Cas9 enrichment for mtDNA: The genomic DNA samples were treated to maximize the available mitochondrial target fragments for the sequencing process using the Cas9 targeted sequencing method described by Gilpatrick et al (2020) with a few variations (Fig 1). More specifically, the crRNA-tracrRNA duplexes were first assembled individually by incubating 1 μl of each 100 μM crRNA, 1 μl of 100 μM Alt-R® CRISPR-Cas9 tracrRNA and 8 μl of duplex buffer (IDT) at 95 °C for 5 min in separate tubes. Five Alt-R CRISPR-Cas9 tracrRNA and guide RNA molecules hybridizations were subsequently combined at 10 µM each to form the ribonucleoprotein (RNP) complexes by adding 4 µl of Alt-R HiFi Cas9 V3 Nuclease (0.8 µl per guide included, IDT) and 10 μl of 10 × CutSmart® buffer (New England Biolabs, Ipswich, MA, USA - NEB), 36 μl of nuclease-free H2O and incubated at room temperature for 30 min. In the meantime, the DNA was dephosphorylated in a reaction that included 24 μl genomic DNA (aiming for >210 ng μl-1), 3 μl of 10 × CutSmart® buffer, 3 μl nuclease-free H2O, and 3 μl Quick phosphatase CIP (NEB). Dephosphorylation time was increased to 20 min at 37 °C because it proved to augment the on-target sequences ratio in preliminary tests (results not shown) followed by inactivation at 80 °C for 2 min. The dephosphorylated DNA sample was then subjected to cleavage and dA-tailing in a reaction that comprised 10 μl of Cas9 RNPs, 1 μl 10 mM dATP (NEB) and 1 μl Taq  DNA polymerase (5,000 U/ml) (NEB). The reaction was incubated at 37 °C for 45 min followed by an inactivation at 72 °C for 5 min. These newly generated A-tailed fragments were ready for ligation of the adapters using the LSK109 or LSK110 sequencing kits (detailed protocol in S1).