genetic nomenclature

Rogene Schnell rogene at MOLBIO.CBS.UMN.EDU
Wed Jul 6 22:45:40 EST 1994



I want to thank Susan Dutcher for proposing that we adopt a standard set 
of rules for the nomenclature of genes identified by mutations in 
Chlamydomonas.  Change is always difficult.  Nevertheless, I believe that 
the adoption of a more precise and universal nomenclature will be crucial 
to the future of Chlamydomonas as an experimental organism.  
 
As a geneticist, I am not comfortable with the ambiguity that arises when 
one symbol is given multiple meanings.  For example, the symbol nit-1 (in 
italics) can denote either the wild-type or a mutant allele.  The proposed 
rules elimitate the ambiguity by using NIT1 and nit1-1 to denote wild-type 
and mutant alleles, respectively.  
 
Hyphens within the locus name should be omitted since they are not 
recognized by some widely-used database search strategies.  For a few 
loci in which the third letter might be mistaken for a number, an optional 
hyphen could be introduced for clarity, as suggested by Robin Wright (eg., 
bcl1 may be designated bcl-1).  I've noticed that the genotypes listed for 
strains available at the stock center seldom indicate allele designations, 
even in cases where multiple alleles of a locus have been identified.  The 
proposed nomenclature rules will prevent this kind of information loss 
simply by ensuring that future alleles will be given a unique designation.
 
Two different proposals have been made for the use of capital letters.  The 
debate is whether to use capital letters to indicate that an allele is 
dominant (proposal #1) or that it is wild type (proposal #2).  Thoughtful 
concerns regarding each of these proposals have been raised, but I do 
not believe these concerns outweigh the inherent benefits of adopting one 
of the proposals.  Proposal #1 and #2 have already achieved universal 
acceptance within the yeast and Arabidopsis communities, respectively.  I 
think this particular debate deserves more discussion, and that it should 
ultimately be resolved by one or more geneticists who will take all of our 
comments into consideration.  The issue seems much too important to be 
decided by a haphazard vote over the internet (no offence to the net 
intended).
 
In addition to the enhanced precision and clarity that Susan Dutcher's 
proposed nomenclature conventions would offer, there is a second crucial 
advantage.  The specific rules she proposes are already widely accepted 
and should be familiar to virtually anyone that has taken a graduate level 
genetics course within the last couple of decades.  Inevitably, the 
literature of Chlamydomonas genetic analysis would be accessible to a 
broader audience of biologists.  This would no doubt have a very positive 
effect on the overall perception of the Chlamydomonas community by 
prospective graduate students, post-docs, and grant reviewers.
 
 
Rogene Schnell
rogene at molbio.cbs.umn.edu
 






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