Fig. 2
From: The allotetraploid origin and asymmetrical genome evolution of the common carp Cyprinus carpio
Allotetraploid origin and evolution history of C. carpio. a Phylogenetic relationship of rag2 orthologues of C. carpio and its tetraploid and diploid close relatives in the subfamily Cyprininae. The pentagrams indicate three selected diploid species (Poropuntius huangchuchieni, Hampala macrolepidota, and Onychostoma barbatulum) as progenitor-like diploid candidates, and one species from a relatively distant lineage (Cirrhinus molitorella) for genome sequencing to represent the closely related diploid lineages from Cyprininae. b A histogram shows the coverage of P. huangchuchieni genome sequence mapping to 50 chromosomes of C. carpio. Chromosome IDs have been re-assigned to represent two sets of homoeologous chromosomes. c Boxplots show the genome coverage and similarity comparisons of diploid relatives to the tetraploid genome of C. carpio. d The distribution of the synonymous substitution rates (Ks) of homologous genes between D. rerio and C. carpio, C. carpio and Sinocyclocheilus, and homoeologous genes between two subgenomes of C. carpio. Three peaks (Ks = 0.42, 0.16 and 0.068) of Ks distribution indicate the divergences of D. rerio and C. carpio, C. carpio and Sinocyclocheilus, and two progenitors of C. carpio. e The distribution of sequence divergence rates of transposable elements (TEs) as percentages of subgenome sizes of C. carpio. The TE content segregation between subgenomes A and B indicates the events of diploid progenitor divergence and subgenome merger
