Much of the basic information concerning the Atlantic salmon genome is known. For example, the C value for Atlantic salmon has been estimated as 3.27 pg , which translates into a haploid genome size of ~3 × 109 bp. The G+C content of the Atlantic salmon genome is 44.4% . Although the Atlantic salmon genome is fairly similar to those of warm-blooded vertebrates with respect to size and overall base composition, it seems to be devoid of isochore structures like other coldwater fish genomes . This is reflected in the inability to obtain G-banding patterns in Atlantic salmon chromosomes . It has been suggested that the diploid ancestor of salmonids possessed a karyotype with 48 acrocentric chromosomes, resulting in 96 acrocentrics after the genome duplication . Comparisons of the karyotypes of several salmonid species, including Atlantic salmon, revealed that many gross chromosomal rearrangements (fusions and inversions) have occurred along the different lineages since the ancestral whole genome duplication occurred . The Atlantic salmon whose genome has been chosen to be sequenced represents the European subspecies (S. salar europensis), with 29 pairs of chromosomes [17, 18].
Approximately 200 cDNA libraries have been constructed from many different tissues and developmental stages of Atlantic salmon [19–27]. As of 2 April 2010, there were 495,257 Atlantic salmon Expressed Sequence Tags (ESTs) . Atlantic salmon ranked 20th by organism with respect to total number of ESTs, and almost all of the other organisms in the top 20 have had their genomes sequenced or are in progress of so doing. The ESTs have been placed in over 81,000 contigs and annotated . As of 2 April 2010, 33,709 Atlantic salmon UniGenes had been identified  and over 9,057 reference quality full-length cDNA coding sequences had been confirmed . All of this information can be viewed on publicly available websites [29–32]. The EST databases provide a rich source of material for identifying genetic markers, such as microsatellites [33, 34] and single nucleotide polymorphisms (SNPs) [35, 36], that have been used to place genes on linkage maps [37, 38]. In addition, the ESTs enabled the construction of microarrays for expression analyses [22, 25, 39–41]. More than 60 groups around the world are using these microarrays, indicating that there is a large salmonid research community actively engaged in functional genomics. Moreover, the EST databases, especially the full-length cDNA coding sequences, will form the basis for building gene models during the annotation of the Atlantic salmon genome.
A publicly available Atlantic salmon bacterial artificial chromosome (BAC) library (CHORI-214) was constructed from the DNA of an individual male from a Norwegian aquaculture strain and arrayed on nylon membranes . HindIII fingerprinting of the CHORI-214 Atlantic salmon BACs was used to create the first physical map of a salmonid genome, consisting of 223,781 BACs in ~4,565 contigs and 33,217 singletons . 207,869 BAC end sequences with an average length of 666 bp (~3.5% of the genome) were produced to yield a snapshot of the Atlantic salmon genome and to identify putative syntenic relationships between the Atlantic salmon physical map and the fish genomes that have been sequenced ( and KA Boroevich, KP Lubieniecki, W Chow, P de Jong, J Schein, M Field, R Moore, JG de Boer, BFK, WSD, unpublished results). Several linkage maps based on microsatellites, amplified fragment length polymorphisms (AFLPs) and SNPs have been constructed for Atlantic salmon [37, 38, 45–47]. The BAC end sequences also provide a rich source of microsatellite markers and SNPs, which were used to integrate the physical and linkage maps [37, 47]. Fluorescent in situ hybridization (FISH) analysis with BACs that contain microsatellite markers map was used to assign chromosome arms to linkage groups . All of these genomic resources have been made publicly accessible through a website ( and KA Boroevich, KP Lubieniecki, W Chow, P de Jong, J Schein, M Field, R Moore, JG de Boer, BFK, WSD, unpublished results).
An Illumina iSelect bead-array, designed to interrogate ~16,500 putative Atlantic Salmon SNPs, was developed at the Center for Integrative Genetics (CIGENE). Approximately 55% of the SNPs on the array were identified from EST alignments, with most of the remainder coming from a random genomic sampling following construction of reduced representation libraries produced from individual and pooled DNA samples and high-throughput 454 pyrosequencing (MP Kent, B Hayes, Q Xiang, PR Berg, RA Gibbs, S Lien, personal communication). The SNP array is currently being used to genotype a mapping population consisting of 3,500 individuals and construct a high-resolution SNP map for Atlantic salmon, which will be beneficial in assembling the Atlantic salmon genome sequence.
More than 60 Atlantic salmon BACs have been sequenced so far ([50–58], and see  for list). Along with the BAC end sequences these provide a snapshot of the organization of the Atlantic salmon genome. It is estimated that repetitive DNA accounts for 30-35% of the Atlantic salmon genome. Fourteen families of DNA transposons (twelve Tc1-like and two piggyBac-like) constituting 6-10% of the genome have been identified. These DNA transposons are approximately 1,500 bp in length, with different repeat families ranging in similarity from 80% to 94% . An Atlantic salmon repeat database has been developed, and a salmonid repeat masking tool is publicly available .