Fig. 3
From: Asymmetric and parallel subgenome selection co-shape common carp domestication
Genome-wide selection signatures associated with skin color variation in common carp domestication. a Genome-wide selection signals. Tracks A and B are Tajima’s D in the skin-vibrant domesticated group and the skin-caesious wild group, respectively; Tracks C and D are CLR scores in the skin-vibrant domesticated group and the skin-caesious wild group, respectively; Track E is FST between the skin-vibrant domesticated group and the skin-caesious wild group; Track F is the synteny between subgenomes A and B. Chromosomes with signatures of selection are highlighted with larger font size of names (Additional file 2: Table S4). b Genomic regions with selection sweep signals on chromosomes of A06 and B06. Tajima’s D and CLR scores are calculated in the skin-vibrant domesticated group (red lines) and the skin-caesious wild group (blue lines), respectively. FST is calculated between the skin-vibrant domesticated group and the skin-caesious wild group (gray line), between the skin-vibrant domesticated group and the skin-caesious (wild and domesticated) group (orange line), and between the skin-vibrant group and the skin-caesious Asian wild group (pink line). Light blue vertical bars which indicate the selection regions. Genes in the genomic regions (light blue vertical bars) with selection sweep signals are listed. Lines between chromosomes of A06 and B06 show synteny between the two paralogous chromosomes. c The GO in genomic regions with selection sweep signals related to skin color variation. d Genotypes of SNPs in three pairs of paralogous genes on A06 and B06 and extended haplotype homozygosity around the crucial SNPs in each of the six genes. e Expression in skin of the three pairs of ohnologs with selection signals associated with color variation in common carps (Additional file 2: Table S10)