Comparative maps. The rainbow trout genetic map serves as a comparative map within its own genome and with the genome sequences of zebrafish (DRE), medaka (OLA), and tetraodon (TNI). Assignments for fugu scaffolds are reported in Additional File 1 Worksheets 2 (ESTs – Comparative Annotation) and 5 (Comparative Info – BACs). Figure 4 shows rainbow trout chromosomes 1, 2, 3, 8, 10, 15, 16, 19, 20, 21, 23 and 28 represented on the left, with regions of homeology identified through duplicated markers from the genetic map reported under the OMY column on the right. Figure 5 similarly shows the comparative map for chromosomes 6, 7, 11, 12, 13, 14, 17, 18, and 26, Figure 6 contains the comparative information for chromosomes 4, 5, 9, 22, 24, 25, 27 and Sex. Chromosomes showing large regions of homeology are grouped together. Further to the right chromosome homology assignments identified through comparative annotation are reported for each species (DRE, OLA, TNI). Many assignments have been made through comparative mapping of single loci, however wherever two or more loci define a region of conserved synteny we have not tried to estimate the size of the conserved fragment.