Fig. 1

Genomic features and genome evolution of Spinacia oleracea “Cornell-NO. 9” (YY genome), and Sex determination region (SDR) definition. a Genomic features of “Cornell-NO. 9” (YY) of S. oleracea. (i) Gene density; (ii) LTR transposable elements (Copia); (iii) LTR transposable elements (Gypsy); (iv) DNA transposable elements; (v) Predicted miRNA density. b LTR burst patterns and fractions of different repeat elements among the genomes of S. oleracea “Cornell-NO. 9” (YY) and congener species within the Amaranthaceae family. c Identification of the sex chromosome and SDR (sex determination region) among six chromosomes of the YY genome. (i) Density distribution of co-segregation bins (contigs) (100-kb window); (ii) GWAS Manhattan plot of two sex phenotypes (26 females and 44 males); (iii) Density distribution of male-specific SNPs (20-kb window); (iv) genetic differentiation (Fst) between females and males (1000-kb window); (v) Tajima’s D of males (red line) and females (blue line) (200-kb window). d Close-up view of the identified SDR (sex determination region) along chromosome Y. Two clear boundaries of the sex determination region (SDR) (145.31–162.73 Mb, size = 17.42 Mb) were defined using the overlapping region of following evidence (from top to bottom): (i) Elevated density of sex co-segregation bins (contigs) with top 1% cutoff = 1.29; (ii) GWAS plot of two sex phenotypes with cutoff of −log₁₀(P) = 6; (iii) Density distribution of male-specific SNPs with top 1% cutoff = 0.083; (iv) Fst between females and males with top 5% cutoff = 0.022; (v) Tajima’s D of males (red line) and females (blue line) with top 5% cutoff of male/female Tajima’s D ratios =1.83