*3.1. Elimination*

Considering the high transfer frequencies of organellar DNA to nuclear genome and the relatively low percentage of NUPTs/NUMTs in the plant genome, it is expected that a considerable number of these transferred organellar DNA fragments would be eliminated to prevent rapid genomic enlargement. The fate of the newly integrated chloroplast fragments (kanamycin resistance gene, *neo*) in tobacco reveals that four of nine lines show different level of kanamycin resistance instability, which is caused by the deletion of *neo*. The loss of the organellar transferred fragments usually occurs during mitosis, because intraspecific variation of NUPTs is observed frequently. However, it can also occur during meiosis occasionally [48,62]. A comprehensive analysis of the NUPTs existing in the rice genome showed that 80% of the NUPTs were eliminated within a million years following their integration. The average half-lives of these NUPTs are estimated to be 0.5 million years (Myr) for large insertions and 2.2 Myr for small insertions. Thus, the nuclear genome is in balance between continual integration and fast deletion of the organellar DNA [36]. The rapid elimination is a counterbalance mechanism of the frequent integration of plastid DNAs. Investigation of organellar DNA integrants in the nuclear genomes of *Arabidopsis* and rice have suggested that replication slippage is a mechanism for such deletion events, because short direct repeats are found frequently in the flanking regions of the deleted sequences [33,38].

**Figure 2.** Diagrammatic sketch summarizing the fate of integrated organellar DNA in nuclear genome. See details in text.

#### *3.2. Mutation*

As an intrinsic property of DNA, mutation is a predominant post-integration fate of organelle DNA. Organelle-derived sequences in the nuclear genome are unavoidably subject to the evolutionary forces that act on nuclear DNA [4]. Given that mutation rates vary greatly among organellar and nuclear DNAs, the integrated sequences show different mutation rates compared with the organellar sequences that they derive. In most animals, the mutation rate of mitochondrial DNA is approximately ten times faster than that of the nuclear DNA [63–65]. Thus, NUMTs inserted into the nucleus reserve ancestral mitochondria information and become "molecular fossils" that can be useful phylogenetic markers to study the evolutionary route of related taxa [66,67]. By contrast, the mutation rate of organellar DNA in plant species is much slower than that in the nuclear genome [68]. Organellar DNA is evolved with approximately one or fewer mutations per kb per million years [69], and the mutation rate is approximately seven mutations per kb per million years for the nuclear genome [70]. Thus, the NUPTs/NUMTs inserted into the plant nuclear genome evolve much more rapidly. With the evolutionary process, NUPT/NUMT mutation accumulates until they are not recognized as NUPTs/NUMTs because of the large sequence divergence between the evolved integrated sequences and the ancestral organellar DNAs. A previous investigation of recently acquired insertions of nuclear organellar DNA in *Arabidopsis* and rice revealed that the C → T and G → A transition mutations have occurred far more frequently than other point mutations. The 5-methylcytosine hypermutation frequency is approximately 5.6-fold and 9.5-fold higher than other point mutations in *Arabidopsis* NUMTs and rice NUPTs, respectively. In addition, most of the short insertion and deletion mutations occurred at homopolymeric regions and were less frequent than point mutations [33,38]. Thus, the 5-methylcytosine hypermutations may be a major mechanism of mutational decay for the newly integrated organellar sequences.
