Fig. 2

(a) Syntenic analyses of genome regions possessing ApoD clusters. The same color between spotted gar and the chicken represents orthologous chromosomes. Two paralogous duplicated segments in teleost fishes (chromosomes (chrs)/linkage groups (LGs) indicated in red) can be traced back to one corresponding orthologous region in spotted gar and the chicken (chrs/LGs labelled in black), linked by colorful lines. Arrows show the regions in which apolipoprotein D (ApoD) clusters are located in. (b) ApoD clusters next to the breakpoints of genome rearrangements before teleost genome duplication (TGD). The same color between spotted gar and the chicken represents orthologous chromosomes. The red arrows show breakpoints, and the black arrows show gene directions. Neighboring genes are named according to the Ensembl database. (c) Inversion with ApoD clusters next to the breakpoints occurred again in cichlid fishes. The haplochromine lineage, the most species-rich lineage of cichlid fishes, is labelled. (d) ApoD domains and protein-protein association predictions. a. Conserved domains include a single peptide of approx. 20 amino acids (AA) and a lipocalin domain of approx. 144 AA. b. Different paralogs exhibited differential associations. The common associations are with pla2g15, lcat and MAPK genes. One class (copies A2, B2a and B1) is associated with multiple forkhead transcription factors. The other class (copies A1 and B2b) lost this association. Instead, it is associated with the lipoprotein-related gene apoa1. The single ApoD gene in coelacanth possesses both associations