The mitochondrial genome (mitogenome) has proven to be important for the taxonomy, systematics,
and population genetics of ticks. However, current methods to generate mitogenomes can be costprohibitive
at scale. To address this issue, we developed a cost-effective approach to amplify and
sequence the whole mitogenome of individual tick specimens. Using two different primer sites, this
approach generated two full-length mitogenome amplicons that were sequenced using the Oxford
Nanopore Technologies’ Mk1B sequencer. We used this approach to generate 85 individual tick
mitogenomes from samples comprised of the three tick families, 11 genera, and 57 species. Twentysix
of these species did not have a complete mitogenome available on GenBank prior to this work.
We benchmarked the accuracy of this approach using a subset of samples that had been previously
sequenced by low-coverage Illumina genome skimming. We found our assemblies were comparable
or exceeded the Illumina method, achieving a median sequence concordance of 99.98%. We further
analyzed our mitogenome dataset in a mitophylogenomic analysis in the context of all three tick
families. We were able to sequence 72 samples in one run and achieved a cost/sample of ~ $10
USD. This cost-effective strategy is applicable for sample identification, taxonomy, systematics,
and population genetics for not only ticks but likely other metazoans; thus, making mitogenome
sequencing equitable for the wider scientific community.