funtik at ecoclub.nsu.ru (Eugene Berezikov) wrote:
>I have a question concerning use of rDNAs and others multiple genes in phylogenetic
>rRNA genes are known to be organized in tandem repeats so that many copies of the
>are present in genome (by the way, does anybody know how many?). These copies may
>differences. Than, which one to chose for phylogenetic analysis?
>How this problem has been circumvated?
First of all tandem arrays of ribosomal genes are only found in certain eukaryotes
- many protozoa and all prokaryotes have other arrangements of these genes.
The number of copies per genome varies from one in some prokaryotes and around four
in some protozoa to several thousand in certain eukaryotes. However, when multiple
copies of the gene are present the sequences are very closely related in almost
every case. Where sequence differences do occur they are almost always located
in regions of the gene that are excluded from phylogenetic analyses because these
regions are so divergent that unambiguous alignments cannot be obtained.
Therefore, although multiple copies are present any divergence in sequence does
not interfere with phylogenetic studies using these genes. In any case, many rDNA
sequences are now obtained from either multiple clones from the same organism,
pools of clones, or total PCR products directly. In all cases a consensus sequence
would be used.
C. Graham Clark, Ph.D.
Department of Medical Parasitology,
London School of Hygiene and Tropical Medicine,
Keppel Street, London WC1E 7HT, England, G.B.