Jonathan A. Eisen wrote:
-So I ask Mark and others out there, are there examples of significant
-differences between rRNA genes within a single organism in eukaryotes?
-Or, in other words, how rapid is the homogenization process, and how
-complete is it (do all of the 1000s of rRNA genes evolve in concert?).
There are certainly differences within genomes and within species but
whether one considers them 'significant' is another question. Where
multiple rRNA gene sequences from the same organism are available there
are almost always differences - is it real or is it artifact? Probably
a bit of both.
In almost every case real differences are minor and fall within the
variable/expansion/divergent (depending on who's terminology you follow)
regions and are therefore excluded from alignments in most phylogenetic
analyses. One exception to this may be the rDNA of Plasmodium species
(the malaria parasites) where there is life-cycle-stage specific of
rRNA genes. Whether the resulting ribosomes are functionally distinct
has yet to be proven I think. Another example is the 5S gene of Xenopus
where there are oocyte specific forms. The sequence differences here are
minor but appear to be involved in the tissue specificity of expression
(if I am remembering correctly).
Also please remember that many organisms do NOT have 1000s of ribosomal
genes. I think Plasmodium holds the record in eukaryotes with an
estimate of 4-8, some bacteria have only one, and the fungus fly Sciara
has only ca. 45, etc.....