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.
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.