Cosmid clones from Atlantic salmon: physical genome mapping

Abstract

Cosmids are valuable tools in physical mapping of genomes. They are commonly used in low resolution physical mapping, as markers for Fluorescence In Situ Hybridization (FISH) of chromosomes. In addition, they are used in high resolution physical mapping, i.e., cosmid contigs, restriction mapping, sequencing. With aims of physically mapping the salmon ( Salmo salar) genome we have constructed a partial (incomplete genome coverage) salmon cosmid library. A strategy has been adopted where anonymous, randomly picked, cosmids are isolated, characterized by partial shotgun nucleotide sequencing and used as markers for FISH. By multicolour multiprobe FISH a low resolution physical map can be established. Identifying on the cosmids, genes, whose homologs in other organisms are mapped, enables comparative mapping. Identifying genetic markers like microsatellites enables linkage of physical and genetic maps. This strategy has sofar proven to be effective: on one cosmid clone the salmon U2 snRNP-specific A′ protein gene (U2 small nuclear ribonucleoprotein particle) (U2A′) was identified. (This is the first identified genomic sequence of a U2A′ gene from any organism). In addition a tetranucleotide microsatellite was identified within an intron. On another cosmid clone the salmon RAN gene was identified. The cosmid containing the U2A′ gene was assigned to a metacentric salmon chromosome.