Extended Data Fig. 8: Fate and cis-regulatory evolution of ohnologs after WGD.

a, b, Gene Ontology enrichment analysis of ohnologs in the hagfish (a) and the chicken (b). Top 20 terms are shown, majority of which are related with development. c, Cumulative distribution of distance of ACRs from the closest TSSs normalized by the average length of intergenic regions in each genome. d, Distribution of the distance from ACRs to closest TSS of developmental ohnologs (Devel.), non-developmental ohnologs (Non-dev.) and non-ohnologous (Non-ohnol.) genes. e, Distribution of the number of ACRs per gene, normalized by the GREAT region length, for developmental ohnologs (Devel.), non-developmental ohnologs (Non-dev.) and non-ohnologous (Non-ohnol.) genes. Sample size for groups in (d) and (e) are identical. n = 143 (Devel.), n = 816 (Non-dev.), n = 7303 (Non-ohnol.). f, Proportion of distal ACRs across different gene functional categories. Within a GREAT-defined region, proximal regulatory sequences were defined as those from 5 kb upstream to 1 kb downstream of a TSS, and the rest of the region was treated as distal. g, Distribution of the number of ACRs of hagfish ohnologs for each category (special., specialization). n = 344 (Redundancy), n = 178 (Subfunction.), n = 334 (Mild special.), n = 240 (Strong special.). h, Distribution of pairwise protein identity for hagfish ohnologous pairs for each category. n = 170 (Redundancy), n = 88 (Subfunction.), n = 165 (Mild special.), n = 120 (Strong special.). i, Distribution of pairwise protein identity for chicken ohnologous pairs for each category. n = 275 (Redundancy), n = 178 (Subfunction.), n = 318 (Mild special.), n = 167 (Strong special.). j, Number of ohnologues with strong specialization in chicken expressed in each tissue. Only the gene in a pair with narrower expression breadth is analyzed. In panels d, e, g-i P values correspond to two-sided Wilcoxon rank sum test between the indicated groups; boxes correspond to the median (centre line) and the first and third quartiles; whiskers extend to the last point no further than 1.5 times the interquartile range from the first and third quartiles. All statistical information for panels d, e, g-i is provided in Supplementary Tables 58–62. Animal illustrations kindly provided by Tamara de Dios Fernández and reproduced with permission from REF. ¹³³.