We have started to clone some
C.briggsae mutations for which there are clear elegans orthologs, and
have thought about names. What do you think of the following general
nomenclature for other nematodes? Thanks.
Paul
DRAFT1:Possible revision of gene names for non-C.
elegans nematode species.
Under the current nomenclature system for non-C.
elegans nematode species, each gene class in a given species
has a unique three-letter gene class name which does not overlap with
other species. e.g. the C. briggsae
equivalent of dpy is cby, the
equivalent of unc is mip. However,
with over 1100 gene classes in C. elegans and an
increasing number of species under study, this will soon become
unmanageable. We therefore propose an alternative nomenclature system,
one which will allow genes with similar mutant phenotypes in other
species to keep the same gene class name.
When a gene is identified in another species that belongs to a gene
class with a clear equivalent in C. elegans, it
should be given the same gene class name, but with a species
identifier in square brackets as a postfix. For example, a new Tra
mutation in C. briggsae could be named
"tra[Cb]-1", and a new Unc mutation in P.
redivivus could be named "unc[Pr]-1".
Gene classes with no equivalent in C. elegans or
other species will be given unique identifiers. The postfix indicates
the equivalent gene class but does not indicate orthologous
relationship. In other words, C briggsae genes
tra[Cb]-1, tra[Cb]-2 and tra[Cb]-3
do not necessarily correspond to C. elegans
tra-1, tra-2 and
tra-3.
The preexisting system of indicating orthology by a prefix (e.g.
Cb-tra-1 for briggsae ortholog of
C. elegans tra-1) will be retained and used in
parallel. If tra[Cb]-1 is discovered to be the
C. briggsae ortholog of C. elegans
tra-2, it would be renamed Cb-tra-2
and tra[Cb]-1 would be treated as a synonym.
Although this system would lead to similar names with different
meanings (e.g. tra[Cb]-1, Cb-tra-1, Ce-tra[Cb]-1
etc.), it should be easy to follow if one keeps in mind that prefix
indicates orthology at the gene level and postfix indicates the
equivalent gene class. Preexisting species-specific gene names like
cby could be renamed (dpy[Cb]) or
retained.
Discussion
Bhagwati suggests that gene numbers should start from 101 or some
other high number to avoid confusion (e.g. between
Cb-lin-11 and lin[Cb]-11). (Or,
higher with unc and let).
Takao prefers low numbers for several reasons.
1) High number would be redundant with the postfix.
2) Three digit gene names like let-617 are hard to
remember.
3) We can start tra[Cb] with 101, but if we start
other species with 101 also, there would be confusion among
non-C. elegans species. If we assign different number
blocks to different species, numbers would get very large very soon.
Also, this would require someone to keep track of which numbers
correspond to which species.
4) If we assign an unique number block for C.
briggsae, the tendency would be to abbreviate the postfix,
which could cause problems later, especially if other species have the
same number block. Having overlapping numbers would enforce the use of
postfix.
5) Gene names would get very long with the postfix and three-digit
gene numbers.
Takao is most concerned with the redundancy and awkwardness of
three-digit gene names.
26 squared is 676 and 26 cubed is 17,576; neither is sufficient.