Fig. 2

Overview of the included MHC class Ia and Ib haplotypes from Atlantic salmon (Salmo salar), Rainbow trout (Oncorhynchus mykiss) and Coho salmon (Oncorhynchys kisutch) in addition to the assumed Northern pike (Esox lucius) allelic haplotypes represented by the Chr. 10 region (Ia) and the unplaced genomic scaffolds NW80 (NW_017859580.1) and NW71 (NW_017859271.1). Color coding for individual genes are shown on the bottom of the figure. Sequences originate from either previously published BAC sequences [Rainbow trout haplotype Ia_#A and Ib_#A: [42]; Atlantic salmon haplotypes Ia_#A&#B, Ib_#A&#B: [37, 38]], from genomes available in GenBank [Atlantic salmon Ia_#C and Ib_#C: [39], Northern pike: [41]] or unpublished genome assemblies for rainbow trout and Coho salmon. See Materials and Methods for additional references. A 7.2 Mb region dividing MHCI-related genes in the Atlantic genome Ib region is indicated by a black line. Gene boxes are colored red for MHCIA, dark green for PSMB subunits, yellow for TAP2, blue for TAPBP and grey for remaining genes. Individual genes are shown above the boxes using abbreviations B, C, D, E, F, L, G for individual U lineage genes; Z for Z lineage genes; 8, 8F, 9, 10, 12, 13 for individual PSMB genes; 1 through 7 for undefined MHCI lineage genes in Northern pike. X denotes pseudogenes. More regional details can be found in Additional file 1: Figure S1