Mosaic mitochondrial-plastid insertions into the nuclear genome show evidence of both non-homologous end joining and homologous recombination

Abstract

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.

Keywords: Gene conversion; Mosaic insertions; Non-homologous end joining; Numins; Numts; Nupts.

Fig. 1

Distribution of organelle insertions in the genome of nine plant species. Simple numts composed of a single mitochondrial fragment (pink), simple nupts composed of a single plastid fragment (blue), complex numts composed of a number of mitochondrial fragments (red), complex nupts composed of a number of plastid fragments (green) and numins composed of at least one mitochondrial and one plastid fragment (yellow). The total number of inferred insertions is indicated for each species

Fig. 2

An inferred numin in the genome of Z. mays shows NHEJ signatures. a The total length of this inferred insertion located on chr5:210,342,490-210,346,062 is 3,573 bp (light blue) and it is composed of four fragments: two originating from the mitochondria (red) and two originating from the plastid (green). The junction number is indicated above the nuclear DNA and the length of each DNA fragment is indicated. Note that only junctions between organelle fragments are analyzed (1–3) while the terminal junctions with the nuclear genome (0,4) are not analyzed. b Two junctions between mitochondria and plastid fragments are shown at the base pair level. Junction 1 between fragments A (plastid) and B (mitochondrial) shows blunt-end signature while junction 3 between fragments C (mitochondrial) and D (plastid) shows microhomology of three bases (ATT, in orange)

Fig. 3

Microhomology length distribution for internal junctions of complex insertions in nine plants. Single origin insertions are shown in purple and mosaic origin insertions are shown in gray. Blunt end is shown as microhomology of length 0

Fig. 4

An inferred numin in the genome of Z. mays shows long homology. a A complex insertion located in chr4:156,747,273-156,755,671 is composed of two fragments that are 5,534 bp and 3,057 bp overlapping by 186 bp. b The junction between mitochondria and plastid fragments is shown at the base pair level. Overlapping between mitochondrial and plastid fragment is of 186 bp and identity in the overlapping region is 100%. The overlapping region is trimmed and the size is indicated

Fig. 5

Distribution of p-distance in NHEJ (orange) and non-NHEJ (blue) mosaic insertions in seven species. NHEJ insertions are defined as insertions with at least one junction with 0–10 base pairs overlap between fragments. Non-NHEJ is defined as insertions where all of their fragments are spaced by at least 1 base pair