Chlamydomonas nomenclature vote

Susan Dutcher dutcher at beagle.Colorado.EDU
Tue Aug 2 14:54:21 EST 1994

Dear Members of the Chlamydomonas Community:

It is time for a vote on the  nomenclature for genetic loci.  This proposal 
does not cover sequenced genes, which will be covered by the Commission on 
Plant Gene Nomenclature or chloroplast encoded genes. (See the Supplement to 
the Plant Molecular Biology Reporter, June 1994).  After having read the discussion 
over the net for the last six weeks, it seems that there are proponents of 
many different formats. 

Why should the nomenclature be changed?  One of the goals of this vote is to 
standardize the nomenclature for nuclear genetic loci.  If you read the genetic 
literature in Chlamydomonas, you rapidly see that we all use something a little 
bit different.  Second, we are part of a larger community and it  would be 
useful for scientists who work on other organisms to be able to read our literature 
and grants without a great deal of effort.  The proposal that was made in June 
(and at the Chlamydomonas meeting in May) is similar to the nomenclature that 
is used in Arabidopsis and S. cerevisiae.  I would argue that these are two 
important groups of readers.  A third reason is the increase in the number 
of  loci that are being identified by insertional mutagenesis.  With  the number 
of screens that are being performed, it seems like an appropriate time to make 
our nomenclature more amenable to having multiple alleles as well as tagged 
alleles.  Finally, the adoption of the d and r as part of the allele designation 
provide additional information to the reader.

Below is the modified proposal that I am submitting for a vote.   Please vote 
Yes or No by August 10.
1.  Acronyms for loci will be three letters with the exception that previously 
named loci would remain as  two letter acronyms (pf, lf, sr, ac, mt, etc.) 
 and the y loci would remain as a single letter.  Loci names would not include 
superscripts or subscripts. The acronym will pertain to some aspect of the 
mutant phenotype. This will be followed by a number to identify one locus from 
another with the same mutant phenotype. Numbers would be chosen sequentially. 
 There will be no dash between the acronym and the number.  Alleles will be 
designated by a number and separated from the locus name by a hyphen.  As an 
example, the first mutant allele at a locus  would be abc1-1.   This name would 
be in italics or underlined.
2.  The loci and mutant alleles would be in italics or underlined.
3.  We would use capital letters for wild-type alleles.  We would use lower 
case letters for mutant alleles. 
4.  If dominance tests are performed on mutant alleles (against a wild-type 
allele), the mutant name would include that information: abc1-1r  for recessive 
alleles, abc1-1d for dominant alleles, and abc1-1c for codominant alleles.

If this vote fails, we would retain the nomenclature described in the Sourcebook 
(Harris, 1989). The prefix would be one to three lower case letter followed 
by a hyphen.  The locus would be indicated by a number.  Numbers would be sequential. 
 Alleles would be designated by a number or a letter.   Wild-type allele would 
have a + superscript, if desired by the authors.

Regardless of the outcome of the vote, the nomenclature will be described in 
Trends in Genetics that will appearing late in 1994.

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