Abstract
DNA transfer from organelles to the nucleus is one of the most dynamic evolutionary processes in eukaryotes and occurs frequently, even in the present day. However, the fate of sequences translocated into the nucleus has been unknown. The draft sequence of the rice (Oryza sativa L. ssp. japonica) nuclear genome provides an opportunity to undertake a genome-wide analysis of the nuclear-localized chloroplast DNA fragments, nupDNAs. The rice nuclear genome has at least 700 loci containing nupDNAs, constituting up to 0.2% of the total nuclear genome. Here we show that the chloroplast DNA fragments integrated into the nuclear genome are rapidly fragmented and shuffled, with 80% of nupDNAs eliminated from the nuclear genome within a million years. The rates of integration and elimination of nupDNAs are markedly higher in the pericentromeric regions, where large nupDNA fragments are frequently found. This suggests that pericentromeric regions play an important role in nupDNA metabolism.
