Fig. 3
From: The allotetraploid origin and asymmetrical genome evolution of the common carp Cyprinus carpio
Asymmetrical homoeologous gene expression in C. carpio. a Circos plot distribution of homoeologous gene pairs in 25 chromosome pairs across subgenomes A and B. b Boxplot of the Ka/Ks ratio distribution of protein-coding genes in 50 chromosomes of C. carpio. Orange and blue boxplots indicate that the chromosomes belong to subgenomes A and B, respectively. c Histograms of the genome-wide expression of homoeologous genes among the indicated tissues of C. carpio. Log2(FPKM_A/FPKM_B) indicates the degree of expression difference of homoeologous gene pairs. N values indicate the number of dominant genes in subgenomes A and B. d Heatmaps of three divergently expressed triplet clusters (each triplet includes two homoeologous genes of C. carpio and their orthologue of C. idella), indicate potential subfunctionalization and neofunctionalization in the allotetraploid genome of C. carpio. The orders of 12 tissues in both C. idella and C. carpio are the same as 3c. e Histograms of the genome-wide expression divergence of homoeologous genes of C. carpio in stress treatments and controls. N values indicate the number of dominant genes in subgenomes A and B, respectively. f Histogram of the ratio of homoeologous expression divergence in the stress treatment and controls [(A/B)treatment/(A/B)control], which indicates accelerated homoeologous expression divergence in stress treatments compared to controls
