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% GC content and 16S phylogeny

Graham Clark G.CLARK at lshtm.ac.uk
Wed Aug 14 08:04:37 EST 1996

Small subunit rRNA has two components that differ in their G+C content.
The 'core' ribosomal RNA are the regions largely conserved across the
phylogenetic spectrum and those vary little in G+C content (generally
a little over 50%). The second component is made up of the so-called
'variable regions'/'divergent regions''/'expansion segments' depending
on which terminology you use. This component is very variable in G+C
content and largely reflects the tendency of the genome as a whole.
For example in Giardia these regions are very G+C rich (80%-ish) 
while in Plasmodium they are very low in G+C (less than 20%). This
nucleotide bias is very similar to that seen in the 3rd codon position.
The result of this is that the overall G+C of ribosomal RNA will be less
than that of the genome as a whole if the genome is very G+C rich and
more than that of the genome as a whole if the genome is very A+T rich.
It will also depend on the relative size of the variable regions w.r.t
the core region.


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