*4.2. E*ff*ects on Gene Structure and Evolution*

Certain NUPTs and NUMTs are related to genes. For example, two NUMTs are located within genes in the yeast genome [79]. In the *Arabidopsis* and rice genomes, approximately 25% of NUMTs and NUPTs are found within genes [39]. In some cases, NUMT/NUPT sequences that fuse to non-organelle-derived nuclear DNA are transcribed, suggesting that NUMTs/NUPTs can remodel genes and their products by providing novel exons [19,80,81]. The mosaic genes with one or more exons originated from organellar DNA were analyzed in detail in yeast, *Homo sapiens*, *Arabidopsis*, and rice. In that study, a total of 474 NUMTs and NUPTs were detected within, or adjacent to the annotated genes. Among these NUMTs and NUPTs, 45 insertions are involved in a total of 49 protein-coding exons belonged to 34 genes [23]. Moreover, considering that the sequence divergence between NUMT/NUPT and the donor organellar sequences was constantly enlarged with evolutionary time, some organelle-originated exon sequences may be difficult to directly detect through conventional methods. Thus, organelle-derived DNA integrations might contribute to many ancient functional exon acquisitions that are not found thus far [23]. In addition, the Ka/Ks ratios (non-synonymous substitutions/synonymous substitutions) of the nuclear protein-coding exon derived from organellar

reading frames are higher than 1, thereby suggesting the non-neutral evolution of these integrants and their adaptation to their novel functions [23].

In addition to recruiting as exons, NUMTs/NUPTs can also be associated with the regulatory elements of genes. Some organellar DNA sequences are integrated into introns, as well as regions of 5 and 3 to nuclear genes; these integrated sequences might be associated with changes in the gene regulation [80]. Specifically, two organelle-derived sequences, namely, *Arabidopsis* enhancer 12-7 and 12-Q, make the reporter genes show cell-specific expression in transgenic tobacco [82]. However, the influence of the organellar insertions on gene expression still needs further investigation.

## *4.3. Roles Played in the Sex Chromosome Evolution*

Several reports revealed that NUPTs and NUMTs are strongly accumulated in the sex chromosomes of dioecious plants than other plants [74,83,84]. The first discovery of this phenomenon is in the model dioecious plant *Silene latifolia*, in which a bacterial artificial chromosome clone containing partial plastid genome sequences shows strong hybridization signals on the Y chromosome; however, the signals are very weak on the X chromosome and the autosomes. The large size of the Y chromosome in this species may be partially due to the accumulation of such NUPTs [83]. In another dioecious plant, *Carica papaya*, NUPTs are localized within the male-specific region of the Y chromosome (MSY) and HSY approximately 12 times the rate in the X chromosome counterpart and four times that of the genome wide average [74]. NUPTs/NUMTs accumulate in the sex chromosomes of other dioecious plants, such as *Rumex acetosa* [84] and *Coccinia grandis* [85]. In *A. o*ffi*cinalis*, the number and total length of NUPTs in Y chromosome were larger than those in other chromosomes. Sequence alignment and cytogenetic analysis show a 47-kb centromeric region in the Y chromosome with very high density of NUPTs, i.e., more than three-quarters of the sequences of this region originate from the plastid. However, the MSY and the nearby regions did not have NUPT integrations. Thus, NUPTs may play important roles in the centromere building of the sex chromosome of *A. o*ffi*cinalis* but are not implicated in MSY formation [21]. These studies reveal that the organellar DNA accumulation is strongly related to the evolution of plant sex chromosomes.

These integrated organellar DNA sequences are predicted as one of the evolutionary forces that drive the formation of sex chromosomes in dioecious plants. It is believed that the sex chromosomes originate from autosomes, and the evolutionary process involves some essential events, such as sex-determining gene emergence, recombination restriction, and Y chromosome degeneration [86]. In addition, sex chromosomes can recruit abundant TEs and organellar DNAs [74,85], and these novel sequences may benefit the structural differentiation and recombination restriction of sex chromosomes and contribute to Y chromosome degeneration [49]. The gathering of such novel sequences in sex chromosomes can promote recombination suppression of the sex chromosomes; when recombination is suppressed, such sequences can accumulate rapidly in the recombination-free region. The lack of recombination and release from purifying selection avoids their deletion from the recombination-suppressed region [87,88].
