Fig. 2

Distribution of conserved gene blocks, TRs, indels, and SNPs in the plastomes of T. ascendens. Circle 1: plastome map of T. ascendens with coding genes labeled in blue, tRNAs labeled in red, and rRNAs in purple. Circle 2: conserved blocks of genes relative to the cp genome of Cycas. Circle 3: location of 639 TRs reported by phobos software. TRs of different length are marked with different colors, with green representing repeats ≥20 bp, rose red representing 10~19 bp, and orange representing < 10 bp. The relative height of the dot position in the figure represents the relative number of polymorphic loci within non-overlapping bins of 200 bp. Repeats in the three different colors were treated separately in statistical analysis. Dots with a high relative position represent more loci belonging to TRs within the 200 bp window. Circle 4: counts of indels (blue). Circle 5: counts of SNPs (red). Dots with a high relative position, represent more polymorphic loci in the 200 bp window. The red rectangle (HR01-HR11) showed the locations of the 11 selected hypervariable regions. The number or relative position of dots of indel and/or SNP inner rectangles were higher that outside