Gene nomenclature

Pete Lefebvre pete at MOLBIO.CBS.UMN.EDU
Tue Jul 12 17:03:56 EST 1994

I am writing to support Susan Dutcher's proposed standardization of the 
Chlamydomonas genetic nomenclature. The field clearly needs to be 
speaking one genetic language in press. The existing nomenclature has 
some awkward elements which has led my lab and others to adopt a 
different style in recent papers. That is, we have de facto voted against 
the current system not because we are rebels (most of us being hard-core 
Yankees), but because it is difficult to write papers gracefully using the 
current system.

The "status quo", as far as I can tell, has been justified largely 
because of its historic momentum rather than its intrinsic value.  There 
is in the current system, for example, no clear way to identify the wild 
type protein product of a gene.  Is it the ac-17+ protein product, or the 
"wild-type product of the ac-17 locus", or some other long phrase?  Under 
the new system the gene product would be the AC17 protein.  I favor the 
use of CAPS for the wild-type, and some additional notation, to be 
decided later, for a dominant allele.  

On the matter of hyphens, I have found it awkward to include hyphens both
for the locus name and for alleles.  As more of us generate more alleles
at popular loci (as has already happened at apm1) there will be increasing
use of allele names. Why not just remove the hyphen from the locus name
and use it for alleles, as practiced in other systems?  In fact, a reading
of the genetic literature in the past decade will show more new locus
names without hyphens than with.  As to the problem of "l"s looking like
"one"s, we can certainly allow extra hyphens or some other designator to
take care of that problem; we can even avoid naming our genes with "l" in
the third position. 

Thanks again to Susan for promoting this discussion at the Chlamy
meetings. Pete Lefebvre (pete at molbio.cbs.umn.edu)

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