Worm Breeder's Gazette 15(1): 26 (October 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.

The C. briggsae Physical Map: An Update

Jacqueline Schein, and The Washington University Genome Sequencing Center Staff

Genome Sequencing Center Washington University School of Medicine 4444 Forest Park Blvd. St. Louis, MO 63108

Approximately 18,000 C. briggsae fosmid clones have been fingerprinted, and thus far a total of 1660 contigs have been constructed through automated assembly and manual editing. The average edited contig length spans 1.8 clones (approximately 72 kb). The largest contig is approximately 400 kb in length. At the time of this writing, 106 fosmid clones representing 3.3 megabases, containing an estimated 600 genes, have been sequenced and finished, with an additional 100 clones in the pipeline. The regions of the C.elegans genome with matching C. briggsae fosmids are indicated in the accompanying figure. The C. briggsae sequences are distributed across the C. elegans genome, as a result of random selection of fosmid clones during the early part of the project. The sequence data and a blast server are available at our website (http://genome.wustl.edu.gsc/gscmpg.html), and a list of the matches to the C. elegans genome will also soon be available.

Currently, sequencing of some C. briggsae fosmid clones is being done at the request of investigators in the C. elegans community. C. briggsae fosmids containing homology to genes of interest can be indentified by hybridization to high density, gridded filters containing the 18,000 fingerprinted C. briggsae fosmid clones. These filters can be purchased from Genome Systems Inc. (genome@genomesystems.com). Researchers can contact Marco Marra at the GSC (mmarra@watson.wustl.edu) with results of hybridizations to the filters. On a cautionary note, a small fraction of the gridded clones appear to be contaminated with vector DNA, and light up as false positives if probe DNAs are not completely free of vector sequences. A list of these artifacts will be available on our website, and we request that hybridization results be compared against this list prior to contacting us. If the positive clones reside in a contig, or one can be constructed based on their fingerprints, a clone will be selected and placed into the sequencing queue. We recommend that researchers obtain the selected fosmid from us prior to sequencing and verify the presence of the gene by PCR or Southern blot, in order to ensure that the clone contains the gene of interest. Previous hybridization results provided to us by C. elegans researchers, including members of the Horvitz, Aamodt, Baillie, Hekimi, Kramer, Miller, Rose and Wood labs, have proven to be very useful for the construction of contigs. Continuing input of this type from the C. elegans community will be essential as we continue building the C. briggsae map.