*3.5. Proliferation*

The integrated organellar DNAs can amplify themselves to increase the copy number in the nuclear genome. The amplified fragment can be arranged in tandem arrays or distributed separately in the host genome. For example, in *A. o*ffi*cinalis*, we identified several NUPT clusters arranged by a number of nearly identical chloroplast DNA sequences [21]. In *Carica papaya*, a plastid-derived sequence containing *rsp15* gene has been proliferated 23 times in the hermaphrodite-specific regions of the Yh chromosome (HSY) [74]. The NUPTs/NUMTs themselves are not able to duplicate; thus, their proliferation in the nuclear genome is probably duplicated, co-amplified with neighboring retrotransposons, which can easily increase their copy number via "copy-and-paste" retrotransposition. Indeed, intact *Ty3-pypsy* retrotransposable elements are presented less than 1.5 kb upstream of most *rsp15* NUPT sequences, suggesting that the NUPT proliferation is probably mediated via retrotransposons [74].

We summarized the various fates of the organellar DNA integrated into the host nuclear genome. It is worth noting that the occurrence of the abovementioned events is not isolated and that these events usually occur integrated within one NUPT or NUMT sequence. Thus, after the organellar DNA integrated into the nuclear genome, they are fragmented, shuffled, and accompanied by nucleotide mutation. During this process, a considerable number of NUPTs/NUMTs are deleted from the nuclear genome. Thus, the current repertoire of NUPTs/NUMTs is in rapid variation of fragmentation, mutation, and rearrangement and in dynamic equilibrium between continuous integration and frequent deletion.

In addition, we only discuss the fate of the NUPTs/NUMTs with simple origin, that is, individual organellar fragment from chloroplast or mitochondrial genome transferred to the nucleus. However, the transferred sequence not only comes from one fragment of plastid or mitochondria but it can be derived from both plastids and mitochondria. In this case, the disparate fragments from plastids and mitochondria are combined and/or rearranged and then integrated into the nuclear genome [38,62]. Such integrants can undergo the abovementioned various evolutionary events and complicate the structure of NUPTs/NUMTs.
