Background: Mitochondrial and plastid DNA fragments are continuously transferred into eukaryotic nuclear genomes, giving rise to nuclear copies of mitochondrial DNA (numts) and nuclear copies of plastid DNA (nupts). Numts and nupts are classified as simple if they are composed of a single organelle fragment or as complex if they are composed of multiple fragments. Mosaic insertions are complex insertions composed of fragments of both mitochondrial and plastid DNA. Simple numts and nupts in eukaryotes have been extensively studied, their mechanism of insertion involves non-homologous end joining (NHEJ). Mosaic insertions have been less well-studied and their mechanisms of integration are unknown. Results: Here we estimated the number of nuclear mosaic insertions (numins) in nine plant genomes. We show that numins compose up to 10% of the total nuclear insertions of organelle DNA in these plant genomes. The NHEJ hallmarks typical for numts and nupts were also identified in mosaic insertions. However, the number of identified insertions that integrated via NHEJ mechanism is underestimated, as NHEJ signatures are conserved only in recent insertions and mutationally eroded in older ones. A few complex insertions show signatures of long homology that cannot be attributed to NHEJ, a novel observation that implicates gene conversion or single strand annealing mechanisms in organelle nuclear insertions. Conclusions: The common NHEJ signature that was identified here reveals that, in plant cells, mitochondria and plastid fragments in numins must meet during or prior to integration into the nuclear genome.
Bibliographical noteFunding Information:
We thank the following funding agencies: the German-Israeli Foundation grant I-1321-203.13/2015 (E.H.-C., W.F.M.), the European Research Council grants 666053 (W.F.M.); and the Open University of Israel Research Fund (E.H.-C.). SP is a fellow of the Edmond J. Safra Center for Bioinformatics at Tel Aviv University. The funding bodies had no role in the design of the study, collection, analysis and interpretation of data and in writing of the manuscript.
© 2018 The Author(s).
- Gene conversion
- Mosaic insertions
- Non-homologous end joining