Fig. 5: Impact of WGD events on the regulatory genome. | Nature Ecology & Evolution

Fig. 5: Impact of WGD events on the regulatory genome.

From: Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences

Fig. 5: Impact of WGD events on the regulatory genome.The alternative text for this image may have been generated using AI.

a, Distributions of the ACR numbers within the cis-regulatory regions of each gene (see Methods). n = 28,497 (amphioxus), n = 23,183 (zebrafish), n = 22,184 (medaka), n = 15,213 (chicken), n = 23,256 (mouse) and n = 16,951 (hagfish) genes. ***P < 2.2 × 10−16, Bonferroni-adjusted, two-sided Wilcoxon rank-sum tests. b, Numbers and fractions of ACRs with respect to genomic annotations in each species. Promoters, between 1 kb upstream and 0.5 kb downstream of annotated transcription start sites (TSSs); proximal, within 5 kb upstream and 1 kb downstream of annotated TSSs, but not overlapping promoters; exonic, within exons of protein-coding genes but not overlapping proximal regions; distal, not in aforementioned locations. c, Cumulative proportion of the distance of ACRs from the closest TSSs in each species. For the result with scaling based on the average length of intergenic regions of each species genome, see Extended Data Fig. 8c. d, The distribution of ACR numbers across different classes of genes, according to PANTHER Gene Ontology database (devel., developmental ohnologues; non-dev., non-developmental ohnologues; non-ohnol., singletons). n = 143 (devel. ohnol.), n = 816 (non-devel. ohnol.) and n = 7,303 (non-ohnol.) genes. P values from Bonferroni-adjusted two-sided Wilcoxon rank-sum tests are indicated. e, Distribution of fates of ohnologous families after WGD. Red., potential redundancy; Subf., potential subfunctionalization; Spec., potential specialization. f, Number of ohnologues with strong specialization expressed in hagfish tissues. In a and d, boxes correspond to the median (centre line) and the first and third quartiles. Whiskers extend to the last point no further than 1.5× the interquartile range from the first and third quartiles. For a–d, see Supplementary Tables 52–57 for detailed statistical information, including P value for each pairwise comparison. Animal illustrations kindly provided by Tamara de Dios Fernández; chicken and hagfish illustrations reproduced with permission from ref. 133.

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