I'm in agreement with using 3-letter designations for genes in general.
This would be in conformity with common usage in many other organisms. There
would be nothing wrong with extending some designations to 4 or even 5 letters
if desirable, for descriptive and mnemonic purposes. After all, there are only
19,683 3-letter combinations (and many of those would not be particularly
suitable for any gene), and Chlamy therefore may have more genes than there are
appropriate 3-letter combinations.
I'm also in agreement with the use of italics. Ordinary non-italic letters
could be used for the gene-PRODUCTS, in conformity with fairly widespread usage
in some areas (human genetics, for example).
However, using capital letters for dominant and lower case for recessive
(Susan Dutcher's suggestion), or capital letters for wild-type and lower case
for mutant (Robin Wright's suggestion), might both lead eventually to some
confusion and/or inconsistencies. For example:
1. How to designate partial dominants? And would you have to do dom/rec
tests in diploids prior to designating every mutant allele? What about alleles
that are dominant in some circumstances and recessive in others?
2. "Wild-type" does not have a universal meaning. If and when people get
around to doing real population genetics on Chlamy isolated from natural
sources, it will be found that there is often more than one allele that could
be called "wild-type." (This is what in fact has been found for virtually
every plant, animal, and bacterial species that have been studied genetically
at the population level so far.)
So, at the risk of making muddy waters even murkier, I'd like to suggest
using lower case letters for all genes and all their alleles at all times.
This would have the following advantages:
1. Gene designations would always be the same, so there wouldn't be any
ambiguity about whether capitals vs. lower case meant dominant vs. recessive or
wild-type vs. mutant. (Those sorts of qualifications could always be added as
hyphenated or superscripted additions, as needed, and they could be flexible.)
2. You could drop the hyphen for different loci, because the number would
usually stand up higher than the letters; e.g., mbo2.
3. As indicated above, you could always indicate the dom/rec/wt/mutant
status with superscripts or hyphenated additions, as required for particular
circumstances; e.g., mbo2-1, mbo2-2, mbo2-3 for different alleles of the mbo2
gene; mbo2-wt (or mbo2+) where wild-type is meant, in contrast to just mbo2 for
a mutant allele.
Dept. of Biology
Univ. of Miami