Worm Breeder's Gazette 14(5): 12 (February 1, 1997)
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.
| 1 | MRC-LMB, Hills Road, Cambridge CB2 2QH, England |
| 2 | The Sanger Centre, Hinxton, Cambridge CB10 1SA, England |
1997 Genetic Map
The deadline for new genetic map data to be incorporated into the
1997 Genetic Map of Caenorhabditis elegans (Printed Version) is 30 April
1997. Data can be sent:
(preferably) by e-mail to: cgc@mrc-lmb.cam.ac.uk. Forms for data
submission are available by e-mail or fax, on request to this address.
(or alternatively) by fax or mail, to: Jonathan Hodgkin, MRC-LMB, Hills
Road, Cambridge CB2 2QH, England [fax (+44) 1223 412142]
Genetic Nomenclature
Recommendations for genetic nomenclature have been based on the
original paper by Horvitz et al. (1979), plus further recommendations
published in The Worm Breeder's Gazette. Summaries of current
recommendations can be found in Trends in Genetics (1995) and C. elegans
II (1997) and will be added to websites at the GSA (Genetics Society of
America), the Sanger Centre, and the UTSW C. elegans WWW site. As
indicated in the original paper, these recommendations should be
regarded as flexible guidelines, to be extended and modified when
necessary.
Laboratory Designations
At the end of 1996, 216 laboratories had strain and allele
designations registered with the CGC. New Principal Investigators
should seek approval for proposed new designations, by e-mail to:
jah@mrc-lmb.cam.ac.uk.
In 1994, 18 new labs desginations were assigned; in 1995, 29; in
1996, 24. At this rate of growth, there is no danger of running short
of 2-letter strain and allele designations until well into the next
century. We have, however, established a 3-letter strain category, for
use by nematologists who like the idea of systematized strain names for
isolates of other nematode species. Also, there is an increasing number
of laboratories who are making only minor use of C. elegans as an
experimental tool, and are therefore unlikely to generate more than a
few strains or alleles. For these we have established a group
designation, "XA" (for strains) and "qa" (for alleles). Successive
blocks of 100 XA and qa numbers are assigned to separate laboratories in
the "minor user" category.
Gene Names
Recommendations for new 3-letter gene names are included in the
Nomenclature Guidelines. We appreciate notification of proposed new
gene names before publication or submission to databases, especially for
genes inferred from the genomic sequence data. Consultation on proposed
names also helps sort out potential problems with multiple names for the
same gene, or with the same name being used for different genes.
Occasionally, we are asked to approve a new name in confidence, which we
are willing to do. Otherwise, new gene names will be added to the
"Gene_Class" list in ACeDB. A total of 40 new gene names were
registered in 1995, and 41 in 1996.
Genetic Map
Data for new genes and rearrangements are solicited from the
community, and also obtained from the published literature. E-mail
forms for the efficient communication of data are available from us, and
have been used successfully by many researchers. All such data are
scrutinized before entry into ACeDB, because some correction or
modification is often necessary. For many genes, no data are
communicated, which means that the relevant information must be
extracted by us from publications. For example, the following numbers
apply to 135 genes added to the map over the past year:
Genes defined by mutation Genes defined by
sequence
E-mail submission 24 3
(no revision needed)
E-mail submission 30 4
(revision needed)
Extracted from publications 28 46
The genetic map available through ACeDB is periodically updated
and corrected, ideally (though not always) with every new data release.
This process is partly manual, since there is no computer program
capable of generating the entire map de novo from the available data.
Assessing contradictions within the genetic data, resolving conflicts
between the genetic and physical map data, and optimizing the
representations of the genetic map, are all difficult and time-consuming
tasks. A full revision and updating of the map is carried out every two
years, and a printed version of the ACeDB map is then published and
distributed as an issue of The Worm Breeder's Gazette. This issue also
includes full lists of laboratory designations, gene names and
definitions, and all registered genes, rearrangements and balancers.
As more and more genes are included on the map, it has become
increasingly difficult to provide representations that will please
everyone. Using ACeDB, it is possible for any user to generate a
customized map incorporating only the features desired. S.M. can
provide instructions for doing this on request to: sylvia@sanger.ac.uk.
For the printed map, our options are necessarily more limited.
Nevertheless, we have been encouraged, by various members of the
Caenorhabditis research community, to remove from the printed map all
lethals, all poorly mapped genes, all rearrangements, and all genes
defined only from physical map data. These suggestions have been noted,
but not implemented, since we believe in incorporating the maximum
amount of information into the printed map, in so far as this is
possible. We have also been asked to improve the aesthetic properties
of the map, but have received few useful suggestions as to how this
might be achieved.
Corrections to the map and to the data in ACeDB, however minor,
are always appreciated, and we would like to thank the many researchers
who have noticed errors and communicated them to us.