*3.3. Fragmentation*

As discussed above, the sequence similarity between NUPTs/NUMTs and their original chloroplast/mitochondrial DNAs will decrease over evolutionary time. Such sequence similarity is correlated positively with the size of NUPTs/NUMTs. In addition, dot plot analysis showed many separate but tightly linked NUPTs, which are collinear with the chloroplast genome in *A. o*ffi*cinalis* [21]. These pieces of evidence indicate that the original insertions are large and then break into smaller fragments [36,39]. The insertion of TEs and other non-organelle DNA sequences into NUPTs and NUMTs plays a significant role in this fragmentation process [36,39]. Some NUPT/NUMT clusters were formed by such process of organellar DNA insertion and subsequent fragmentation accompanied by incorporation of non-organellar DNA.
