes
in some Echinoderms...one kind appears to be expressed more abundantly
than the other. These are probably not allelic variants, but might
represent two different kinds of ribosome (don't quote me on this). One
of the first references that I came across on this subject was
Mylvaganam and Dennis (1992), but I can't be sure that it was the first
report of this occurrence.
As to the second part of your question- whether it would have an effect
on phylogeny reconstruction.....YES, a very dramatic effect.=20
Apparently, the Echinoderm data makes no sense if the wrong ribosomal
RNAs are used. It is therefore quite important to ensure that there is
only one kind of rRNA in your organism.
Hope this helps a little,
James.
Cited reference.
Mylvaganam, S. and Dennis, P. P. (1992). =93Sequence Heterogeneity
Between the 2 Genes Encoding 16S rRNA from the Halophilic
Archaebacterium Haloarcula marismortui.=94 Genetics 130(3): 399-410.
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James O. McInerney Phone/Voicemail: +44 171 938 9247
Senior Scientific Officer, email:j.mcinerney at nhm.ac.uk
The Natural History Museum, =20
Cromwell Road,
London SW7 5BD
UK
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