Synteny between Atlantic cod and selected teleosts. The co-occurrence of orthologous genes (with a minimum of 50% sequence identity over 50% of the alignment) located on 23 Atlantic cod linkage groups⁸ reveals synteny with the chromosomes of four teleosts. Multiple genes located on the stickleback XIV, tetraodon 4 and medaka 12 chromosomes indicate a lineage-specific chromosomal rearrangement in Atlantic cod.

Functional haemoglobin polymorphisms in Atlantic cod (a) Schematic of the head-to-head organized α1 and β1 globin genes, the intergenic promoter region and transcription start sites (red arrows). A 73 bp insert promoter polymorphism (red box) segregates in linkage disequilibrium with two amino acid substitution polymorphisms at position 55 and 62 (vertical lines), which affect oxygen-binding affinity. This linkage disequilibrium results in two predominant haplotypes, Long-Val-Ala and Short-Met-Lys. (b) Normalized luciferase luminescence ratios in salmon kidney cells. Cells were transfected using the long (black symbol) or short (white symbol) promoter and incubated at 4, 15 or 20 °C (n = 3 for each treatment level). Error bars show 95% confidence intervals.

Major histocompatibility complex (MHC) I diversity in Atlantic cod (a) MHCI α3 domain copy number estimates. Estimates are based on qPCR Cp ratios (Supplementary Note 28) of the MHCI α3 domain and a single copy reference gene. For Atlantic cod, β-2-microglobulin and topoisomerase-III-α (*) are used as single copy reference gene, for human and stickleback β-2-microglobulin is used. 95% bootstrap confidence intervals (black dots) were calculated by bootstrapping (n = 50,000). The human and stickleback estimates agree with the expected number of α3 domains found in both reference genomes (Supplementary Table 15) (b) Phylogeny of teleost MHCI α1-3 domain amino acid sequences. The Atlantic cod sequences are derived from cDNA and comprise classical U-lineage MHCI only. The other teleost sequences were obtained from Ensembl and NCBI and contain classical and non-classical U-lineage MHCI. Alignments were visually inspected and corrected where necessary. Maximum Likelihood (ML) values and bayesian posterior probabilities (dots) support the main branches on the ML topology. Distance represents the average number of substitutions per site (scale). The ratio of non-synonymous over synonymous variable sites (Ka/Ks), average nucleotide diversity per site (π) and Tajimas D (D) were calculated for the two main clades in Atlantic cod.

Phylogeny of Toll-like receptor (TLR) families in Atlantic cod. TLR protein sequences were selected based on the conserved TIR domain for Atlantic cod, including known sequences from stickleback, zebrafish, tetraodon, fugu, medaka and human as reference. TLR clades with (*) or without (⁻) Atlantic cod sequences are denoted according to human or teleost orthologs (summary tree topology, top left). Distance represents the average number of substitutions per site (scale). Maximum Likelihood (ML) values and bayesian posterior probabilities over 75/0.75 support the ML topology. Detailed topologies of TLR 7 (blue) -8 (purple) -9 (green) -22 (grey) show gene expansions for Atlantic cod (red).