Chlamydomonas correct nomenclature vote and ballot

Susan Dutcher dutcher at beagle.Colorado.EDU
Tue Aug 2 16:02:41 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. 
**************************************************************
                 PLEASE CAST YOUR VOTES BY EMAIL 
to kmills at beagle.colorado.edu and to chlamy at acpub.duke.edu. 
by August 12.  Lib and I will compile the votes independently and the outcome 
will be put on the news and in the Trends in Genetics article.
***************************************************************
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,r and c as part of 
the allele designation provide additional information to the reader.

Below is a description of the modified proposal that the nomenclature committee 
is submitting for a vote.   Please vote in favor or opposed by August 12. 
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 to designate a locus and its reference allele. 
which would normally be the wild-type allele.  We would use lower case letters 
for mutant alleles.   Thus, we would have the ABC1 locus with mutant alleles 
abc1-1, abc1-2, etc.
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.
5.  The nomenclature in the Sourcebook by Lib Harris (1989) (pp 447-449) 
is as follows and would be used if the outcome of the vote 
is opposed to the ballot proposals below.
a. The prefix would be one to three lower case letter followed by a hyphen.
b.  The locus is indicated by a number.  Numbers would be sequential.
c.  Alleles would be designated by a number or a letter.
d.  Wild-type alleles would have a + superscript, if desired by the authors.

One final nomenclature issue that has arisen is 
what to do about insertions. In other organisms, 
insertional alleles are often designated with the insertion. 
For example abc1-1::NIT1  would indicate that the mutant allele was made by 
an insertion of the NIT1 gene.  abc1-1::TEC1 or abc1-1::Gulliver would indicate 
an insertion of a transposon TEC1 or Gulliver.

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

                       BALLOT
****Summit by email to kmills at beagle.colorado.edu and to chlamy at acpub.duke.edu 
by August 12.

1.  A three-letter designation followed by number
    In Favor      ___________
    Opposed       ___________

2.  Omitting the hyphen between the letter designation and number (abc1)
    In Favor      ___________
    Opposed       ___________

3.  Pick one alternative:
 
    Designating locus in upper case letters 
      (ABC1)
    In Favor      ___________

    Designating locus in lower case letters 
      (abc1)

    In Favor      ___________

4. Pick one alternative: 

   Designating  wild-type allele in upper case letters

    In Favor      ___________

   Designating wild-type allele in lower case with + superscript (abc1+)

    In Favor      ___________

5.  Using d, r, and c to indicate dominant, recessive and codominant alleles
    In Favor      ___________
    Opposed       ___________

6.  Use of the double colon and the inserting DNA to indicate an insertion
    In Favor      ___________
    Opposed       ___________

 





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