Patterns of Genomic Integration of Nuclear Chloroplast DNA Fragments in Plant Species

Abstract

The transfer of organelle DNA fragments to the nuclear genome is frequently observed in eukaryotes. These transfers are thought to play an important role in gene and genome evolution of eukaryotes. In plants, such transfers occur from plastid to nuclear [nuclear plastid DNAs (NUPTs)] and mitochondrial to nuclear (nuclear mitochondrial DNAs) genomes. The amount and genomic organization of organelle DNA fragments have been studied in model plant species, such as Arabidopsis thaliana and rice. At present, publicly available genomic data can be used to conduct such studies in non-model plants. In this study, we analysed the amount and genomic organization of NUPTs in 17 plant species for which genome sequences are available. The amount and distribution of NUPTs varied among the species. We also estimated the distribution of NUPTs according to the time of integration (relative age) by conducting sequence similarity analysis between NUPTs and the plastid genome. The age distributions suggested that the present genomic constitutions of NUPTs could be explained by the combination of the rapidly eliminated deleterious parts and few but constantly existing less deleterious parts.

Analysis of nuclear mitochondrial DNAs and factors affecting patterns of integration in plant species

“…The results revealed two types of age distributions, as seen in NUPTs (Yoshida et al, 2014). In addition, they suggest that patterns of incorporation of NUMTs are related to the complexity of mitochondrial genomes.…”

“…A larger p-distance indicates a more ancient integration into the nuclear genome. As in the previous study of NUPTs (Yoshida et al, 2014), BLAST hits of 100 bp or longer and with relatively low p-distances (≤ 0.1) were selected. Compared with NUPTs, BLAST searches with mitochondrial genomes resulted in a larger number of partially/completely overlapping BLAST hit coordinates (start position, end position) in nuclear genomes.…”

“…This makes it difficult to estimate the corrected number of substitution events between NUMTs and mitochondrial genomes. Thus, as in Yoshida et al (2014), p-distance was used as an indicator of relative time since integration into the nuclear genome. For each species, the age distribution of NUMTs, as indicated by their p-distance, was estimated.…”

“…In previous studies, the patterns of integration in the model plants Arabidopsis thaliana and Oryza sativa have been extensively analyzed (e.g., Richly and Leister, 2004;Matsuo et al, 2005;Noutsos et al, 2005). Recently, other species also have been analyzed to reveal the patterns of integration (Smith et al, 2011;Michalovova et al, 2013;Yoshida et al, 2014). In addition, research has been conducted using tobacco plants to estimate the transfer rate (Lloyd and Timmis, 2011;Stegemann et al, 2013).…”

“…The general patterns of genomic integration of NUPTs in 17 plant species have been analyzed (Yoshida et al, 2014). The esti-mated age distribution of NUPTs for those species was of two types.…”