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.
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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.
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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 ___________
