Fig. 2

Degeneration of the Y-SDRs. A Comparison of the synonymous substitution rates (Ks) of genes between X-, Y-SDR, and different species (genes on Chr01). Significant values of the Mann-Whitney U test are marked above. Sar: S. arbutifolia; Sch: S. chaenomeloides; Spu: S. purpurea; Ptr: P. trichocarpa; shared and pseudo: shared and pseudo genes. B Types and proportions of the repetitive sequences in each region of S. chaenomeloides and S. arbutifolia. C Estimated divergence values and insertion times of full-length long terminal repeat retrotransposons (LTR-RTs) in Y-SDRs. The orange and blue lines represent LTRs around the RR partial duplicates, and their corresponding positions are shown below. D Comparison of deleterious mutations in S. chaenomeloides (yellow) and S. arbutifolia (blue). Chr07 and chr15 represent all genomic regions of the chromosome. Chr07’ represents the autosomal genomic region in S. arbutifolia (which has the SDR on Chr15) that is collinear with the S. chaenomeloides SDR, and Chr15’ represents the autosomal genomic region in S. chaenomeloides (which has the SDR on Chr07) that is collinear with the S. arbutifolia SDR. Significant values from the Mann-Whitney U test are indicated with asterisks: ***p<0.001. Sch: S. chaenomeloides; Sar: S. arbutifolia; DEL: deleterious variants; SYN: synonymous variants