Worm Breeder's Gazette 9(2): 10

These abstracts should not be cited in bibliographies. Material contained herein should be treated as personal communication and should be cited as such only with the consent of the author.

A Suggested Nomenclature for Cloned C. elegans Genomic DNAs

S. Ward and other discussants

As more and more genes become cloned and assigned to John Sulston 
and Alan Coulson's growing physical map, the need for a simple, 
standard nomenclature for cloned genomic DNAs is apparent.  After 
discussion with John, Alan and several others the following simple 
system is recommended for naming cloned genomic DNAs, especially those 
that will be physically mapped.  Suggestions for improvement are 
welcomed; some points of contention are noted below.
A vector containing a cloned DNA can be thought of as equivalent to 
a mutant strain.  Each such clone should be named with your two letter 
(upper case) lab designation followed by the # symbol and a number 
assigned serially by your lab.  Thus BA#2 is the second named cloned 
DNA from my lab.  The # indicated cloned DNA and distinguishes clones 
from worm strains.
The genes contained in this clone can be named in the same way as 
ordinary genes, except that the criteria for determining what 
constitutes a gene are different from the genetic criteria used for 
defining a gene with mutations.  In addition it will be rarely known 
how many other genes might be contained in a large genomic clone.  
Thus clone BA#2 contains gene msp-32.  One could write BA#2[msp-32].  
Note use of brackets rather than parentheses to avoid confusion with 
genes and alleles.  Other gene names, or the presence of TCl 
insertions, could be added if they are found in the same clone.  The 
chromosome assignment can also be added if it is known.  Cloned mutant 
alleles could be designated as alleles of the genes using standard 
genetic nomenclature.  It would be useful to be able to distinguish 
pseudogenes from functional genes, (particularly for MSP genes because 
there are many of each kind) so I suggest adding a Greek phi, (symbol) 
,to a gene name if one knows for certain (by sequence or probing) that 
it is in fact a pseudogene.  Note that it is easier to be sure that a 
gene is, rather than that it is not, a pseudogene.  For example, msp-
24(phi) is a pseudogene because it is missing an ATG start codon and 
has a 17bp insertion, relative to other MSP genes, in its coding 
sequence.  The added phi is an optional descriptor and is not an part 
of the gene name.
This suggested nomenclature is simple and flexible because it puts 
no information except the laboratory of origin in the clone name 
itself.  Several people have pointed out that it is inconsistent with 
'standard' cloning nomenclature because it does not indicate the 
vector.  Plasmids are usually named with a lower case 'p' first and 
lambda clones preceded by 'lambda ', and cosmids by a lower case 'c'(
sometimes).  There is no provision in this suggested nomenclature for 
naming cDNA clones nor is there a way to describe cloned gene 
fragments.  It doesn't seem necessary to standardize the naming of 
these at present.