*4.1. Contribution to the Genetic Diversity*

Organellar DNA integration is a substantial and ongoing process that generates genetic diversity. The NUMT/NUPT numbers, sizes, and densities show large divergence between different species. Even in the same species, different lines or ecotypes represent sequence variation of NUMTs and NUPTs. Among the 40 investigated NUMTs in humans, 12 are polymorphic [29]. In *Arabidopsis*, a 3.9-kb NUMT is presented in a polyubiquitin gene in four ecotypes, including Columbia, Eifel, Enkheim, and Hilversum [75,76]. However, this NUMT loci did not exist in five other ecotypes investigated [75]. Another 104-bp rearrangement NUMT derived from different mitochondrial DNA fragments is detected at the subtelomeric region of the short arm of chromosome 1 in 12 out of the 35 *Arabidopsis* accessions examined [77]. Similar results were found in rice and maize. A NUPT with length of 131 kb was detected on chromosome 10 of *O. sativa* subsp. *japonica*, but not detected in *O. sativa* subsp. *indica* or *O. rufipogon* nuclear genomes [33]. Fluorescence in situ hybridization (FISH) analyses using overlapping mitochondrial/chloroplast DNA fragments as probes revealed that the number and positions of detectable NUMTs/NUPTs varied markedly among different maize inbred lines [13,78]. For example, a mix of cosmids containing overlapping mitochondrial DNA fragments was probed, and only B73 showed a strong hybridization signal on 9L among the examined inbred lines; thus, this site may represent a recent mitochondrial DNA insertion [78]. Some NUMT sites are diverse even within the same maize inbred line collected from different laboratories (sources) [78]. Such diversity may be attributed to different mechanisms, such as integration of a new fragment of mitochondrial DNA, proliferation of an existing NUMT fragment, or deletion and degradation of NUMT sequences at a particular site [78]. The interspecific diversity in NUPT and NUMT accumulation might be affected by the number and stability of plastid and mitochondria in the germline; another factor is the species-specific mechanisms regulating nuclear DNA acquisition and deletion [37]. These results strongly suggested that the organelle DNA transfer is a frequently ongoing process, and the insertions of organelle-derived segments are components of the dynamic fraction of plant nuclear genomes.
