Fig. 1: Genome assemblies of C. gibelio and C. auratus.
From: Comparative genome anatomy reveals evolutionary insights into a unique amphitriploid fish
a, Syntenic relationship between and within C. auratus and C. gibelio genomes. The outermost circle shows the 50 chromosomes of C. auratus (left) and C. gibelio (right); the subsequent coloured lines represent the syntenic relationship between subgenomes A and B in each species; the innermost coloured lines represent the syntenic relationship between the homologous chromosomes of C. auratus and C. gibelio. b, Localization of subgenome-specific repeats in C. auratus and C. gibelio chromosomes. Two TEs (blue) are mainly distributed in subgenome A, whereas three TEs (tan) are mainly distributed in subgenome B. c, Allele frequencies of alternative alleles in each chromosome of C. auratus and C. gibelio. The average frequencies were close to 0.50 and 0.33 in C. auratus and C. gibelio, respectively (red dashed line); this indicated two and three haplotypes for their genomes, respectively. The order of chromosomes is consistent with that in a. d, Density of read depth for reference or alternative alleles in C. auratus and C. gibelio. The left panel shows a similar read depth of reference and alternative alleles, whereas the right panel shows twice as much coverage of the reference alleles than the alternative alleles. e, The read depth relative to the single haplotype in each chromosome of C. auratus and C. gibelio. The order of chromosomes is consistent with that in a.
