Characteristics of genetic variations in NUPTs compared with the plastid genome. The density feature of NUPTs in different regions of the plastid genome is based on non-overlapping 1-kb windows, including A) insertion frequency (depth), B) single nuclear polymorphism (SNP) density, and C) InDel density. NUPTs were first aligned to the plastid genomes and then examined for each feature. LSC, large single-copy region; SSC, small single-copy region; IRa, repeat region a; IRb, repeat region b. D) The proportion of different types of SNPs. E) The proportion of different types of insertions and deletions. The error bars in D) and E) indicate the Sd among different genomes/subgenomes. F and G) The UpSet plot based on the intersection matrix of SNPs F) and InDels G) in each variation site among genomes/subgenomes. The total number of SNPs and InDels including core, dispersed, and specific classes were also shown. H and I) The NJ tree topology is based on the intersection matrix of SNPs H) and InDels I) used in F) and G). The corresponding information on NUMTs is shown in Supplemental Fig. S6.