Repetitive landscape of the Atlantic salmon genome

The duplication of genes and genomes is considered a major force in evolution. Ohno, in 1970, theorized that with two copies of the genome, one copy would be under normal evolutionary constraints while the other copy could serve as raw material for evolution. Salmonids are a classical example of species containing duplicated genomes, and they offer an opportunity to investigate how such genomes undergo reorganization as they attain a stable diploid state. Repetitive elements play an important role in genome reorganization. Therefore, I investigated the repeat structure and organization of the Atlantic salmon genome. An analysis of the fingerprinted CHON-214 BACs classified the singletons, or those that contained few restriction sites, into three categories of repetitive structures. The first group contains histone genes in a tandemly repeating cluster of H4 - H2B - H1 - H2A - H3. A second group contains the ribosomal DNA (rDNA) cistron. Intriguingly, fluorescent in situ hybridization (FISH) analysis indicated that one of each of the duplicated histone and rDNA clusters was lost or rearranged in the genome. The remaining group of BACs contains novel repetitive sequences and tRNA clusters. The Atlantic salmon EST libraries and BAC-end sequences were data-mined for simple sequence repeats (SSRs) and 2,497 SSRs were recovered. 154 SSR loci gave clean PCR amplicons and 94 produced polymorphic banding patterns with eleven of the EST-SSRs indicating duplicated loci. These loci were mapped on the Atlantic salmon linkage map. Novel repetitive elements were detected in the sequences of Atlantic salmon BACs and ESTs. Using computational tools for data-mining, repetitive elements were identified and classified based on sequence similarity to other known repetitive elements such as SINES, LINES and retrotransposons. A repeat database that can be used to mask repetitive elements, is now available for the Atlantic salmon genome. A website was developed to host the Atlantic salmon linkage and physical maps, correlating them based on marker hybridization. A BAC annotation pipeline analyzes the BAC sequences for ORFs, transcript similarity and repetitive elements. Information generated from sequence annotation, microsatellite development and repetitive element identification provides essential resources for investigating salmonid genomes.