Fig. 2

Genomic features of the Y-chromosome SDR and its X counterpart in spinach. a Genomic landscape of the SDR and its X counterpart. The red and black lines connecting gene pairs identified using MCscan and blast search, respectively. The region is featured by two Y-specific insertions (INS1 and INS2) and two inversions (Inversion 1 and Inversion 2). b Comparison of 126 conserved gene pairs from the SDR and its X counterpart. Sequence identities (identities 1 without sliding window, identities 2 with sliding window in 500kb window and 200kb step), numbers of SNPs, and INDELs were plotted between each gene pair. Inversion 1 and 2 were classified as two strata separated by INS2. c Comparison of gene densities among different regions. Gene densities in 200-kb window were plotted in four genomic regions, i.e., ChrX-PAR, ChrY-PAR, the SDR, and its X counterpart. Mean separation was performed using t-test and ANOVA (alpha = 0.05). d Gene pair divergence among different genomic regions. The SDR was classified into two strata based on two inversions. An estimated divergence time (T = Ks/2r, r = 2.8e−9) was plotted for each stratum with pairwise t-tests. e Similarly, Ka/Ks ratios for each gene pair from respective strata were plotted. f Comparison of LTR-RTs insertion times among different genomic regions. Density distributions of intact LTR-RTs insertion times in the SDR and its X counterpart, entire X and Y chromosomes, and whole YY and XX genomes were plotted. g Insertion times of LTR-RTs across the SDR and its X counterpart, including collinear regions, two inversions and two insertions