ciliate genome

David Roos droos at sas.upenn.edu
Wed Jun 7 08:42:34 EST 1995


giuliano at ib.pi.cnr.it (Giuliano Colombetti) wrote:

> I am currently working on a marine ciliate, Fabrea salina, using a PCR
> approach to try to identify some particular genes. Unfortunately, I do not
> know whether the ciliate genome is generally more similar (with regard to
> base composition, gene organization a.s.o.) to that one of higher or lower
> organisms. I ned this piece of information in order to design appropriate
> primers for PCR cloning.

Unfortunately, there is no general way to predict base composition, codon 
usage, gene organization for ciliates as a group (or for "higher" or 
"lower" organisms, whatever those groups may signify).  For a start, I 
would assume roughly equal frequencies for all for nucleotides, and few 
introns.  If you know anything about ANY gene in Fabrea salina that would 
give you some idea of how far off these assumptions are.  Also, use ITP 
nucleotides for degenerate positions, and try to PCR short fragments 
(~200 nt) to minimize the possibility of introns.  Good luck

D.S.Roos (droos at sas.upenn.edu)



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