A fingerprinting map of the zebrafish genome has been generated in collaboration by three laboratories;

A bacterial clone physical map of the genome was constructed using restriction enzyme fingerprinting (Marra et al., 1997). Fingerprints were generated by digesting clones with HindIII. Following electrophoresis on agarose and data collection using a fluorimager, raw images are entered using the software IMAGE. This produces an output of normalised band values and gel traces. Analysis of data takes place in FPC. Clones are contiguated on the basis of shared bands. We have generated 20x coverage across the 1.6Gb genome.

The map is providing a template for clone tile path selection, as a prerequisite for sequencing, which is taking place at the Sanger Institute. It will also aid positional cloning experiments, by providing a resource for clone walking. Contigs will be anchored to the existing genome maps by radiation hybrid mapping and hybridization approaches. However, contigs of interest for positional cloning can be immediately identified by screening library pools or filters and then searching the database for these clones.

List of libraries being used and nomenclature;

Data coordination, map assembly and manipulation will take place at the Sanger.

Currently there are 218656 fingerprints assembled into 2013 reference sequence contigs. These data represent the output of a stringent automated assembly resulting in contigs of highly overlapping set of clones. The aim is to merge these contigs by relaxing the stringency required for overlap, as well interrogating all other available data, such as contig localisation to RH and genetic maps. Contigs identified as of special interest to the community can be prioritised for walking.

The database will be updated as maps are refined. Contigs can be viewed using WebFPC. Please select small WebFPC or large WebFPC to view the appropriate Java display for your screen size. Sequence clone selection is under way.

In collaboration with Dr. Charles Lee at Brigham and Women's Hospital, Boston, and with the Sanger Cytogenetics group we have begun to place contigs onto the genome using Fluorescent InSitu Hybridisation (FISH) on metaphase spreads of chromosomes derived from embryo tissue. We hope to define chromosomal locations for many of the unplaced contigs this way. Gap sizes between anchored contigs can be determined using fibre FISH. An improving view of the cytogenetics of the Zebrafish will enable more accurate chromosome sizing and identification.