Abstract
BackgroundMitochondrial DNA is remarkably polymorphic. This is why animal geneticists survey mitochondrial genomes variations for fundamental and applied purposes. We present here an approach to sequence whole mitochondrial genomes using nanopore long-read sequencing. Our method relies on the selective elimination of nuclear DNA using an exonuclease treatment and on the amplification of circular mitochondrial DNA using a multiple displacement amplification step.ResultsWe optimized each preparative step to obtain a 100 million-fold enrichment of horse mitochondrial DNA relative to nuclear DNA. We sequenced these amplified mitochondrial DNA using nanopore sequencing technology and obtained mitochondrial DNA reads that represented up to half of the sequencing output. The sequence reads were 2.3 kb of mean length and provided an even coverage of the mitochondrial genome. Long-reads spanning half or more of the whole mtDNA provided a coverage that varied between 118X and 488X. We evaluated SNPs identified using these long-reads by Sanger sequencing as ground truth and found a precision of 100.0%; a recall of 93.1% and a F1-score of 0.964 using the Twilight horse mtDNA reference. The choice of the mtDNA reference impacted variant calling efficiency with F1-scores varying between 0.947 and 0.964.ConclusionsOur method to amplify mtDNA and to sequence it using the nanopore technology is usable for mitochondrial DNA variant analysis. With minor modifications, this approach could easily be applied to other large circular DNA molecules.
Highlights
The presence of DNA segments transferred from the mitochondria to the nuclear DNA, the so-called Nuclear Mitochondrial DNA Sequences (NUMTs), can seriously complicate mtDNA analysis in a variety of animals from bees to humans [10,11,12]
Since the amount of nuDNA vastly exceeds that of mtDNA, we tried four conditions of nuclear DNA removal and evaluated their efficiency using qPCR (Fig. 1a)
We found that the best condition was 2 h of incubation with 10 Units of Exonuclease V, since it resulted in a ratio of mtDNA over nuDNA of 3755+/− 0.7 (Fig. 1a)
Summary
The ratio of mtDNA over nuclear DNA mutation rate is usually above 20 [8] This means that mtDNA polymorphisms may occur relatively often in animal populations with the potential for associated disorders, and this is why sequencing these organelle genomes is an important component of contemporaneous animal genetics. The presence of DNA segments transferred from the mitochondria to the nuclear DNA, the so-called Nuclear Mitochondrial DNA Sequences (NUMTs), can seriously complicate mtDNA analysis in a variety of animals from bees to humans [10,11,12] Such NUMTs can span several kilobases, can be nearly identical to mtDNA sequence and can exhibit variation between individuals of the same species [13]
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