Fig. 2

Circos plot representation of NUPTs in the moringa nuclear genome. Nuclear and chloroplast chromosomes are represented as grey and green filled blocks, respectively, forming a circumference. Results are shown for the 14 nuclear chromosomes, hosting 4812 NUPTs (92.49% of the total number) spanning 8,928,478 bp (91.28% of the total length). The block corresponding to the chloroplast genome is located at 12 o’clock, and the 14 nuclear chromosomes are arranged clockwise. Nuclear chromosomes are drawn to scale, with lengths proportional to size and expressed in Mb, while the chloroplast genome has been upscaled to occupy a quarter of the image circumference; its size unit was set to 10,000 bp. Line plots representing the respective density distributions of NUPTs-I (red) and NUPTs-II (blue) are displayed. Windows of 500,000 and 100 bp were selected for the nuclear and chloroplast chromosomes, respectively. Local BLASTN sequence alignments between the chloroplast and the nuclear genome corresponding to individual NUPTs are represented as ribbons. Ribbons are colored according to the percentage of sequence identity of the local alignments (NUPTs) grouped by quartiles (with yellow, light orange, orange, and red corresponding to the first, second, third and fourth quartiles, respectively). LSC, Large Single Copy; IRA, Inverted Repeat A; IRB, Inverted Repeat B; SSC, Small Single Copy