Fig. 4

Graphical representation of the ten largest clusters of NUPTs for every episode in terms of number of integrants and the corresponding donor regions in the chloroplast genome (A) NUPTs-I. B NUPTs-II. For every cluster, donor regions in the chloroplast genome are shown as green blocks, while NUPTs-I and NUPTs-II are depicted as red and blue blocks, respectively. For every NUPT, the corresponding BLASTN sequence alignment between the chloroplast and the nuclear genome is represented as a ribbon. Ribbons are colored according to the percentage of sequence identity of the underlying alignment grouped by quartiles (with yellow, light orange, orange, and red corresponding to the first, second, third and fourth quartiles, respectively). The different elements in the diagram are drawn to scale, with the chloroplast genome and its four canonical regions (LSC, Large Single Copy; IRA, Inverted Repeat A; IRB, Inverted Repeat B; SSC, Small Single Copy) displayed on top as a reference for size