A new method for long-read sequencing of animal mitochondrial genomes: application to the identification of equine mitochondrial DNA variants

Sophie Dhorne-Pollet (1) , Eric Barrey (1) , Nicolas Pollet (2)

1 GABI - Génétique Animale et Biologie Intégrative
2 EGCE - Evolution, génomes, comportement et écologie

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 2.3kb 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.

Mots clés: Mitochondria; mtDNA; Horse; Nanopore sequencing; MinION device; Single nucleotide polymorphism

Domaines: Génétique animale; Zoologie des vertébrés; Interactions cellulaires [q-bio.CB]; Embryologie et organogenèse; Morphogenèse; Bio-Informatique, Biologie Systémique [q-bio.QM]; Evolution [q-bio.PE]; Systématique, phylogénie et taxonomie; Biologie moléculaire; Génétique des populations [q-bio.PE]; Génomique, Transcriptomique et Protéomique [q-bio.GN]; Organisation et fonctions cellulaires [q-bio.SC]

Sophie Dhorne-Pollet, Eric Barrey, Nicolas Pollet. A new method for long-read sequencing of animal mitochondrial genomes: application to the identification of equine mitochondrial DNA variants. BMC Genomics, 2020, 21 (1), ⟨10.1186/s12864-020-07183-9⟩. ⟨hal-03104281⟩