Fig. 3

Structural variations and allelic gene comparisons between the two haplotypes. a Structural variations detected between two haplotypes and synteny analyses between allele genes in M. bimucrnata. Outer to inner tracks: (a) chromosome karyotype, (b) duplications (DUPs), (c) inversions (INVs), (d) inverted duplications (INVDPs), (e) inverted translocations (INVTRs), (f) translocations (TRANSs), (g) synteny analyses between allele genes. All distributions are drawn in a window size of 1 Mb. b Distribution of Ka/Ks between allele gene pairs. c Box plot of the FPKM (fragments per kilobase of transcript per million fragments mapped) value of allelic genes between two haplotypes. Light blue and dark blue represent haplotype A and haplotype B, respectively. d Four genes with different expression patterns in the two haplotypes. Red indicates high expression, and blue indicates low expression. The average FPKM of three biological replicates was used as the expression level, and they were normalized by Log2 (FPKM + 1). e Venn diagram of SV-related genes and allele-specific expression genes