**1. Introduction**

Three genetic compartments coexist in the plant cells: the nucleus and two cytoplasmic organelles, namely, chloroplast (plastid) and mitochondria. Among these cellular parts, the nucleus harbors the majority of the genetic material, and chloroplast and mitochondria contain relatively little but essential genetic substance. It is widely accepted that chloroplasts and mitochondria in eukaryotic cells are descended from erstwhile free-living organisms (α-proteobacteria and cyanobacteria) by endosymbiosis more than a billion years ago [1–3]. When the three genetic compartments were involved in one cell, genetic flux among them occurred frequently [4–6]. In theory, there are six types of DNA transfer occur among the three genetic compartments. At least five types, including mitochondrion-to-nucleus, plastid-to-nucleus, plastid-to-mitochondrion, nucleus-to-mitochondrion, and mitochondrion-to-plastid DNA transfer, have been observed presently based on experimental and bioinformatics data [4]. The transfer frequency is remarked different among the different types of genetic flow. Mitochondrion and chloroplast DNA have been integrated to the nuclear genome with high frequency, whereas other types of transfer occur rarely. In fact, along with the evolutionary process of the plastid and mitochondrion, many genes have relocated from the organelle to host nuclear genomes. Such events combined with the deletion of dispensable organelle genes considerably reduced the genome size of the mitochondrion and plastid during the evolution from their progenitors [4,7]. Organellar DNA transfer into the nuclear genome not just occurred during the establishment of symbiosis; it still actively occurs continuously [8–13]. The organelle-derived DNAs in the nucleus are designated as nuclear integrants of plastid DNA (NUPTs)

and nuclear integrants of mitochondrial DNA (NUMTs). The NUPTs and NUMTs discussed here refer to the nuclear organellar DNAs, which still have homologous copies in the organelles and do not include the relocated organellar genes that were previously reviewed [4,7,14].

With the rapid development of high-throughput sequencing technology, the plastid, mitochondrial, and nuclear genomes of a number of plant species have been deciphered. This makes the large-scale analysis of NUPTs and NUMTs in plants be possible. Currently, NUPTs and NUMTs in some plant genomes have been characterized [15–21]. The characterization of nuclear organellar DNAs in plants adds new insights into the role of NUPTs and NUMTs in genome structure and evolution. Growing pieces of evidence has revealed that DNA transfer from organelles contributes considerably to gene and genome evolution and provides a major source of genetic diversity [4,22–24]. In this review, we summarized recent advances in organelle-derived sequences and genome evolution in plants, with focus on the evolutionary fate of these insertions and the roles of NUPTs/NUMTs in the structure and evolution of plant genomes.
