Extreme-Depth Re-sequencing of Mitochondrial DNA Finds No Evidence of Paternal Transmission in Humans

Abstract

Recent reports have questioned the accepted dogma that mammalian mitochondrial DNA (mtDNA) is strictly maternally inherited. In humans, the argument hinges on detecting a signature of inter-molecular recombination in mtDNA sequences sampled at the population level, inferring a paternal source for the mixed haplotypes. However, interpreting these data is fraught with difficulty, and direct experimental evidence is lacking. Using extreme-high depth mtDNA re-sequencing up to ~1.2 million-fold coverage, we find no evidence that paternal mtDNA haplotypes are transmitted to offspring in humans, thus excluding a simple dilution mechanism for uniparental transmission of mtDNA present in all healthy individuals. Our findings indicate that an active mechanism eliminates paternal mtDNA which likely acts at the molecular level.

Fig 1. Extreme deep sequencing in trios with discordant paternal and maternal mitochondrial DNA.

(a) Position of the discordant haplotypes on the mitochondrial genome. Thick horizontal bars show the position of the PCR amplicons. (b) Average sequencing depth +/- 95% confidence intervals for the two amplicons in all four trios. (c) Population variant allele frequencies for the two amplicons, indicating position of motif variants.

Fig 2. Power to detect paternally transmitted mtDNA in the children studied here based on the observed ultra-deep mtDNA sequence data.

Calculations are based on the comparison of two Poisson distributions as described by Skellam [25], assuming the same mtDNA fold coverage in mothers and offspring (see text for a full description of the methods). Each graph shows the power to detect a paternal contribution to the mtDNA in the offspring of the trios studied here based for different degrees of ultra-deep sequencing coverage, and for different background levels of mtDNA heteroplasmy seen in the mothers, which in this study were 4.3 x 10^–5, 6.0 x 10^–5, 5.7 x 10^–5, and 7.6 x 10^–5.