**6. Conclusions and Perspective**

Organellar DNA integrated into the nuclear genome plays important functional roles in gene and genome evolution. The characterization and distribution patterns of organellar-derived sequences of the nuclear genome are crucial to the elucidation of the dynamics and evolution of the genome in plants and other eukaryotes. Nevertheless, many unanswered questions about organellar integrated nuclear sequences remain. For example, the precise mechanism of organellar DNA transfer, the extent and variety of the effects of organellar DNA transfer on gene activity regulation, and the genome instability and defense mechanism caused by organellar DNA transfer are still poorly understood. Thus, bioinformatics approaches, cytogenetic analysis, and experimental studies illustrating transfer events are necessary to answer these questions.

Currently, the experimental analysis of DNA transfer from organelle to nucleus has been performed only in tobacco and yeast. Studies that used these model organisms have presented considerable information on NUMT/NUPT insertion events, such as the transfer frequency, the size of transferred genome fragments, the environmental conditions favoring the transfer, and the mechanism of transfer. However, that such events are universal is not yet certain and should be further studied in other plant species. Experimental models involving other plant species should be established to provide more insights into the transfer event.

Similar to TE, organellar DNA integrated into nuclear genome is considered alien genetic material to the nuclear genome. Such sequences could result in nuclear genome instability, and the nuclear genome can initiate defense mechanisms [49,50]. A recent report showed that DNA methylation might play an important role in this process [51]. Future studies on DNA methylation and heterochromatization of organellar DNA insertions may improve our understanding of the organellar DNA integrants involved in dynamic genome evolution.

**Supplementary Materials:** The following are available online at http://www.mdpi.com/1422-0067/21/3/707/s1, Table S1, information of genome size, chloroplast genome size, and NUPT statistics results in sequenced plants. Table S2, information of genome size, mitochondrial genome size, and NUMT statistics results in sequenced plants.

**Author Contributions:** W.-J.G. and H.-X.N. conceived the whole project; G.-J.Z. and R.D. wrote the paper; L.-N.L. and S.-F.L. analyzed the NUPT and NUMT data. All authors have read and agreed to the published version of the manuscript.

**Funding:** This work was funded by the National Natural Science foundation of China (31970240), and the Key Scientific Research Projects of Colleges and Universities in Henan Province (19A180003).

**Conflicts of Interest:** The authors declare no conflicts of interest.
