a. Genes identified in the nine BACs using our in-house annotation pipeline http://grasp.mbb.sfu.ca/. b. Order of the genes within the minimum tiling path. Comparative synteny analysis against the four published fish genomes (medaka, Oryzias latipes; tiger pufferfish, Takifugu rubripes; green spotted pufferfish, Tetraodon nigriviridis; zebrafish, Danio rerio and stickleback, Gasterosteus aculeatus) enabled the ordering of the gene-containing contigs in the GS FLX assembly of shotgun reads only. This order was confirmed when contigs were assembled into scaffolds with the addition of GS FLX Long Paired End reads. Numbers correspond to contig identity in the Atlantic salmon assemblies; colors coordinate with genes listed in Figure 4a. The grey boxes that correspond to sequence contigs 5 and 685 indicate matches to hypothetical genes. The genes for gonadotropin releasing hormone receptor and the novel protein similar to vertebrate perilipin were found within the Sanger-sequenced BAC and the remaining genes were within the eight BACs sequenced by GS FLX pyrosequencing.