Cosmid clones from Atlantic salmon: physical genome mapping

Cosmids are valuable tools in physical mapping of genomes. They are commonl y used in low resolution physical mapping, as markers for Fluorescence In S itu Hybridization (FISH) of chromosomes. In addition, they are used in high resolution physical mapping, i.e., cosmid contigs, restriction mapping, se quencing. With aims of physically mapping the salmon (Salmo salar) genome w e have constructed a partial (incomplete genome coverage) salmon cosmid lib rary. A strategy has been adopted where anonymous, randomly picked, cosmids are isolated, characterized by partial shotgun nucleotide sequencing and u sed as markers for FISH. By multicolour multiprobe FISH a low resolution ph ysical map can be established. Identifying on the cosmids, genes, whose hom ologs in other organisms are mapped, enables comparative mapping. Identifyi ng genetic markers like microsatellites enables linkage of physical and gen etic maps. This strategy has sofar proven to be effective: on one cosmid cl one the salmon U2 snRNP-specific A' protein gene (U2 small nuclear ribonucl eoprotein particle) (U2A') was identified. (This is the first identified ge nomic sequence of a U2A' gene from any organism). In addition a tetranucleo tide microsatellite was identified within an intron. On another cosmid clon e the salmon RAN gene was identified. The cosmid containing the U2A' gene w as assigned to a metacentric salmon chromosome. (C) 1999 Elsevier Science B .V. All rights reserved.