Extended Data Fig. 7: Overlapping ratio and clustering analysis of ohnologous and orthologous chromosomes.

a, b, AC1 corresponds to five and six mutually paralogous chromosomes in hagfish (a) and sea lamprey (b) genomes, respectively. Numbers in colour-coded cells (bottom left triangle) indicate the OR between two chromosomes. Numbers in white cells (top right triangle) indicate the number of shared retained genes between two chromosomes. Numbers on the diagonal line from top left to bottom right (thick-lined cells) indicate the total number of retained genes of a chromosome. Overlapping rations corresponding to all hagfish chromosomes and lamprey scaffolds are provided in Supplementary File 9. c, Retention profile clustering analysis of gnathostome orthologous chromosomes deriving from AC1. Retained genes are denoted by dark cyan lines. Four orthologous chromosome pairs are defined. d, The clustering found in (c) is the same as that found in the phylogenetic analysis (Extended Data Fig. 5a), demonstrating the reliability of the OR approach.