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.