The problems that Rob Last describes with respect to nomenclature are only too
common. It has long been of immense irritation to me that the style of nomen
clature changes depending on whether you work on bacteria, plants, fungi, or
mammalian systems, making it impossible to tell at a glance whether the marker
referred to is a phenotypic marker, a defined mutation in a known structural
gene, or a mutation at a mapped locus UNLESS you are familiar with the system
in use. Many of the problems Rob describes are due to only using 3 letters to
identify most genes. To my mind the microbial geneticists have got it right:
1. When a mutation is isolated and identified, it is identified by three lower
case letters to define its general function (e.g. trp=tryptophan metabolism)
and an isolation number. These mutations are termed trp-1, trp-2, trp-3 etc.
The phenotypes of such mutants are designated Trp1, Trp2, Trp3 etc. (without
italics - all genotypes are italicised)
2. When the exact function of the locus is identified, the only thing to change
is that an upper case letter is added to identify the particular gene
involved, so that if trp-2 is a mutation in trypophan synthase beta subunit,
the gene is trpB, the allele is trpB2 - note that it retains its isol-
ation number - and the phenotype is TrpB2 (again no italics).
3. When second (or third or fourth) copies are identified, there should remain
plenty of spare letters in the alphabet.
The key point to note is that numbers are never used to identify genes, only
alleles, and that the former terms are implicit in the latter ones, so that
the use of the new nomenclature shouldn't confuse people. Of course,
persuading people to use this or any other coherent nomenclature is not going
to be easy. Perhaps the current nomenclature could be amended so as to follow
these general principles, but in a different way.
Anyone wanting to look up bacterial genetic nomenclature in detail should refer
to Demerec et al. (1966) Genetics 54:61-76.
Any other suggestions?