Abstract
The natural transfer of DNA from mitochondria to the nucleus generates nuclear copies of mitochondrial DNA (numts) and is an ongoing evolutionary process, as genome sequences attest. In humans, five different numts cause genetic disease and a dozen human loci are polymorphic for the presence of numts, underscoring the rapid rate at which mitochondrial sequences reach the nucleus over evolutionary time. In the laboratory and in nature, numts enter the nuclear DNA via non-homolgous end joining (NHEJ) at double-strand breaks (DSBs). The frequency of numt insertions among 85 sequenced eukaryotic genomes reveal that numt content is strongly correlated with genome size, suggesting that the numt insertion rate might be limited by DSB frequency. Polymorphic numts in humans link maternally inherited mitochondrial genotypes to nuclear DNA haplotypes during the past, offering new opportunities to associate nuclear markers with mitochondrial markers back in time.
Highlights
Endosymbiosis is germane to eukaryote evolution, and gene transfers from organelles to the nucleus were an important mechanism of genetic variation that helped to forge the prokaryote-to-eukaryote transition [1,2,3]
Based on whole genome alignments, more than 80% of the numts in the human and chimpanzee genomes were found to be orthologous in that they are present at the same loci in the two species [21], but non-orthologous numts stemming from recent numt insertions, deletions, and tandem duplications were identified
The highest total numt content was found in the opossum Monodelphis domestica, whose genome sequence contains over 2000 kb of numt nucleotides
Summary
Endosymbiosis is germane to eukaryote evolution, and gene transfers from organelles to the nucleus were an important mechanism of genetic variation that helped to forge the prokaryote-to-eukaryote transition [1,2,3]. ¤ Current address: Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America Due to their sequence similarity to mitochondrial DNA, numts are responsible for many instances of misidentification, both in mitochondrial disease studies and phylogenetic reconstruction. Ricchetti et al [30] used a PCR analysis with primers from both the nuclear flanking regions and the numt sequence to identify recent numt insertions that appear only in the human genome but not in the chimpanzee genome. Based on whole genome alignments, more than 80% of the numts in the human and chimpanzee genomes were found to be orthologous in that they are present at the same loci in the two species [21], but non-orthologous numts stemming from recent numt insertions, deletions, and tandem duplications were identified. With the increasing availability of structural variation data in populations, the number of loci polymorphic for numts is predicted to increase, and it should be possible to identify variable more numts that are missing in the reference genome(s) but appear in the variation data
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